Contacts of the helix formed by residues 81 - 101 (chain R) in PDB entry 1VQ4
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 PRO 81 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20500 G 3.8 0.9 - - - +
20510 G 3.8 12.8 - - - +
27R HIS* 3.6 31.2 - - + +
31R ILE* 4.4 9.0 - - + -
50R VAL* 4.1 1.3 - - + -
57R VAL* 3.9 19.7 - - + -
59R PHE* 3.5 31.6 - - + -
79R ARG* 3.3 9.4 - - + +
80R TYR* 1.3 81.8 - - - +
82R GLU* 1.3 56.4 + - - +
83R LYS 3.5 1.6 - - - -
84R ALA* 4.3 2.0 - - + -
85R SER* 2.4 36.7 + - - -
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Residues in contact with GLU 82 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20500 G 3.1 41.9 + - - +
20510 G 3.4 7.4 + - - +
51R ILE* 4.4 32.1 - - + +
80R TYR 2.7 10.8 + - - +
81R PRO* 1.3 69.4 - - - +
83R LYS* 1.3 68.9 + - - +
85R SER* 3.4 5.7 - - - -
86R LYS* 2.8 61.2 + - - +
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Residues in contact with LYS 83 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14330 G 4.6 10.1 + - - -
20510 G 3.0 36.0 + - - +
20520 U 3.0 33.2 + - - +
22R GLN* 3.2 27.1 + - - +
23R MET* 4.5 9.2 - - + -
24R SER 5.9 0.2 - - - +
82R GLU* 1.3 86.1 - - - +
84R ALA* 1.3 64.3 + - - +
86R LYS* 3.1 16.7 + - - +
87R ALA* 3.2 12.7 + - + +
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Residues in contact with ALA 84 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20510 G 4.3 2.0 + - - -
23R MET* 4.0 25.3 - - + +
24R SER 4.6 3.1 - - - +
27R HIS* 3.9 24.7 - - + +
28R SER* 4.3 6.5 - - - +
31R ILE* 3.6 19.3 - - + -
81R PRO* 3.8 4.2 + - + +
82R GLU 3.4 0.4 - - - -
83R LYS* 1.3 79.8 - - - +
85R SER* 1.3 59.6 + - - +
87R ALA* 3.3 2.6 + - - +
88R PHE* 3.0 30.1 + - - -
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Residues in contact with SER 85 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31R ILE* 3.6 15.8 - - - +
47R LEU* 4.0 18.1 - - - +
50R VAL* 3.8 13.3 - - - +
51R ILE* 3.9 19.5 - - - -
81R PRO* 2.4 25.4 + - - +
82R GLU* 3.4 4.3 - - - -
83R LYS 3.1 0.2 - - - -
84R ALA* 1.3 74.0 - - - +
86R LYS* 1.3 66.8 + - - +
87R ALA 3.0 2.0 - - - -
88R PHE* 3.0 7.0 + - - +
89R LEU* 2.9 26.6 + - - +
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Residues in contact with LYS 86 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51R ILE* 3.8 27.8 - - + -
82R GLU* 2.8 53.5 + - - +
83R LYS* 3.6 7.4 - - - +
85R SER* 1.3 73.3 - - - +
87R ALA* 1.3 62.5 + - - +
89R LEU* 3.3 11.4 + - + +
90R ASP* 3.2 25.6 + - - +
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Residues in contact with ALA 87 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18R LEU* 3.3 17.4 - - + +
21R ARG* 3.9 26.0 - - - +
23R MET* 3.7 25.4 - - + -
83R LYS* 3.2 10.6 + - + +
84R ALA 3.4 10.1 - - - +
85R SER 3.0 0.6 - - - -
86R LYS* 1.3 75.4 - - - +
88R PHE* 1.3 64.0 + - - +
90R ASP* 3.1 8.6 + - - +
91R LEU 3.1 16.3 + - - -
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Residues in contact with PHE 88 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18R LEU* 4.6 1.8 - - + -
23R MET* 4.0 11.7 - - + -
28R SER* 3.9 44.6 - - - -
31R ILE* 3.8 22.0 - - + -
32R ALA* 4.1 8.1 - - + -
35R ILE* 3.9 13.5 - - + -
47R LEU* 3.6 21.3 - - + -
84R ALA 3.0 26.6 + - - +
85R SER 3.0 4.7 + - - +
87R ALA* 1.3 76.3 - - - +
89R LEU* 1.3 56.4 + - - +
91R LEU* 3.0 17.8 + - + +
92R LEU* 2.7 38.0 + - + +
114R VAL* 4.1 14.1 - - + -
116R ALA* 4.9 1.1 - - + -
143R VAL* 4.0 28.3 - - + -
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Residues in contact with LEU 89 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44R VAL* 3.9 38.1 - - + +
47R LEU* 3.7 23.3 - - + -
48R GLU* 4.0 16.6 - - + +
51R ILE* 3.4 32.5 - - + -
85R SER 2.9 13.0 + - - +
86R LYS* 3.4 12.1 - - + +
87R ALA 3.2 0.2 - - - -
88R PHE* 1.3 78.1 - - - +
90R ASP* 1.3 58.4 + - - +
92R LEU* 3.7 3.9 - - + +
93R GLU* 2.8 28.4 + - - +
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Residues in contact with ASP 90 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4960 G 5.7 0.7 - - - +
18R LEU* 4.6 2.0 - - + -
21R ARG* 3.1 34.9 + - - +
86R LYS 3.2 12.5 + - - +
87R ALA* 3.1 9.7 + - - +
88R PHE 3.0 0.6 - - - -
89R LEU* 1.3 77.9 - - - +
91R LEU* 1.3 67.4 + - - +
93R GLU* 3.1 19.6 + - - +
94R ASN* 3.0 24.9 + - - +
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Residues in contact with LEU 91 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16R ALA* 3.5 14.4 - - + +
17R MET* 3.4 46.7 - - - +
18R LEU* 3.8 16.6 - - + +
87R ALA 3.1 5.3 + - - +
88R PHE* 3.0 21.2 + - + +
90R ASP* 1.3 80.5 - - - +
92R LEU* 1.3 56.1 + - + +
94R ASN* 3.4 5.4 + - + +
95R ALA* 2.9 28.8 + - - +
114R VAL* 4.8 1.1 - - + -
143R VAL* 3.4 35.9 - - + +
145R LEU* 3.8 25.8 - - + -
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Residues in contact with LEU 92 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35R ILE* 4.8 6.5 - - + -
40R ALA* 4.3 19.7 - - + -
43R ALA* 3.8 22.2 - - + -
44R VAL* 4.0 24.5 - - + +
47R LEU* 3.9 20.2 - - + -
88R PHE* 2.7 20.8 + - + +
89R LEU* 3.8 5.8 - - + +
91R LEU* 1.3 75.4 - - + +
93R GLU* 1.3 65.1 + - - +
94R ASN 3.1 1.8 - - - -
95R ALA* 4.4 3.1 - - + -
96R VAL* 3.0 30.6 + - + +
111R ILE* 4.1 17.5 - - + -
145R LEU* 3.6 25.1 - - + -
147R LEU* 5.1 1.3 - - + -
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Residues in contact with GLU 93 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4930 U 4.6 4.3 + - - +
4940 C 3.7 44.7 + - - +
4950 A 5.2 2.1 + - - -
89R LEU 2.8 18.4 + - - +
90R ASP* 3.1 20.5 + - - +
92R LEU* 1.3 76.2 - - - +
94R ASN* 1.3 57.1 + - - +
96R VAL* 4.1 3.4 - - - +
97R GLY* 3.1 22.2 + - - -
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Residues in contact with ASN 94 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4930 U 4.1 12.2 + - - +
4990 G 3.1 28.7 + - - +
5000 G 2.7 47.6 + - - +
16R ALA* 3.6 9.6 - - + +
17R MET 4.8 1.3 + - - +
90R ASP 3.0 15.4 + - - +
91R LEU* 3.5 6.3 - - - +
93R GLU* 1.3 77.1 - - - +
95R ALA* 1.3 55.4 + - - +
97R GLY* 2.8 2.9 + - - -
98R ASN* 2.7 56.0 + - - -
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Residues in contact with ALA 95 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14R ALA* 4.2 2.1 - - - +
15R LYS 4.1 9.0 - - - +
16R ALA* 3.6 19.5 - - + -
91R LEU 2.9 17.9 + - - +
92R LEU* 4.0 3.6 - - + +
94R ASN* 1.3 77.5 - - - +
96R VAL* 1.3 58.1 + - + +
97R GLY 3.2 0.2 + - - -
98R ASN* 3.3 2.3 + - - +
99R ALA* 2.9 30.0 + - - +
145R LEU* 4.3 12.3 - - + -
147R LEU* 3.5 26.2 - - + +
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Residues in contact with VAL 96 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40R ALA* 3.5 33.2 - - + -
44R VAL* 5.6 3.1 - - + -
92R LEU* 3.0 24.2 + - + +
93R GLU* 4.4 3.8 - - - +
95R ALA* 1.3 75.4 - - - +
97R GLY* 1.3 62.1 + - - +
99R ALA* 3.6 7.4 - - - +
100R ASP* 2.8 40.7 + - - +
106R GLY* 3.9 5.6 - - - -
107R GLU* 3.9 29.2 - - + +
147R LEU* 4.3 4.5 - - + -
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Residues in contact with GLY 97 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4920 C 5.3 1.0 + - - -
4930 U 5.4 14.6 - - - -
93R GLU 3.1 14.6 + - - -
94R ASN* 2.8 10.1 + - - -
96R VAL* 1.3 75.7 - - - +
98R ASN* 1.3 65.5 + - - -
100R ASP* 3.0 18.2 + - - +
101R HIS* 3.1 14.0 + - - +
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Residues in contact with ASN 98 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4920 C 4.6 2.4 + - - -
4930 U 5.1 3.4 + - - -
5000 G 3.1 27.5 - - - +
5010 G 2.6 43.0 + - - +
14R ALA* 5.3 1.3 - - + -
15R LYS 3.1 14.5 - - - +
94R ASN* 2.7 36.4 + - - -
95R ALA 3.6 5.8 - - - +
97R GLY* 1.3 72.4 - - - +
99R ALA* 1.3 63.0 + - - +
101R HIS* 3.3 8.4 + - - +
102R GLN* 3.2 32.4 + - - +
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Residues in contact with ALA 99 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14R ALA* 3.8 14.5 - - + +
95R ALA 2.9 18.2 + - - +
96R VAL* 3.6 7.9 - - - +
98R ASN* 1.3 77.3 - - - +
100R ASP* 1.3 62.6 + - - +
102R GLN* 3.1 7.5 + - - +
104R PHE* 3.0 33.5 + - - -
106R GLY* 4.0 3.1 - - - -
109R MET* 3.1 33.2 - - + -
147R LEU* 4.5 0.7 - - + -
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Residues in contact with ASP 100 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96R VAL* 2.8 26.0 - - - +
97R GLY* 3.0 9.2 + - - +
99R ALA* 1.3 70.9 - - - +
101R HIS* 1.3 56.4 + - - +
102R GLN 2.7 6.1 + - - -
103R GLY* 2.6 25.8 + - - -
104R PHE 3.3 12.2 - - - +
105R ASP* 4.2 1.7 - - - +
106R GLY* 3.2 23.1 + - - -
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Residues in contact with HIS 101 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4910 C 4.3 11.4 + - - -
4920 C 3.3 54.4 + - - +
5010 G 4.3 13.2 + - - -
5020 A 6.1 1.8 - - - -
97R GLY 3.1 10.1 + - - +
98R ASN* 3.6 11.4 - - - +
100R ASP* 1.3 77.6 - - - +
102R GLN* 1.3 61.7 + - + +
103R GLY 3.9 0.2 + - - -
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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