Contacts of the helix formed by residues 74 - 86 (chain A) in PDB entry 3VTV
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 ASN 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A HIS 3.4 3.6 + - - +
73A VAL* 1.3 79.5 - - - +
75A MET* 1.3 66.8 + - - +
76A SER* 3.0 14.9 + - - -
77A GLU* 2.8 50.7 + - - +
78A LEU* 3.0 18.0 + - - +
106A VAL 5.5 0.7 - - - +
107A SER 4.0 11.9 + - - +
108A THR 3.8 17.5 - - - +
109A PRO* 4.3 4.0 - - + -
110A ILE 4.4 0.4 - - - +
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Residues in contact with MET 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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74A ASN* 1.3 77.0 - - - +
76A SER* 1.3 57.6 + - - +
78A LEU* 3.7 18.5 - - + +
79A ILE* 2.9 35.8 + - + +
96A LEU* 4.9 2.2 - - - -
103A MET* 3.3 48.7 - - + +
104A VAL 4.9 0.4 - - - +
106A VAL* 3.5 35.3 + - + +
108A THR 4.3 2.2 + - - -
109A PRO 4.8 0.4 - - - -
110A ILE* 3.5 50.0 - - + +
113A VAL* 3.9 7.4 - - + -
126A MET* 4.5 7.2 - - + -
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Residues in contact with SER 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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74A ASN* 3.0 14.3 + - - -
75A MET* 1.3 78.0 - - - +
77A GLU* 1.3 68.5 + - - +
79A ILE* 3.5 11.8 + - - +
80A LYS* 3.2 21.3 + - - +
104A VAL 5.1 8.6 + - - -
106A VAL 5.2 2.9 + - - -
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Residues in contact with GLU 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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72A HIS* 4.1 5.8 + - - +
73A VAL* 3.4 19.1 - - + +
74A ASN* 2.8 52.2 + - - +
76A SER* 1.3 82.8 + - - +
78A LEU* 1.3 61.8 + - - +
80A LYS* 3.2 9.1 + - - +
81A ILE* 3.0 31.3 + - + +
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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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50A ILE* 4.7 6.7 - - + -
69A VAL* 4.4 24.7 - - + -
73A VAL* 4.1 5.8 - - + +
74A ASN 3.0 16.6 + - - +
75A MET* 3.2 12.1 + - - +
77A GLU* 1.3 73.4 - - - +
79A ILE* 1.3 62.6 + - - +
81A ILE* 3.1 19.9 + - + +
82A ILE* 2.9 53.0 + - + +
96A LEU* 4.2 7.2 - - + -
110A ILE* 4.2 15.5 - - + -
126A MET* 3.7 37.9 - - + -
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Residues in contact with ILE 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 MET* 2.9 23.1 + - + +
76A SER* 3.7 9.6 - - - +
78A LEU* 1.3 76.3 - - - +
80A LYS* 1.3 64.1 + - - +
82A ILE* 3.2 2.6 + - - +
83A ARG* 2.9 47.3 + - - +
94A PHE* 4.0 21.7 - - + +
95A PHE* 6.4 0.2 - - - -
96A LEU* 4.1 28.7 - - + +
103A MET 4.5 2.5 - - - -
104A VAL* 3.9 37.7 - - + +
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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 SER 3.2 10.9 + - - +
77A GLU* 3.2 12.0 + - - +
78A LEU 3.2 0.6 - - - -
79A ILE* 1.3 81.7 - - - +
81A ILE* 1.3 57.9 - - + +
83A ARG* 3.5 8.0 + - + +
84A ARG* 3.0 54.4 + - - +
500A SO4 4.6 7.1 + - - -
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Residues in contact with ILE 81 (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 VAL* 6.3 0.7 - - + -
73A VAL* 4.7 15.3 - - + -
77A GLU* 3.0 22.7 + - + +
78A LEU* 3.1 20.8 + - + +
80A LYS* 1.3 78.0 - - + +
82A ILE* 1.3 60.5 + - + +
84A ARG* 3.4 25.0 + - - +
85A ARG* 2.9 33.1 + - + +
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Residues in contact with ILE 82 (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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50A ILE* 3.8 32.3 - - + -
62A LEU* 4.4 17.3 - - + -
78A LEU* 2.9 38.7 + - + +
79A ILE 4.0 0.9 - - - +
81A ILE* 1.3 76.1 - - + +
83A ARG* 1.3 66.0 + - - +
85A ARG* 3.2 6.9 + - - +
86A LEU* 2.9 31.6 + - + +
94A PHE* 3.4 28.3 - - + -
96A LEU* 4.0 29.4 - - + -
128A TYR* 4.8 1.1 - - + -
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Residues in contact with ARG 83 (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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79A ILE* 2.9 35.7 + - - +
80A LYS* 3.9 7.9 - - - +
82A ILE* 1.3 78.6 - - - +
84A ARG* 1.4 61.8 + - - +
86A LEU* 3.4 1.0 + - - -
87A GLN 3.2 3.5 + - - -
88A LEU* 3.0 52.3 + - + +
89A ASN 3.0 30.1 + - - -
90A ALA* 4.1 7.5 + - - +
92A GLN 3.0 23.4 + - - -
93A ALA* 4.3 0.4 - - - +
94A PHE* 3.4 43.2 + - + +
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Residues in contact with ARG 84 (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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80A LYS* 3.0 49.1 + - - +
81A ILE* 3.5 30.9 - - - +
83A ARG* 1.4 74.3 - - - +
85A ARG* 1.3 62.3 + - - +
87A GLN* 2.9 25.4 + - - +
88A LEU 5.2 0.2 - - - +
500A SO4 2.9 44.2 + - - +
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Residues in contact with ARG 85 (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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62A LEU* 3.9 16.9 - - + +
63A ASP* 2.7 44.9 + - - +
64A LYS* 4.1 15.0 - - - +
67A PHE* 3.8 26.8 - - - -
81A ILE* 2.9 23.5 + - + +
82A ILE* 3.2 6.9 + - - +
84A ARG* 1.3 78.2 - - - +
86A LEU* 1.3 60.0 + - - +
87A GLN* 3.4 8.1 + - - +
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Residues in contact with LEU 86 (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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59A LEU* 5.2 1.1 - - + -
60A PRO* 3.5 43.6 - - + +
61A VAL 3.9 4.0 - - - +
62A LEU* 3.6 28.0 - - + +
82A ILE* 2.9 22.1 + - + +
83A ARG 3.4 0.2 + - - -
85A ARG* 1.3 73.3 - - - +
87A GLN* 1.3 69.9 - - - +
88A LEU* 3.4 23.8 + - + +
94A PHE* 3.6 36.6 - - + -
128A TYR* 3.5 21.5 - - + +
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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