Contacts of the helix formed by residues 70 - 91 (chain t) in PDB entry 3J9X
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 70 (chain t).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827 T 3.5 26.8 + - - +
837 A 4.4 2.0 + - - -
111q PHE* 3.5 18.3 - - - -
90r ILE* 5.6 0.6 - - - +
99r MET* 5.3 0.4 - - - +
69t THR* 1.3 76.1 - - - +
71t PRO* 1.3 66.2 - - - +
72t ASN 3.0 0.2 - - - -
73t ARG* 2.9 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 71 (chain t).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827 T 3.6 24.0 - - + +
837 A 3.9 32.8 - - - +
71q PRO* 3.6 18.9 - - + +
74q ALA* 4.8 2.0 - - + -
75q ILE* 3.5 38.4 - - + +
107q TYR* 6.5 0.9 - - + -
111q PHE* 4.6 7.4 - - + -
70t GLY* 1.3 82.3 - - - +
72t ASN* 1.3 65.1 + - - +
73t ARG 3.1 0.4 - - - -
74t ALA* 3.1 4.8 + - - +
75t ILE* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 72 (chain t).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72q ASN* 3.1 24.4 - - - +
75q ILE* 3.5 11.8 - - - +
111q PHE* 3.3 25.5 + - - +
112q ASN* 4.8 8.1 + - - +
68t ILE* 3.5 16.2 - - + -
69t THR* 3.3 14.2 + - - +
70t GLY 3.0 0.6 - - - -
71t PRO* 1.3 74.5 - - - +
73t ARG* 1.3 64.5 + - - +
75t ILE* 3.3 18.9 + - + +
76t TYR* 3.0 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain t).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827 T 3.0 36.0 + - - +
89r ARG 4.6 0.8 + - - -
90r ILE* 3.7 27.2 + - - +
60t SER* 2.7 46.5 + - - +
63t LEU* 3.5 15.9 - - + +
64t THR* 2.9 32.1 + - - +
68t ILE* 2.8 55.6 + - + +
69t THR* 3.8 8.3 - - - +
70t GLY 2.9 15.6 + - - +
72t ASN* 1.3 76.2 - - - +
74t ALA* 1.3 59.6 + - - +
76t TYR* 3.0 4.9 + - - -
77t GLN* 2.8 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain t).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817 A 4.1 15.8 - - + +
827 T 3.0 41.8 + - + +
2678 A 4.7 5.4 - - + -
2688 T 4.4 5.4 - - - +
71q PRO* 4.8 3.4 - - + -
70t GLY 3.6 0.8 + - - -
71t PRO* 3.1 9.7 + - + +
73t ARG* 1.3 77.6 - - - +
75t ILE* 1.3 64.1 + - - +
77t GLN* 3.6 10.3 - - - +
78t GLY* 2.9 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain t).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2688 T 5.8 0.2 - - - -
71q PRO* 3.6 26.4 - - + +
72q ASN* 3.5 36.6 - - - +
71t PRO 3.0 14.4 + - - +
72t ASN* 3.4 22.4 - - + +
73t ARG 3.2 0.4 - - - -
74t ALA* 1.3 77.2 - - - +
76t TYR* 1.3 66.1 + - + +
78t GLY* 3.4 1.1 + - - -
79t PHE* 3.1 21.3 + - - +
107t TYR* 3.5 30.5 - - + -
111t PHE* 4.6 11.0 - - + +
112t ASN 5.9 0.4 - - - +
113t ALA* 4.1 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 76 (chain t).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59t VAL* 4.4 3.3 - - - +
63t LEU* 3.6 28.5 - - + -
68t ILE* 4.0 17.6 - - + +
72t ASN* 3.0 28.3 - - + -
73t ARG 3.0 6.0 + - - +
75t ILE* 1.3 80.9 - - + +
77t GLN* 1.3 61.0 + - - +
79t PHE* 3.3 6.0 + - - +
80t GLY* 2.8 26.9 + - - -
112t ASN 5.0 0.3 + - - -
113t ALA* 3.9 8.6 - - + -
114t ASN* 2.9 37.7 + - - +
117t VAL* 3.7 31.1 - - + +
118t LEU* 3.7 30.7 - - + -
121t VAL* 4.2 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 77 (chain t).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817 A 3.4 33.3 + - + +
827 T 3.1 20.9 + - - +
55t VAL* 5.4 0.7 - - - +
56t ASN* 3.4 24.8 + - - +
59t VAL* 3.3 20.9 - - - +
60t SER* 3.5 26.5 - - - +
63t LEU* 4.0 2.1 - - + +
73t ARG 2.8 22.8 + - - +
74t ALA* 3.2 9.4 + - - +
76t TYR* 1.3 77.2 - - - +
78t GLY* 1.3 56.3 + - - +
80t GLY* 3.3 0.9 + - - -
81t LEU* 2.9 41.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 78 (chain t).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817 A 5.4 1.2 + - - -
2688 T 5.1 3.4 - - - -
2698 A 4.1 26.2 - - - +
74t ALA 2.9 16.0 + - - -
75t ILE 3.8 1.8 - - - -
77t GLN* 1.3 76.6 - - - +
79t PHE* 1.3 61.5 + - - +
81t LEU* 3.4 5.5 + - - +
82t LYS* 3.0 23.9 + - - +
107t TYR* 3.5 13.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain t).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75t ILE 3.1 13.6 + - - +
76t TYR 3.5 7.4 - - - +
78t GLY* 1.3 76.1 - - - +
80t GLY* 1.3 64.5 + - - +
82t LYS* 3.1 5.6 + - - +
83t VAL* 2.9 33.1 + - + +
100t ILE* 5.1 2.0 - - + -
103t LEU* 3.7 24.0 - - + -
104t LYS* 3.8 23.6 - - + -
107t TYR* 3.5 33.9 + + + -
118t LEU* 3.3 52.7 - - + -
121t VAL* 3.8 16.8 - - + -
122t VAL* 3.7 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 80 (chain t).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55t VAL* 4.5 6.1 - - - -
59t VAL* 5.0 2.0 - - - -
76t TYR 2.8 16.5 + - - -
77t GLN* 3.8 1.3 - - - -
79t PHE* 1.3 73.4 - - - +
81t LEU* 1.3 62.5 + - - +
83t VAL* 3.1 2.9 + - - -
84t ALA* 3.0 19.2 + - - +
121t VAL* 3.5 26.9 - - - -
125t ILE* 3.1 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain t).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807 T 5.5 1.3 - - - +
817 A 5.6 3.6 - - - +
2698 A 4.1 19.1 - - + +
2708 T 3.4 36.3 - - - +
52t PHE* 3.5 43.1 - - + +
55t VAL* 4.5 6.2 - - + +
56t ASN* 3.4 30.7 - - - +
77t GLN* 2.9 28.5 + - + +
78t GLY* 3.7 5.2 - - - +
80t GLY* 1.3 75.6 - - - +
82t LYS* 1.3 58.2 + - - +
84t ALA* 3.2 4.1 + - - -
85t ARG 2.9 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 82 (chain t).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717 A 6.3 0.2 - - - -
727 T 3.2 14.3 + - - -
2698 A 3.7 25.1 + - - +
2708 T 3.3 29.4 + - - +
106s TYR* 2.8 33.2 + - - -
78t GLY 3.0 17.3 + - - +
79t PHE* 3.5 5.4 - - - +
81t LEU* 1.3 74.6 - - - +
83t VAL* 1.3 65.4 + - - +
85t ARG* 3.3 11.0 + - - +
86t ALA* 3.1 21.3 + - - +
99t MET* 5.9 2.4 - - - -
103t LEU* 3.5 34.6 - - + +
106t TYR* 5.0 6.3 - - + -
107t TYR* 4.6 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain t).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79t PHE* 2.9 42.3 + - + +
80t GLY* 3.1 8.3 + - - +
82t LYS* 1.3 76.6 - - - +
84t ALA* 1.3 61.9 + - - +
86t ALA* 3.3 7.7 + - - +
87t LEU* 3.0 20.3 + - + +
96t LEU* 4.5 2.6 - - + +
100t ILE* 4.3 28.3 - - + -
103t LEU* 3.7 19.1 - - + -
122t VAL* 4.6 7.6 - - + -
125t ILE* 3.8 27.4 - - + -
126t THR* 4.5 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain t).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51t LYS 5.7 0.4 - - - +
52t PHE* 3.6 20.9 - - + -
55t VAL* 4.2 19.5 - - + -
80t GLY 3.0 12.2 + - - +
81t LEU* 3.5 7.9 - - - +
83t VAL* 1.3 73.9 - - - +
85t ARG* 1.3 65.6 + - - +
87t LEU* 3.1 13.0 + - + +
88t ASN* 3.0 25.4 + - - +
125t ILE* 4.4 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 85 (chain t).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717 A 3.8 35.9 + - - -
727 T 2.9 33.7 + - - +
2708 T 3.0 36.1 + - - +
2718 A 3.4 28.8 + - - +
52t PHE* 3.5 11.1 - - - -
81t LEU 2.9 12.8 + - - +
82t LYS* 3.3 20.2 - - - +
83t VAL 3.2 0.2 - - - -
84t ALA* 1.3 75.2 - - - +
86t ALA* 1.3 65.1 + - - +
88t ASN* 3.0 6.3 + - - +
89t ARG* 3.0 46.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain t).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717 A 5.6 2.5 - - - -
82t LYS 3.1 9.5 + - - +
83t VAL* 3.3 9.6 + - - +
85t ARG* 1.3 78.6 - - - +
87t LEU* 1.3 58.3 + - - +
89t ARG* 4.5 2.7 - - - +
90t ILE* 2.7 47.1 + - + +
96t LEU* 3.8 17.3 - - + -
99t MET* 3.8 27.6 - - + -
100t ILE* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain t).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83t VAL* 3.0 13.6 + - + +
84t ALA* 3.1 12.1 + - + +
86t ALA* 1.3 75.8 - - - +
88t ASN* 1.3 64.0 + - - +
91t GLY* 2.7 31.0 + - - +
92t SER* 3.6 28.9 - - - +
96t LEU* 3.6 24.3 - - + +
125t ILE* 4.5 25.6 - - + +
126t THR* 6.0 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 88 (chain t).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2718 A 5.8 1.1 - - - +
48t ASN* 4.9 6.0 + - - +
51t LYS* 3.8 32.7 + - - +
52t PHE* 3.4 33.7 - - + -
84t ALA* 3.0 12.5 + - - +
85t ARG* 3.0 8.3 + - - +
87t LEU* 1.3 85.8 - - - +
89t ARG* 1.3 64.1 + - + +
90t ILE 3.7 0.3 + - - -
91t GLY* 4.5 1.4 + - - -
7u SER* 4.6 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 89 (chain t).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697 A 4.6 9.9 + - - -
707 T 3.6 29.2 + - - +
717 A 3.3 32.7 + - - +
2718 A 4.1 17.5 + - - +
2728 T 4.3 15.4 + - - -
85t ARG* 3.0 45.8 + - - +
86t ALA* 4.3 2.0 - - - +
88t ASN* 1.3 80.7 - - + +
90t ILE* 1.3 62.9 + - + +
7u SER* 4.1 32.7 - - - +
8u ARG* 6.2 0.2 - - - +
60v SER* 4.5 6.1 + - - -
73v ARG* 4.6 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 90 (chain t).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707 T 5.6 0.4 - - - +
717 A 4.5 12.1 - - - +
86t ALA* 2.7 29.7 + - + +
88t ASN 4.8 0.4 - - - -
89t ARG* 1.3 78.0 - - - +
91t GLY* 1.3 68.7 - - - +
95t ALA* 3.6 26.2 - - + +
96t LEU* 4.0 5.4 - - + +
99t MET* 3.8 38.4 - - + -
60v SER* 4.9 1.9 + - - -
61v ALA* 5.8 0.7 - - - -
64v THR* 2.6 36.8 + - + +
69v THR* 4.4 10.3 - - + -
73v ARG* 3.7 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 91 (chain t).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86t ALA 3.6 0.6 + - - -
87t LEU* 2.7 30.4 + - - -
88t ASN 4.5 0.9 - - - -
89t ARG 3.9 0.2 - - - -
90t ILE* 1.3 91.1 - - - +
92t SER* 1.3 68.7 + - - +
96t LEU* 3.4 9.2 - - - +
64v THR* 3.6 1.1 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il