Contacts of the helix formed by residues 62 - 76 (chain A) in PDB entry 3A7H
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 62 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLU* 1.3 91.2 - - - +
63A GLU* 1.3 70.1 + - - +
64A ILE 3.2 2.6 + - - -
65A GLU* 3.8 20.3 + - + +
66A ASP* 3.5 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A SER* 6.3 0.7 - - - -
35A PHE* 3.8 30.1 - - + -
60A ALA* 3.2 19.8 - - + +
61A GLU* 2.8 27.1 + - - +
62A ASP* 1.3 92.0 + - - +
64A ILE* 1.3 60.9 + - - +
65A GLU 3.4 0.4 - - - -
66A ASP* 3.5 11.7 + - - +
67A ILE* 3.0 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 6.4 0.2 - - + -
57A LEU* 3.9 45.1 - - + +
60A ALA* 3.9 13.5 - - + +
61A GLU* 2.8 24.2 + - + +
63A GLU* 1.3 78.3 - - - +
65A GLU* 1.3 65.6 + - - +
67A ILE* 3.2 13.2 + - + +
68A GLN* 2.9 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLU 4.2 1.3 + - - +
62A ASP* 4.1 16.8 - - - +
63A GLU 3.4 0.2 - - - -
64A ILE* 1.3 78.8 - - - +
66A ASP* 1.3 62.6 + - - +
68A GLN* 3.7 9.6 - - - +
69A GLN* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PHE* 3.9 22.4 - - + -
62A ASP 3.5 16.4 - - - +
63A GLU* 3.5 11.6 + - - +
64A ILE 3.2 0.2 - - - -
65A GLU* 1.3 79.8 - - - +
67A ILE* 1.3 61.2 + - - +
69A GLN* 3.7 2.1 - - - +
70A GLU* 2.9 29.8 + - - +
164A GLY* 3.7 21.5 - - - +
165A VAL* 5.2 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 5.5 0.4 - - + -
35A PHE* 3.8 20.2 - - + -
53A LYS* 5.6 0.4 - - - +
55A ILE* 3.4 42.6 - - + -
57A LEU* 5.9 2.7 - - + -
60A ALA* 5.8 0.4 - - + -
63A GLU* 3.0 28.0 - - + +
64A ILE* 3.2 17.0 + - + +
66A ASP* 1.3 75.7 - - - +
68A GLN* 1.3 66.8 + - - +
70A GLU* 3.2 6.5 + - - +
71A ILE* 3.0 27.1 + - + +
95A LEU* 3.9 17.5 - - + -
97A ILE* 3.8 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLY* 2.9 39.0 + - - -
10A LEU* 3.6 24.9 + - + +
64A ILE* 2.9 22.1 + - + +
65A GLU* 3.7 10.5 - - - +
67A ILE* 1.3 77.9 - - - +
69A GLN* 1.3 60.8 + - - +
71A ILE* 3.4 1.6 + - - -
72A THR* 2.9 47.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLU 2.9 18.5 + - - +
66A ASP* 3.7 0.9 - - - +
68A GLN* 1.3 78.2 - - - +
70A GLU* 1.3 66.1 + - - +
72A THR* 3.1 12.4 + - - +
73A VAL* 3.0 33.6 + - + +
164A GLY 3.4 21.3 - - - +
165A VAL* 5.1 1.1 - - - -
166A ALA 4.2 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PHE* 5.0 5.7 - - - -
53A LYS* 4.5 17.0 + - - -
66A ASP 2.9 18.1 + - - +
67A ILE* 3.2 6.7 + - - +
69A GLN* 1.3 76.0 - - - +
71A ILE* 1.3 64.0 + - + +
73A VAL* 3.5 2.0 + - - +
74A LEU* 3.0 40.6 + - + +
99A MET* 5.2 7.3 - - - +
162A ASP* 3.0 36.8 + - - +
163A PHE* 3.7 18.8 - - + +
164A GLY* 3.5 22.5 + - - +
400A ATP 5.5 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.5 43.1 - - + -
11A PRO* 4.1 4.9 - - + +
67A ILE* 3.0 17.0 + - + +
70A GLU* 1.3 77.7 - - + +
72A THR* 1.3 65.3 + - - +
74A LEU* 3.9 5.8 - - + +
75A SER* 3.0 21.3 + - - -
85A TYR* 3.1 43.7 - - + +
88A SER* 3.7 2.2 - - - +
97A ILE* 3.6 40.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLY 4.6 0.2 + - - -
11A PRO* 3.8 15.0 - - + +
68A GLN* 2.9 35.8 + - - +
69A GLN* 3.1 15.9 + - - +
71A ILE* 1.3 76.6 - - - +
73A VAL* 1.3 63.9 + - + +
75A SER* 2.7 24.1 + - - +
76A GLN* 3.4 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLN* 3.0 27.6 + - + +
70A GLU 4.1 2.9 - - - +
72A THR* 1.3 76.8 - - + +
74A LEU* 1.3 64.1 + - - +
76A GLN* 2.9 23.5 + - - +
77A CYS* 3.4 14.0 + - - -
140A LYS* 3.9 24.0 - - + -
163A PHE* 3.7 29.4 - - + -
166A ALA* 4.1 26.5 - - + +
167A GLY 5.8 3.4 - - - +
168A GLN* 5.7 3.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLU* 3.0 36.1 + - + +
71A ILE* 4.1 5.4 - - + +
72A THR 3.4 0.2 - - - -
73A VAL* 1.3 77.1 - - - +
75A SER* 1.3 62.0 + - - +
76A GLN 3.2 0.5 + - - -
77A CYS* 3.3 19.5 + - - +
82A VAL* 3.6 10.3 - - + -
83A THR* 3.5 38.4 - - - +
84A LYS* 4.8 1.3 - - - +
85A TYR* 3.9 30.0 + - + +
99A MET* 4.7 15.0 - - + -
162A ASP 6.2 0.2 - - - +
163A PHE* 3.5 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PRO* 3.2 30.2 - - - +
71A ILE 3.0 11.1 + - - -
72A THR* 2.7 20.8 + - - +
74A LEU* 1.3 77.4 - - - +
76A GLN* 1.3 61.1 + - - +
77A CYS 3.4 3.0 + - - +
85A TYR* 3.9 21.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A THR* 3.5 30.9 - - - +
73A VAL* 2.9 12.7 + - - +
75A SER* 1.3 80.8 - - - +
77A CYS* 1.3 61.3 + - - +
134A TYR* 3.9 5.9 + - - -
138A GLU* 4.9 5.0 - - - +
140A LYS* 3.2 35.7 + - - +
168A GLN* 3.7 6.1 + - - +
----------------------------------------------------------
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