Contacts of the helix formed by residues 75 - 90 (chain a) in PDB entry 5GJQ
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 LEU 75 (chain a).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104X TYR* 4.2 30.1 - - + +
41a ILE* 3.7 4.8 - - - +
66a HIS* 6.1 0.4 - - - -
72a GLU* 6.2 0.4 - - - +
73a PRO 4.6 4.5 - - - +
74a PRO* 1.3 78.9 - - - +
76a VAL* 1.3 65.3 + - - +
77a HIS* 4.1 11.7 - - + +
78a THR* 3.2 36.9 + - - +
79a ALA 3.4 4.7 + - - -
104a ASP* 3.2 30.1 - - - +
106a GLN* 3.8 37.7 - - + +
110a GLN* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 76 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41a ILE* 3.6 17.7 - - + -
74a PRO 3.8 0.4 + - - -
75a LEU* 1.3 73.2 - - - +
77a HIS* 1.3 64.1 + - - +
78a THR 3.1 0.2 + - - -
79a ALA* 3.2 3.5 + - - +
80a ALA* 3.0 21.0 + - - +
100a ILE* 4.0 15.9 - - + +
101a ALA 4.5 0.7 - - - -
102a GLY 3.6 33.9 - - - +
103a TRP 3.9 13.0 - - - +
104a ASP* 3.9 2.6 - - + -
110a GLN* 3.7 34.3 - - + +
112a TYR* 3.9 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 77 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102X PHE 4.2 5.3 + - - -
103X GLY* 4.3 20.5 - - - -
104X TYR* 5.2 5.6 + - + +
75a LEU* 3.2 10.4 - - + +
76a VAL* 1.3 79.5 - - - +
78a THR* 1.3 56.6 + - - +
80a ALA* 3.6 2.6 + - - +
81a SER* 2.9 53.3 + - - -
110a GLN* 4.2 4.2 + - - +
112a TYR* 3.5 41.2 + + - +
120a MET* 4.1 13.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 78 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102X PHE* 3.8 33.9 - - + +
104X TYR* 3.2 27.1 + - + -
63a LEU* 3.6 19.5 - - + -
66a HIS* 4.0 15.0 - - + +
75a LEU* 3.2 28.0 + - - +
76a VAL 3.1 0.6 - - - -
77a HIS* 1.3 74.9 - - - +
79a ALA* 1.3 66.2 + - - +
81a SER* 3.1 2.9 + - - -
82a LEU* 3.0 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37a ILE* 4.6 4.7 - - + -
41a ILE* 3.9 25.4 - - + -
59a VAL* 4.0 2.2 - - + +
63a LEU* 3.7 32.0 - - + +
75a LEU 3.4 2.2 + - - -
76a VAL 3.2 8.2 + - - +
78a THR* 1.3 77.7 - - - +
80a ALA* 1.3 64.8 + - - +
82a LEU* 3.2 7.2 + - - +
83a PHE* 3.0 29.3 + - + -
100a ILE* 4.1 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76a VAL 3.0 13.6 + - - +
77a HIS 3.7 4.3 - - - +
79a ALA* 1.3 82.8 - - - +
81a SER* 1.3 55.6 + - - +
83a PHE* 3.4 3.1 + - - +
84a LYS* 2.9 28.1 + - - +
100a ILE* 4.0 16.5 - - + +
112a TYR* 3.7 28.9 - - + -
114a VAL* 4.2 2.4 - - - +
120a MET* 3.4 22.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 81 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101X ASN 4.5 1.8 - - - -
102X PHE* 3.5 27.0 + - - -
103X GLY* 4.1 2.6 - - - -
77a HIS* 2.9 42.2 + - - -
78a THR 3.1 3.3 + - - -
80a ALA* 1.3 73.2 - - - +
82a LEU* 1.3 61.9 + - - +
84a LYS* 3.3 10.4 + - - +
85a GLU* 3.0 32.6 + - - +
120a MET* 3.8 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101X ASN* 3.3 24.5 - - + +
102X PHE* 3.6 30.5 - - + -
59a VAL* 4.0 15.7 - - + -
62a GLN* 3.8 23.2 - - + +
63a LEU* 3.8 41.3 - - + +
78a THR 3.0 14.1 + - - +
79a ALA 3.2 6.3 + - - +
81a SER* 1.3 75.8 - - - +
83a PHE* 1.3 65.4 + - - +
85a GLU* 3.2 8.1 + - + +
86a MET* 3.1 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 83 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37a ILE* 3.8 25.4 - - + -
43a CYS* 3.9 9.9 - - + -
52a THR 5.3 0.2 - - - -
55a VAL* 3.5 29.6 - - + -
56a ALA* 3.8 25.6 - - + -
59a VAL* 3.5 23.5 - - + +
79a ALA* 3.0 24.4 + - + -
80a ALA 3.6 7.4 - - - +
82a LEU* 1.3 75.5 - - - +
84a LYS* 1.3 57.5 + - - +
86a MET* 3.4 1.2 + - - +
87a CYS* 2.9 36.5 + - - +
98a ILE* 4.0 26.2 - - + -
100a ILE* 3.5 32.5 - - + -
114a VAL* 4.3 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100X SER 4.6 0.4 + - - -
80a ALA 2.9 17.5 + - - +
81a SER* 3.4 14.8 - - - +
82a LEU 3.1 0.2 - - - -
83a PHE* 1.3 74.2 - - - +
85a GLU* 1.3 96.0 + - - +
87a CYS 3.8 0.5 - - - -
88a TYR* 2.9 35.1 + - + +
114a VAL* 4.3 9.8 - - - +
118a GLY 3.2 24.6 - - - +
119a MET 4.2 0.9 - - - -
120a MET* 3.8 30.3 - - + -
61g GLN* 4.2 15.4 - - + +
62g TYR* 6.2 2.0 - - - +
65g GLN* 3.2 19.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100X SER 3.2 18.1 - - - +
101X ASN* 4.1 25.8 - - + +
81a SER* 3.0 19.0 + - - +
82a LEU* 3.6 10.3 - - + +
84a LYS* 1.3 101.9 + - - +
86a MET* 1.3 67.5 + - + +
88a TYR* 3.9 7.9 - - - +
89a ARG* 3.0 46.8 + - - +
65g GLN* 3.5 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 86 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54a ALA 5.2 0.7 - - - +
55a VAL* 3.9 36.1 - - + -
58a ALA* 3.7 32.3 - - + -
59a VAL* 5.1 2.5 - - + -
62a GLN* 4.3 20.0 - - - +
82a LEU 3.1 12.0 + - - +
83a PHE 3.9 4.7 - - - +
85a GLU* 1.3 82.3 - - + +
87a CYS* 1.3 64.6 + - - +
88a TYR 3.2 0.7 + - - -
89a ARG* 6.1 0.2 - - - +
90a TYR* 3.2 52.4 + - + +
94a LEU* 4.0 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 87 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55a VAL* 4.4 16.6 - - - -
83a PHE* 2.9 22.2 + - - +
84a LYS 4.1 0.2 - - - +
86a MET* 1.3 77.9 - - - +
88a TYR* 1.3 60.4 + - - +
90a TYR 4.1 0.9 - - - +
91a ARG* 3.6 21.3 + - - +
94a LEU* 4.1 15.0 - - + +
96a ALA* 4.3 26.9 - - - -
98a ILE* 4.5 12.6 - - - -
114a VAL* 4.4 9.6 - - + -
115a PRO 5.2 0.7 - - - +
116a MET 4.2 8.5 - - - +
117a GLY 3.7 3.8 - - - +
118a GLY* 4.0 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 88 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84a LYS* 2.9 24.8 + - + +
85a GLU* 4.0 7.9 - - - +
87a CYS* 1.3 76.9 - - - +
89a ARG* 1.3 72.1 + - + +
90a TYR 3.2 2.5 + - - -
91a ARG* 3.3 33.9 + - - +
117a GLY 4.0 9.9 - - - -
118a GLY* 3.9 11.2 - - - +
1g THR* 4.7 0.4 + - - -
58g ALA* 4.3 17.0 - - + -
59g ASP* 3.2 28.6 + - - -
62g TYR* 3.5 43.2 - + + -
99g ARG* 3.3 25.6 + - - -
106g LEU* 3.6 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 89 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101X ASN* 5.8 1.4 + - - -
85a GLU* 3.0 40.6 + - - +
86a MET* 4.9 0.4 - - - +
88a TYR* 1.3 86.7 - - + +
90a TYR* 1.3 92.7 + - + +
91a ARG* 3.4 1.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 90 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86a MET* 3.2 48.3 + - + +
87a CYS 4.1 2.5 - - - -
88a TYR 3.2 0.4 - - - -
89a ARG* 1.3 106.3 - - + +
91a ARG* 1.3 62.7 + - - +
92a GLU 3.1 3.8 - - - -
93a ASP* 3.0 28.7 + - + +
94a LEU* 3.1 29.8 + - + +
----------------------------------------------------------
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