Contacts of the helix formed by residues 91 - 109 (chain V) in PDB entry 1V7M
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 GLY 91 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78V ARG* 3.1 23.4 + - - -
88V SER 3.9 2.0 - - - -
89V LEU 2.4 17.2 + - - -
90V LEU* 1.3 69.8 - - - +
92V GLN* 1.3 56.0 + - - -
93V LEU* 2.9 10.5 - - - +
94V SER* 3.1 28.2 - - - -
95V GLY 3.2 4.2 + - - -
98V ARG* 5.3 1.0 + - - -
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Residues in contact with GLN 92 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22V LEU* 3.8 24.8 - - + +
25V ARG* 5.3 4.7 + - - +
88V SER* 3.1 22.2 + - - +
89V LEU* 2.9 53.6 + - - +
91V GLY* 1.3 72.8 - - - +
93V LEU* 1.3 58.1 + - - +
95V GLY* 3.3 6.8 + - - +
96V GLN* 3.1 30.8 + - - +
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Residues in contact with LEU 93 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19V SER* 5.4 7.0 - - - +
22V LEU* 3.9 10.0 - - + +
70V LEU* 5.5 0.4 - - + -
74V VAL* 4.0 24.2 - - + -
89V LEU 3.4 7.5 + - - +
90V LEU* 4.3 5.2 - - + -
91V GLY 3.4 12.3 - - - +
92V GLN* 1.3 76.8 - - - +
94V SER* 1.3 50.4 + - - +
96V GLN* 2.8 26.9 + - + +
97V VAL* 2.8 26.0 + - + +
127V ILE* 4.8 19.3 - - + +
128V PHE* 4.0 37.2 - - + +
131V PHE* 4.0 29.8 - - + -
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Residues in contact with SER 94 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71V LEU* 5.4 4.5 - - - -
74V VAL* 3.1 25.8 - - - +
75V MET* 4.2 9.5 - - - -
78V ARG* 5.1 1.1 + - - -
90V LEU 4.1 0.2 + - - -
91V GLY* 3.1 22.0 + - - -
93V LEU* 1.3 74.1 - - - +
95V GLY* 1.3 63.2 + - - -
97V VAL* 3.8 10.3 - - - +
98V ARG* 3.1 54.6 + - - +
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Residues in contact with GLY 95 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91V GLY 3.2 9.2 + - - -
92V GLN* 3.3 9.6 + - - -
93V LEU 3.2 0.8 - - - -
94V SER* 1.3 79.2 - - - +
96V GLN* 1.3 63.6 + - - +
98V ARG* 3.2 13.3 + - - +
99V LEU* 2.8 29.2 - - - +
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Residues in contact with GLN 96 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15V LEU* 4.0 21.4 - - + +
18V ASP* 2.6 49.6 + - + +
19V SER* 5.3 1.6 - - - -
22V LEU* 4.4 14.4 - - + -
92V GLN 3.1 18.4 + - - +
93V LEU* 2.8 17.8 + - + +
95V GLY* 1.3 71.9 - - - +
97V VAL* 1.3 64.7 + - - +
98V ARG 3.0 1.0 + - - -
99V LEU* 3.3 25.1 + - - +
100V LEU 3.5 7.1 + - - -
131V PHE* 3.7 25.9 - - + -
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Residues in contact with VAL 97 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67V VAL* 3.7 13.6 - - + +
70V LEU* 3.7 31.4 - - + -
71V LEU* 3.6 31.6 - - + -
74V VAL* 4.5 8.3 - - + -
93V LEU* 2.8 42.2 + - + +
94V SER* 3.8 9.6 - - - +
96V GLN* 1.3 73.2 - - - +
98V ARG* 1.3 57.4 + - - +
100V LEU* 3.3 5.0 + - - +
101V LEU* 3.0 24.2 + - + +
131V PHE* 4.0 13.0 - - + -
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Residues in contact with ARG 98 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H THR* 4.3 8.7 - - - +
31H ASP* 3.2 35.8 + - - +
55H VAL* 3.9 24.8 - - + +
71V LEU* 3.5 19.4 - - + +
75V MET* 3.9 31.3 - - - +
91V GLY 5.3 0.8 + - - -
94V SER* 3.1 34.5 + - - +
95V GLY* 3.6 9.9 - - - +
96V GLN 3.0 1.4 + - - -
97V VAL* 1.3 75.4 - - - +
99V LEU* 1.3 69.0 + - + +
101V LEU* 3.3 8.6 + - + +
102V GLY* 3.0 21.0 + - - -
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Residues in contact with LEU 99 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H VAL* 5.3 6.3 - - + -
15V LEU* 3.8 20.2 - - + -
95V GLY* 2.8 30.5 - - - +
96V GLN* 3.6 15.3 - - - +
98V ARG* 1.3 80.3 - - + +
100V LEU* 1.3 64.5 + - - +
102V GLY* 3.2 1.5 + - - -
103V ALA* 3.0 23.7 + - - +
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Residues in contact with LEU 100 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11V VAL* 5.9 2.0 - - + -
15V LEU* 4.0 20.0 - - + +
67V VAL* 3.5 36.8 - - + -
96V GLN 3.5 5.1 + - - +
97V VAL* 3.3 11.1 + - - +
98V ARG 3.3 0.2 - - - -
99V LEU* 1.3 78.3 - - - +
101V LEU* 1.3 63.6 + - - +
103V ALA* 3.2 9.8 + - + +
104V LEU* 3.1 35.9 + - + +
131V PHE* 4.6 6.7 - - + -
134V LEU* 5.9 2.9 - - + -
135V LEU* 4.0 27.4 - - + -
139V VAL* 4.7 20.2 - - + -
143V MET* 5.6 6.5 - - + -
150V LEU* 6.6 0.2 - - + -
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Residues in contact with LEU 101 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H ASP* 5.0 10.1 - - - +
55H VAL* 5.4 6.1 - - + -
101H TRP* 4.4 13.0 - - + -
64V LEU* 4.3 4.4 - - + +
67V VAL* 4.1 15.5 - - + +
68V THR* 3.9 39.9 - - + +
71V LEU* 4.9 16.8 - - + -
97V VAL* 3.0 15.9 + - + +
98V ARG* 3.7 9.2 - - + +
99V LEU 3.2 0.2 - - - -
100V LEU* 1.3 78.9 - - - +
102V GLY* 1.3 56.4 + - - +
104V LEU* 3.7 4.1 - - - +
105V GLN* 2.8 69.5 + - + +
111V GLN* 4.6 1.1 - - - +
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Residues in contact with GLY 102 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55H VAL* 4.4 14.6 - - - +
56H ASN* 3.3 24.2 - - - +
98V ARG 3.0 14.1 + - - -
99V LEU* 3.6 3.6 - - - -
101V LEU* 1.3 74.0 - - - +
103V ALA* 1.3 59.6 + - - +
105V GLN* 4.3 0.4 - - - -
106V SER* 3.0 32.7 + - - -
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Residues in contact with ALA 103 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11V VAL* 5.1 8.3 - - + -
99V LEU 3.0 12.9 + - - +
100V LEU* 3.6 16.2 - - + +
102V GLY* 1.3 76.1 - - - +
104V LEU* 1.3 58.0 + - + +
106V SER* 3.6 4.1 - - - -
107V LEU* 3.1 28.1 + - - +
143V MET* 6.4 0.7 - - + -
150V LEU* 3.9 12.5 - - + +
151V CYS 3.6 31.9 - - - +
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Residues in contact with LEU 104 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60V ALA* 4.5 23.6 - - + +
63V ILE* 3.7 30.5 - - + -
64V LEU* 3.8 24.5 - - + +
67V VAL* 3.7 19.7 - - + -
100V LEU* 3.1 30.0 + - + +
101V LEU 3.9 2.0 - - - +
103V ALA* 1.3 74.3 - - + +
105V GLN* 1.3 66.6 + - - +
106V SER 3.2 1.3 - - - -
107V LEU* 3.5 14.2 + - + +
108V LEU* 3.0 29.9 + - + +
139V VAL* 5.8 1.6 - - + -
142V LEU* 5.1 3.8 - - + -
150V LEU* 5.0 13.7 - - + -
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Residues in contact with GLN 105 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H ASP 5.2 0.5 - - - +
33H TRP* 3.7 17.6 + - + -
53H SER* 4.8 0.9 + - - -
55H VAL* 4.9 0.2 - - - +
56H ASN* 3.1 21.3 + - - +
101H TRP* 3.9 4.8 - - - +
64V LEU* 3.8 16.0 - - + +
68V THR* 5.1 0.4 - - - +
101V LEU* 2.8 56.4 + - - +
102V GLY 4.2 0.2 - - - +
104V LEU* 1.3 72.5 - - - +
106V SER* 1.3 52.8 + - - +
108V LEU 3.1 1.2 + - - -
109V GLY* 2.6 33.4 + - - -
110V THR 3.4 25.4 + - - +
111V GLN* 2.7 41.5 + - + +
112V LEU 5.1 0.2 - - - +
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Residues in contact with SER 106 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52H ARG* 4.8 15.1 + - - +
56H ASN* 3.8 10.9 + - - -
102V GLY 3.0 20.2 + - - -
103V ALA* 3.6 5.8 - - - -
104V LEU 3.2 0.2 - - - -
105V GLN* 1.3 75.5 - - - +
107V LEU* 1.3 66.9 + - - +
108V LEU 3.2 0.7 + - - -
109V GLY* 3.2 10.2 + - - -
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Residues in contact with LEU 107 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60V ALA* 4.7 13.0 - - + -
103V ALA 3.1 14.9 + - - +
104V LEU* 3.8 15.0 - - + +
105V GLN 3.5 0.2 - - - -
106V SER* 1.3 81.1 + - - +
108V LEU* 1.3 75.2 + - + +
109V GLY 3.7 0.2 + - - -
142V LEU* 5.4 2.7 - - + -
148V SER* 3.9 31.0 - - - +
149V THR 4.1 15.0 - - - +
150V LEU* 4.7 17.0 - - + +
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Residues in contact with LEU 108 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90L ARG 5.3 3.3 - - - +
57V GLU* 4.1 26.3 - - + +
60V ALA* 4.2 22.9 - - + +
61V GLN* 3.4 39.7 + - + +
64V LEU* 3.4 25.6 - - + -
104V LEU* 3.0 20.1 + - + +
105V GLN 3.8 2.0 - - - +
107V LEU* 1.3 90.4 - - + +
109V GLY* 1.3 62.4 + - - +
110V THR* 3.1 17.6 + - + +
112V LEU* 3.9 4.5 - - + -
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Residues in contact with GLY 109 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H TRP* 3.6 10.5 - - - -
52H ARG* 4.4 8.5 - - - -
90L ARG 5.6 1.8 - - - -
93L TYR* 3.4 10.3 + - - -
95L ARG* 3.3 28.5 + - - -
105V GLN 2.6 15.0 + - - -
106V SER 3.2 9.7 + - - -
107V LEU 3.7 0.2 + - - -
108V LEU* 1.3 73.6 - - - +
110V THR* 1.3 54.6 + - - -
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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
------------------------------------------------------------
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