Contacts of the helix formed by residues 65 - 80 (chain A) in PDB entry 1GV3
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 LYS 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A LYS 5.4 0.2 - - - -
61A LEU* 2.9 36.9 + - + +
64A ASP* 1.3 85.7 - - + +
66A HIS* 1.3 59.8 + - - +
68A ALA* 3.8 1.3 - - - +
69A ALA* 3.0 31.4 + - - +
212B ASN* 3.9 38.1 + - + +
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Residues in contact with HIS 66 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A LEU* 3.0 25.3 + - + -
62A HIS* 3.3 25.1 - - + +
65A LYS* 1.3 71.1 - - - +
67A HIS* 1.3 65.1 + - - +
69A ALA* 3.3 14.5 + - - +
70A TYR* 3.2 30.6 + - + -
204A HIS* 3.5 36.1 + + + +
203B GLU* 3.7 11.7 - - - -
207B TYR* 2.8 34.2 + + - -
212B ASN* 3.5 26.5 - - + +
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Residues in contact with HIS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 3.5 11.8 - - + +
41A PRO* 3.7 15.5 - - + +
62A HIS 2.9 15.2 + - - +
63A HIS* 3.4 15.5 - - - +
66A HIS* 1.3 72.6 - - - +
68A ALA* 1.3 64.2 + - - +
70A TYR* 3.1 18.4 + - + +
71A VAL* 3.1 9.5 + - + +
113A GLY 4.3 1.3 - - - -
114A HIS* 2.8 42.8 + - - -
117A HIS* 3.4 13.5 - - + +
118A THR* 3.4 33.4 - - - -
121A TRP* 2.9 23.8 + - + +
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 4.0 22.9 - - + +
63A HIS 3.4 3.8 + - - -
64A ASP 3.1 28.9 - - - +
65A LYS 3.8 1.3 - - - +
66A HIS 3.3 0.2 - - - -
67A HIS* 1.3 78.1 - - - +
69A ALA* 1.3 56.2 + - - +
71A VAL* 3.1 7.6 + - - +
72A ASN* 2.9 41.8 + - - +
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Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LYS 3.0 19.0 + - - +
66A HIS* 3.5 7.2 - - - +
67A HIS 3.2 0.2 - - - -
68A ALA* 1.3 77.0 - - - +
70A TYR* 1.3 59.8 + - + +
72A ASN* 3.3 8.7 + - - +
73A ASN* 2.8 46.4 + - - +
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Residues in contact with TYR 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A HIS* 3.2 30.0 + - + -
67A HIS* 3.1 13.2 + - - +
69A ALA* 1.3 79.6 - - + +
71A VAL* 1.3 58.3 + - - +
73A ASN* 5.3 1.1 - - - -
74A LEU* 3.0 29.6 + - - +
109A ASN 4.4 1.1 - - - -
110A ASN* 3.4 45.1 - - - +
113A GLY* 3.8 17.9 - - - -
114A HIS* 4.0 7.6 - - - +
117A HIS* 3.6 23.3 - + - -
185A GLN* 3.0 21.9 + - + -
202A TRP* 4.0 16.5 - - - -
204A HIS* 4.3 7.7 - + - -
162B PHE* 3.9 24.6 - + - -
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ALA* 3.5 33.8 - - + +
39A GLU* 4.2 0.2 - - - -
40A LEU* 4.0 22.9 - - + +
67A HIS* 3.1 18.1 + - + +
68A ALA* 3.1 9.8 + - - +
70A TYR* 1.3 77.0 - - - +
72A ASN* 1.3 67.4 + - - +
74A LEU* 3.3 6.3 + - - +
75A ASN* 3.0 28.2 + - - +
114A HIS* 3.6 37.0 - - + +
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Residues in contact with ASN 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ALA* 2.9 30.1 + - - +
69A ALA* 3.8 7.5 - - - +
71A VAL* 1.3 82.5 - - - +
73A ASN* 1.3 67.7 + - - +
75A ASN* 3.2 11.1 + - - +
76A ASN* 3.0 31.7 + - - +
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Residues in contact with ASN 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ALA* 2.8 29.2 + - - +
70A TYR* 5.3 1.4 - - - -
72A ASN* 1.3 74.7 - - - +
74A LEU* 1.3 61.9 + - - +
76A ASN* 3.5 14.2 + - - +
77A ALA* 3.2 22.3 + - - +
106A THR* 4.3 5.6 - - + +
110A ASN* 3.2 35.2 + - - +
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A THR* 4.5 1.1 - - + -
38A ALA* 4.0 20.9 - - + -
70A TYR 3.0 19.2 + - - +
71A VAL* 3.5 4.7 - - - +
73A ASN* 1.3 74.7 - - - +
75A ASN* 1.3 67.4 + - - +
77A ALA* 3.2 4.7 + - - +
78A LEU* 3.1 49.9 + - + +
89A VAL* 4.0 23.6 - - + -
92A LEU* 5.2 2.2 - - + -
106A THR 5.6 0.4 - - - -
107A VAL* 4.3 27.1 - - + -
110A ASN* 4.0 7.1 - - + +
111A GLY* 4.1 25.4 - - - +
114A HIS* 4.4 8.5 - - + -
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Residues in contact with ASN 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A THR 4.5 2.8 - - - +
37A PRO* 3.6 14.2 - - - +
38A ALA* 2.8 50.6 + - - +
71A VAL* 3.0 22.9 + - - +
72A ASN* 3.6 12.4 + - - +
74A LEU* 1.3 76.9 - - - +
76A ASN* 1.3 62.8 + - - +
78A LEU* 3.3 8.1 + - - +
79A LYS* 3.2 38.1 + - - +
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Residues in contact with ASN 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ASN* 3.0 25.1 + - - +
73A ASN* 3.7 16.8 + - - +
75A ASN* 1.3 79.3 - - - +
77A ALA* 1.3 61.1 + - - +
78A LEU 3.5 0.2 + - - -
79A LYS* 3.6 31.0 + - - +
80A LYS* 3.8 18.6 - - - +
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Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ASN 3.2 9.4 + - - +
74A LEU* 3.2 9.7 + - - +
76A ASN* 1.3 79.5 - - - +
78A LEU* 1.3 61.6 + - - +
80A LYS* 3.5 26.8 + - - +
81A HIS 4.1 0.2 + - - -
103A ILE* 3.4 35.6 - - + +
106A THR* 3.8 24.0 - - + -
107A VAL* 4.7 7.9 - - + -
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A THR* 3.5 43.7 - - + +
74A LEU* 3.1 31.8 + - + +
75A ASN* 3.3 10.0 + - - +
77A ALA* 1.3 72.3 - - - +
79A LYS* 1.3 63.8 + - - +
80A LYS 3.1 2.2 - - - -
81A HIS 3.0 26.7 + - - +
82A PRO 3.4 1.2 - - - -
84A LEU* 4.0 31.4 - - + +
85A GLN* 3.4 18.8 + - + +
92A LEU* 4.3 11.9 - - + -
103A ILE* 4.9 1.1 - - + -
107A VAL* 4.4 16.2 - - + -
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Residues in contact with LYS 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ASN* 3.2 26.5 + - - +
76A ASN* 3.7 23.4 + - - +
77A ALA 3.3 0.6 - - - -
78A LEU* 1.3 76.3 - - - +
80A LYS* 1.3 62.3 + - + +
81A HIS 3.4 0.7 + - - -
82A PRO* 3.5 16.1 - - - +
85A GLN* 3.7 14.4 - - - +
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Residues in contact with LYS 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ASN* 3.8 21.6 - - - +
77A ALA* 3.5 14.0 - - - +
78A LEU 3.1 0.4 - - - -
79A LYS* 1.3 79.1 - - + +
81A HIS* 1.3 77.1 + - + +
82A PRO* 3.6 4.9 - - - +
102A ASP* 5.1 4.7 - - - +
103A ILE* 4.3 16.0 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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