Contacts of the helix formed by residues 93 - 111 (chain l) 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 93 (chain l).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92l SER* 1.3 76.0 - - - +
94l PRO* 1.3 68.2 - - - -
95l ALA 3.3 1.6 - - - -
96l LEU* 2.8 28.7 + - - +
97l VAL* 3.2 16.8 + - - +
133l VAL* 4.5 10.3 - - - -
64n THR* 4.5 0.7 - - - -
65n GLN* 5.3 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 94 (chain l).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92l SER 4.6 0.2 - - - +
93l GLY* 1.3 82.8 - - - -
95l ALA* 1.3 63.1 + - - +
97l VAL* 3.0 6.4 + - - +
98l ASN* 2.9 25.9 + - - +
133l VAL* 3.8 26.8 - - + -
64n THR* 3.3 15.9 - - + +
65n GLN* 3.4 40.4 - - - +
66n TYR 4.7 0.2 - - - -
67n GLY* 3.9 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain l).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90l ILE* 3.6 22.9 - - + -
93l GLY 3.1 0.6 + - - -
94l PRO* 1.3 78.5 - - - +
96l LEU* 1.3 57.3 + - - +
98l ASN* 3.3 1.9 + - - +
99l MET* 3.0 24.6 + - - +
64n THR* 3.2 19.5 + - + +
67n GLY* 3.5 15.9 - - - -
68n ILE 3.6 21.8 - - - +
69n THR* 3.4 14.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain l).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83l VAL* 4.5 3.6 - - + +
86l ALA* 3.8 32.8 - - + +
87l LEU* 3.6 40.2 - - + +
90l ILE* 4.0 5.1 - - + +
91l GLY 3.4 12.6 - - - +
92l SER* 3.8 11.4 - - - -
93l GLY 2.8 16.7 + - - +
95l ALA* 1.3 72.3 - - - +
97l VAL* 1.3 63.0 + - + +
99l MET* 3.1 5.5 + - + +
100l ILE* 2.8 50.2 + - + +
126l THR* 4.8 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain l).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93l GLY 3.2 9.4 + - - +
94l PRO 3.0 8.6 + - - +
96l LEU* 1.3 79.5 - - + +
98l ASN* 1.3 66.5 + - - +
100l ILE* 3.2 5.1 + - + +
101l ASN* 2.9 27.9 + - - +
130l THR* 3.5 21.3 + - - +
131l GLY 3.7 26.9 - - - +
132l TYR 4.2 6.1 - - - +
133l VAL* 3.8 33.9 - - + +
134l SER 5.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 98 (chain l).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109k SER 3.5 21.8 - - - +
110k ALA* 3.6 4.5 - - - +
112k ASN* 5.1 9.8 - - - +
94l PRO* 2.9 12.9 + - - +
95l ALA* 3.4 8.3 - - - +
97l VAL* 1.3 80.3 - - - +
99l MET* 1.3 63.3 + - - +
101l ASN* 3.5 9.4 + - - +
102l GLY 3.3 13.5 + - - -
67n GLY* 3.1 35.4 + - - -
69n THR* 4.4 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 99 (chain l).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1197 A 4.1 13.0 - - - +
106k TYR* 4.6 12.3 - - - +
110k ALA* 3.9 21.5 + - - +
111k PHE* 3.7 31.9 - - + -
82l LYS* 5.9 2.2 - - - -
86l ALA* 3.8 23.1 - - + -
90l ILE* 3.8 21.8 - - + -
95l ALA 3.0 13.2 + - - +
96l LEU* 3.3 12.8 - - + +
98l ASN* 1.3 77.5 - - - +
100l ILE* 1.3 60.1 + - + +
102l GLY* 3.2 3.1 + - - -
103l LEU* 2.9 34.6 + - + +
69n THR* 4.7 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 100 (chain l).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79l PHE* 5.1 1.3 - - + -
83l VAL* 4.3 22.7 - - + -
86l ALA* 6.0 0.2 - - + -
96l LEU* 2.8 47.0 + - + +
97l VAL* 4.7 3.8 - - + -
99l MET* 1.3 75.2 - - + +
101l ASN* 1.3 58.8 + - - +
103l LEU* 4.1 6.5 - - + -
104l LYS* 2.7 34.1 + - + +
122l VAL* 4.3 20.0 - - + -
126l THR* 4.1 24.5 - - + -
130l THR* 3.6 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 101 (chain l).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109k SER* 4.2 7.4 + - - +
97l VAL* 2.9 23.7 + - - +
98l ASN* 3.7 10.1 + - - +
100l ILE* 1.3 76.6 - - - +
102l GLY* 1.3 61.6 + - - +
104l LYS* 3.8 3.3 - - - +
105l GLY* 3.2 18.5 + - - -
130l THR* 2.5 31.4 + - - +
131l GLY* 2.9 32.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 102 (chain l).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105k GLY 4.2 2.0 - - - +
106k TYR* 3.7 12.4 + - - -
109k SER* 2.9 25.7 + - - -
110k ALA* 4.1 11.2 - - - -
98l ASN 3.3 4.4 + - - -
99l MET 3.2 5.8 + - - -
101l ASN* 1.3 76.2 - - - +
103l LEU* 1.3 59.4 + - - +
105l GLY* 3.4 1.8 + - - -
106l TYR* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain l).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106k TYR* 4.0 11.5 - - + -
79l PHE* 3.7 10.5 - - + -
82l LYS* 3.5 51.6 - - + +
83l VAL* 3.7 34.3 - - + +
99l MET* 2.9 24.4 + - + +
100l ILE* 3.6 8.3 - - + +
102l GLY* 1.3 74.7 - - - +
104l LYS* 1.3 65.6 + - - +
106l TYR* 3.2 9.3 - - + +
107l TYR* 3.0 37.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 104 (chain l).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79l PHE* 3.8 17.9 - - + -
100l ILE* 2.7 23.0 + - + +
101l ASN* 3.8 4.7 - - - +
103l LEU* 1.3 73.1 - - - +
105l GLY* 1.3 64.4 + - - +
107l TYR* 3.1 5.2 + - - +
108l ILE* 3.0 46.1 + - + +
115l PRO* 4.4 12.9 - - - +
118l LEU* 4.0 13.1 - - + +
119l ASP* 2.7 39.1 + - - +
122l VAL* 6.0 1.6 - - + -
130l THR* 4.3 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 105 (chain l).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102k GLY* 5.0 1.1 - - - -
105k GLY* 5.9 3.1 - - - -
106k TYR 5.7 0.4 - - - -
101l ASN 3.2 11.7 + - - -
102l GLY* 3.8 2.5 - - - -
104l LYS* 1.3 78.3 - - - +
106l TYR* 1.3 61.1 + - - +
108l ILE* 3.2 12.2 + - - +
109l SER* 3.0 29.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 106 (chain l).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2208 T 4.2 0.2 + - - -
2218 A 3.3 16.2 + - - -
82k LYS* 2.7 34.2 + - - -
99k MET* 4.7 3.3 - - - -
102k GLY 3.5 26.4 + - - -
103k LEU* 4.1 15.3 - - + -
106k TYR* 3.7 25.9 - + + +
82l LYS* 5.0 5.8 - - - -
102l GLY 2.9 19.0 + - - +
103l LEU* 3.2 13.5 - - + +
105l GLY* 1.3 74.5 - - - +
107l TYR* 1.3 81.8 + + - +
109l SER* 3.7 0.2 + - - -
110l ALA* 2.8 44.4 + - + +
111l PHE* 3.7 28.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 107 (chain l).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2208 T 4.4 6.5 + - + +
2218 A 3.4 25.2 + - - -
71i PRO* 6.5 0.9 - - + -
75l ILE* 3.5 37.9 - - + -
78l GLY* 3.5 4.3 - - - -
79l PHE* 3.5 39.4 + + + -
82l LYS* 4.6 4.0 - - + -
103l LEU* 3.0 31.0 + - + +
104l LYS 3.8 5.6 - - - +
106l TYR* 1.3 96.3 - + - +
108l ILE* 1.3 66.3 + - - +
111l PHE* 3.0 46.6 + + - +
113l ALA* 3.1 21.8 + - + +
118l LEU* 4.4 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 108 (chain l).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104l LYS* 3.0 46.1 + - + +
105l GLY* 3.2 10.7 + - - +
107l TYR* 1.3 76.4 - - - +
109l SER* 1.3 62.2 + - - +
112l ASN* 3.0 26.0 - - - +
113l ALA 3.5 16.6 - - - +
115l PRO* 3.9 24.2 - - + -
118l LEU* 3.3 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 109 (chain l).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98k ASN* 3.5 18.4 - - - +
101k ASN* 4.2 6.8 + - - -
102k GLY* 3.0 28.5 + - - -
105l GLY 3.0 11.3 + - - -
108l ILE* 1.3 82.2 - - - +
110l ALA* 1.3 64.4 + - - +
111l PHE 3.4 0.4 - - - -
112l ASN* 4.0 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain l).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69i THR* 2.6 34.0 + - - +
98k ASN* 3.7 13.3 - - - +
99k MET* 4.2 14.3 - - - +
102k GLY* 4.1 11.2 - - - -
106l TYR* 2.8 36.4 + - + +
109l SER* 1.3 77.1 + - - +
111l PHE* 1.3 70.7 + - + +
112l ASN* 5.2 1.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 111 (chain l).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2208 T 3.6 39.0 - - - -
69i THR* 3.4 17.7 - - - +
70i GLY* 3.6 18.8 - - - -
71i PRO* 4.6 2.9 - - + -
72i ASN* 3.2 19.1 + - - +
82k LYS* 6.1 0.2 - - - -
99k MET* 3.8 23.3 - - + -
75l ILE* 4.6 12.6 - - + +
106l TYR* 3.7 37.2 - + - -
107l TYR* 3.0 44.0 + + + +
110l ALA* 1.3 81.8 - - + +
112l ASN* 1.3 74.1 + - - +
113l ALA* 3.2 2.4 + - - +
----------------------------------------------------------
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