Contacts of the helix formed by residues 75 - 86 (chain A) in PDB entry 3V6A
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 ASP 75 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A THR* 4.2 17.8 + - - +
42A LYS* 5.6 0.7 - - - +
43A ARG* 4.2 1.2 + - - -
73A ASP* 2.9 15.1 + - - +
74A GLU* 1.3 78.0 - - - +
76A VAL* 1.3 69.8 + - - +
77A SER* 2.9 27.6 + - - -
78A ILE* 3.1 24.6 + - + +
79A ARG* 3.1 16.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
74A GLU 3.5 4.6 + - - +
75A ASP* 1.3 77.3 + - - +
77A SER* 1.3 61.0 + - - +
79A ARG* 3.2 32.0 + - - +
80A ARG* 2.9 54.2 + - + +
110A ASP* 3.7 26.7 - - + +
113A GLU* 3.5 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ARG* 2.7 36.6 + - - -
75A ASP* 2.9 14.7 + - - -
76A VAL* 1.3 80.5 - - - +
78A ILE* 1.3 63.2 + - - +
80A ARG* 3.6 26.2 + - - +
81A GLN* 3.2 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A THR* 3.7 16.6 - - + +
42A LYS* 4.1 13.9 - - + +
43A ARG* 3.7 45.3 - - + +
46A ALA* 4.6 3.2 - - + +
70A LEU* 4.0 30.7 - - + +
73A ASP* 3.8 19.5 - - + +
75A ASP* 3.1 29.2 + - + +
77A SER* 1.3 75.3 + - - +
79A ARG* 1.3 67.2 + - - +
81A GLN* 3.3 6.2 + - - +
82A ALA* 3.1 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU 3.5 15.0 - - - +
71A CYS* 2.9 27.4 - - - +
72A GLU* 3.8 3.6 - - - +
73A ASP 2.9 37.4 + - - +
74A GLU* 3.4 16.2 + - - +
75A ASP 3.1 6.1 + - - +
76A VAL* 3.5 27.3 - - - +
78A ILE* 1.3 75.9 - - - +
80A ARG* 1.3 52.0 + - - +
82A ALA* 3.3 1.9 + - - +
83A ILE* 2.7 42.6 + - + +
105A LEU* 6.1 0.4 - - - +
108A THR* 4.6 2.4 + - - -
110A ASP* 5.2 1.4 - - - +
113A GLU* 2.8 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL* 2.9 35.3 + - + +
77A SER* 3.7 27.9 - - - +
78A ILE 3.2 0.2 - - - -
79A ARG* 1.3 76.7 - - - +
81A GLN* 1.3 60.9 + - - +
83A ILE* 3.3 4.6 + - - -
84A LYS* 3.0 26.5 + - - +
110A ASP* 3.0 29.3 + - - -
112A ALA* 3.7 27.7 - - - +
113A GLU* 3.8 20.9 - - + +
116A LEU* 3.6 26.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ARG* 4.0 15.8 - - + +
46A ALA* 3.6 21.7 - - + +
47A GLN* 3.6 33.7 + - + +
77A SER 3.2 12.1 + - - +
78A ILE* 3.7 9.2 - - - +
80A ARG* 1.3 79.3 - - - +
82A ALA* 1.3 62.2 + - - +
84A LYS* 3.8 15.5 + - - +
85A GLU* 3.8 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ALA* 3.9 5.3 - - + +
67A GLN* 3.0 32.7 + - - +
70A LEU* 3.6 29.8 - - + -
71A CYS* 3.8 17.5 - - - +
78A ILE 3.1 12.6 + - - +
79A ARG 3.7 2.9 - - - +
81A GLN* 1.3 75.8 - - - +
83A ILE* 1.3 63.7 + - - +
85A GLU 3.3 5.9 + - - -
86A LEU* 3.4 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A CYS* 3.9 23.1 - - - +
79A ARG* 2.7 29.8 + - + +
80A ARG* 3.3 4.9 + - - +
82A ALA* 1.3 69.6 - - - +
84A LYS* 1.3 66.9 + - - +
85A GLU 2.8 3.4 + - - -
86A LEU* 3.1 18.0 + - + +
87A PRO* 3.9 3.5 - - - +
102A LEU* 4.3 12.1 - - + -
105A LEU* 3.9 17.9 - - + -
113A GLU* 3.3 39.0 - - + +
116A LEU* 4.3 7.6 - - + +
117A VAL* 3.8 35.4 - - + +
120A ALA* 4.1 3.8 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
80A ARG 3.0 17.0 + - - +
81A GLN* 3.8 15.5 - - - +
83A ILE* 1.3 78.0 - - - +
85A GLU* 1.3 75.2 + - - +
87A PRO* 3.5 13.0 - - - +
116A LEU* 4.4 30.2 - - + +
120A ALA* 5.3 1.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
46A ALA 3.9 4.3 - - - +
47A GLN* 4.9 3.8 - - - +
50A PRO* 3.5 28.7 - - + -
67A GLN* 4.0 9.6 - - - +
81A GLN* 3.8 22.1 + - - +
82A ALA 3.3 2.0 + - - +
83A ILE 2.8 1.6 + - - -
84A LYS* 1.3 99.2 + - - +
86A LEU* 1.3 65.2 + - - +
87A PRO* 3.2 4.5 - - - -
88A GLN* 2.6 55.2 + - - +
89A PHE* 3.7 6.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLN* 4.1 15.0 - - + -
68A LEU* 4.0 26.2 - - + -
71A CYS* 3.8 18.4 - - - -
82A ALA 3.4 12.5 + - - +
83A ILE* 3.1 12.0 + - - +
85A GLU* 1.3 75.4 - - - +
87A PRO* 1.4 66.9 - - + +
88A GLN 3.0 1.2 + - - -
89A PHE* 3.0 26.9 + - + +
90A ALA 3.6 5.2 + - - -
98A VAL* 3.9 20.6 - - + +
101A ILE* 4.5 11.4 - - + -
102A LEU* 3.6 33.4 - - + -
105A LEU* 4.4 9.9 - - + -
----------------------------------------------------------
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