Contacts of the helix formed by residues 18 - 31 (chain J) in PDB entry 1VQ7
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 ILE 18 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12430 C 3.4 21.3 - - - +
12440 U 2.8 45.1 - - - +
17J CYS* 1.3 68.6 - - - +
19J MET* 1.3 65.8 + - - +
21J ARG* 2.9 44.0 + - + +
22J VAL* 3.0 13.0 + - - +
45J VAL* 3.4 15.0 - - + +
46J ILE* 5.6 0.7 - - - -
47J THR* 4.7 7.2 - - - +
118J GLY 5.3 0.4 - - - +
119J THR* 2.7 19.3 + - - +
120J SER 5.1 3.1 - - - +
121J LEU* 4.6 17.5 - - + -
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Residues in contact with MET 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12420 A 4.9 3.1 - - - +
12430 C 4.1 5.4 - - - +
17J CYS 3.1 4.9 + - - -
18J ILE* 1.3 70.2 - - - +
20J GLY* 1.3 58.7 + - - +
22J VAL* 3.3 3.1 + - - +
23J ALA* 2.9 30.9 + - - +
44J ALA* 4.6 4.7 - - + -
45J VAL 2.9 18.5 + - - +
46J ILE* 5.0 5.4 - - + -
57J TYR* 4.5 11.4 - - - -
78J ILE* 3.4 22.0 - - + -
79J PHE* 3.5 44.8 - - + -
82J THR* 3.5 20.2 - - + +
132J LEU* 3.1 45.8 - - + -
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Residues in contact with GLY 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12420 A 3.0 33.6 + - - -
12430 C 2.8 16.5 + - - -
12470 A 3.5 13.6 + - - -
19J MET* 1.3 75.3 - - - +
21J ARG* 1.3 56.8 + - - +
23J ALA* 3.4 5.9 + - - +
24J SER* 3.0 24.4 + - - -
86J MET* 3.8 3.0 - - - +
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Residues in contact with ARG 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11090 U 2.9 65.6 + - + +
12430 C 3.2 26.4 + - - +
12440 U 2.9 23.2 + - - -
12460 A 3.5 16.8 + - - -
12470 A 2.8 33.4 + - - +
18J ILE* 2.9 27.1 + - + +
20J GLY* 1.3 73.2 - - - +
22J VAL* 1.3 67.8 + - - +
25J GLN* 3.5 21.7 + - - +
118J GLY 3.6 25.6 + - - +
119J THR* 4.3 7.4 - - + -
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Residues in contact with VAL 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J VAL* 4.1 18.8 - - + -
14J ALA* 5.0 6.5 - - + -
17J CYS* 3.7 27.4 - - + -
18J ILE 3.0 17.1 + - - +
19J MET* 3.5 7.0 - - - +
21J ARG* 1.3 76.8 - - - +
23J ALA* 1.3 66.0 + - - +
25J GLN* 2.9 6.8 + - - +
26J VAL* 2.9 38.4 + - + +
38J VAL* 4.8 4.3 - - + -
79J PHE* 3.6 21.5 - - + -
116J LEU* 4.3 5.8 - - + -
119J THR* 3.8 17.3 - - + +
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Residues in contact with ALA 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J MET 2.9 17.1 + - - +
20J GLY 3.7 4.7 - - - +
22J VAL* 1.3 77.2 - - - +
24J SER* 1.3 57.7 + - - +
26J VAL* 3.1 4.9 + - - +
27J ALA* 2.8 33.8 + - - +
79J PHE* 4.1 5.2 - - + -
82J THR* 3.9 19.7 - - + -
83J ILE* 3.6 30.3 - - + +
86J MET* 3.8 9.4 - - - +
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Residues in contact with SER 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11020 C 2.5 37.5 + - - +
11030 C 2.9 20.1 + - - +
11090 U 3.1 23.0 + - - -
12470 A 4.2 0.2 - - - -
20J GLY 3.0 13.3 + - - -
21J ARG 3.8 0.4 - - - -
22J VAL 3.2 0.2 - - - -
23J ALA* 1.3 75.5 - - - +
25J GLN* 1.3 57.2 + - - +
27J ALA* 3.9 1.4 - - - +
28J GLU* 3.2 25.3 + - - +
86J MET* 3.5 13.6 - - - -
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Residues in contact with GLN 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11020 C 5.8 0.2 - - - +
11090 U 4.4 18.5 - - + -
21J ARG 3.5 6.5 + - - +
22J VAL 2.9 8.5 + - - +
24J SER* 1.3 77.4 - - - +
26J VAL* 1.3 61.8 + - - +
27J ALA 3.2 0.4 - - - -
28J GLU* 3.3 8.1 + - + +
29J GLN* 2.9 42.0 + - + +
116J LEU* 3.8 26.0 - - + +
117J ASP* 3.4 14.2 + - - +
119J THR* 3.3 29.6 - - - +
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Residues in contact with VAL 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J VAL* 4.8 2.9 - - + -
22J VAL* 2.9 33.0 + - + +
23J ALA* 3.7 8.7 - - - +
25J GLN* 1.3 77.2 - - - +
27J ALA* 1.3 58.3 + - - +
29J GLN* 3.4 7.3 + - - +
30J ALA* 3.0 28.6 + - - +
36J VAL* 3.6 32.7 - - + +
38J VAL* 4.1 12.1 - - + -
83J ILE* 4.3 9.9 - - + -
101J VAL* 3.9 21.8 - - + -
116J LEU* 4.4 9.2 - - + -
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Residues in contact with ALA 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11030 C 3.4 22.9 - - - +
23J ALA 2.8 17.2 + - - +
24J SER 3.9 1.8 - - - +
26J VAL* 1.3 77.0 - - - +
28J GLU* 1.3 63.4 + - - +
30J ALA* 3.3 1.7 + - - +
31J LEU* 3.1 28.7 + - - +
83J ILE* 4.6 7.3 - - + +
86J MET* 3.8 12.3 - - + -
87J LEU* 3.7 28.8 - - + +
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Residues in contact with GLU 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11030 C 4.0 35.6 + - - -
11040 C 3.9 13.5 + - - -
11060 A 5.5 0.7 + - - -
81070 MG 4.3 9.5 - - - -
24J SER 3.2 16.4 + - - +
25J GLN* 3.6 10.1 - - + +
27J ALA* 1.3 81.2 - - - +
29J GLN* 1.3 62.1 + - + +
31J LEU* 3.6 6.3 + - - +
32J ASP* 2.9 33.7 + - - +
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Residues in contact with GLN 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J VAL* 3.9 27.7 - - - +
12J VAL* 5.3 1.8 - - - +
25J GLN* 2.9 28.9 + - + +
26J VAL* 3.9 5.2 - - - +
28J GLU* 1.3 77.5 - - + +
30J ALA* 1.3 59.0 + - - +
31J LEU 3.0 1.6 - - - -
32J ASP* 2.7 33.6 + - - +
34J GLU* 3.3 31.8 + - + +
36J VAL* 4.5 8.0 - - + +
116J LEU* 4.1 25.3 - - - +
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Residues in contact with ALA 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J VAL 3.0 17.5 + - - +
27J ALA* 3.8 5.8 - - - +
29J GLN* 1.3 76.8 - - - +
31J LEU* 1.3 57.4 + - - +
33J GLY* 3.1 17.8 + - - -
34J GLU* 3.5 15.9 - - - +
36J VAL* 4.8 1.7 - - + +
87J LEU* 4.9 1.6 - - + -
97J ALA* 3.5 30.2 - - + +
100J SER* 4.5 1.0 + - - -
101J VAL* 3.5 28.3 - - + -
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Residues in contact with LEU 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11030 C 4.5 1.3 - - - +
11040 C 3.2 37.7 - - - +
27J ALA 3.1 11.1 + - - +
28J GLU* 3.8 8.5 - - - +
29J GLN 3.0 0.8 - - - -
30J ALA* 1.3 77.5 - - - +
32J ASP* 1.3 60.6 + - - +
33J GLY 3.2 2.3 + - - -
87J LEU* 3.4 28.7 - - + -
88J PRO* 4.7 6.7 - - + -
93J ARG* 4.2 49.8 + - + +
94J GLY* 4.7 1.1 - - - -
97J ALA* 3.7 17.5 - - + -
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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