Contacts of the helix formed by residues 27 - 42 (chain C) in PDB entry 1VQM
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 ARG 27 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6560 G 3.6 7.3 + - - -
6570 G 2.3 30.9 + - - -
25C PRO* 4.2 5.4 + - - +
26C VAL* 1.3 75.9 - - - +
28C SER* 1.3 64.1 + - - +
29C ASP* 2.7 42.9 + - - +
30C LEU* 3.1 35.2 + - + +
31C ILE* 3.0 25.6 + - - +
109C LEU* 5.0 6.3 - - + +
113C SER* 2.5 19.5 + - - +
4O ASN* 3.2 35.9 + - - +
5O PRO* 3.8 6.3 - - - -
6O ARG* 4.3 16.0 - - - +
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Residues in contact with SER 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C VAL* 3.9 8.5 + - - +
27C ARG* 1.3 72.6 - - - +
29C ASP* 1.3 59.2 + - - +
31C ILE* 3.9 2.4 - - - +
32C GLY* 3.0 23.4 + - - -
227C GLY 4.4 4.3 - - - +
229C PRO* 4.0 30.5 - - - -
5O PRO* 4.1 15.8 - - - +
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Residues in contact with ASP 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6560 G 4.4 2.6 - - - +
27C ARG* 2.7 45.2 + - - +
28C SER* 1.3 73.5 + - - +
30C LEU* 1.3 76.8 + - - +
32C GLY* 3.3 1.6 + - - -
33C LYS* 3.0 22.7 + - - +
36C ARG* 5.3 1.9 + - - -
3O THR* 3.2 38.9 - - + +
4O ASN* 3.8 1.4 - - - -
5O PRO* 3.1 17.7 - - + +
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Residues in contact with LEU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6560 G 3.4 25.4 - - - +
6570 G 4.1 3.6 - - - -
27C ARG* 3.1 46.3 + - + +
29C ASP* 1.3 85.0 - - - +
31C ILE* 1.3 64.5 + - - +
33C LYS* 3.3 10.8 + - + +
34C ALA* 3.1 17.5 + - - +
106C GLU* 4.0 21.0 - - + +
109C LEU* 3.5 39.0 - - + -
110C ALA* 3.5 20.4 - - + +
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Residues in contact with ILE 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C VAL* 4.9 0.9 - - + -
27C ARG 3.0 17.9 + - - +
28C SER* 4.0 4.7 - - - +
30C LEU* 1.3 74.5 - - - +
32C GLY* 1.3 67.0 + - - +
34C ALA* 3.0 4.9 + - - +
35C VAL* 2.9 21.3 + - - +
110C ALA* 3.8 21.5 - - - +
113C SER* 3.8 13.0 - - - +
114C ALA* 3.7 26.2 - - - +
220C THR* 3.4 20.4 - - + -
224C ALA* 3.5 21.3 - - + -
227C GLY* 4.0 10.3 - - - +
229C PRO* 3.5 25.8 - - + -
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Residues in contact with GLY 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C SER 3.0 18.9 + - - -
29C ASP* 3.7 1.8 - - - -
30C LEU 3.3 0.2 - - - -
31C ILE* 1.3 77.3 - - - +
33C LYS* 1.3 54.7 + - - +
35C VAL* 3.3 1.4 + - - +
36C ARG* 2.8 48.2 + - - +
227C GLY* 4.4 16.1 + - - -
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Residues in contact with LYS 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6560 G 4.4 5.7 + - - +
7500 A 3.6 45.6 + - - -
7510 U 4.0 16.6 + - - -
29C ASP 3.0 13.5 + - - +
30C LEU* 3.5 16.2 - - + +
31C ILE 3.2 0.2 - - - -
32C GLY* 1.3 74.7 - - - +
34C ALA* 1.3 64.9 + - - +
36C ARG* 3.5 20.1 - - - +
37C ALA* 3.0 23.7 + - + +
101C ASP 5.3 1.1 - - - -
102C LEU* 3.9 18.4 - - + -
106C GLU* 3.0 31.6 + - + +
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Residues in contact with ALA 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LEU 3.1 11.9 + - - +
31C ILE 3.0 8.2 + - - +
33C LYS* 1.3 76.4 - - - +
35C VAL* 1.3 62.6 + - - +
37C ALA* 3.3 4.0 + - - +
38C ALA* 3.1 22.2 + - - +
102C LEU* 3.7 20.9 - - + +
107C ARG* 4.9 7.0 - - + -
110C ALA* 3.8 13.5 - - + -
220C THR* 3.7 26.2 - - + +
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Residues in contact with VAL 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ILE 2.9 19.4 + - - +
32C GLY 3.8 2.9 - - - +
34C ALA* 1.3 71.9 - - - +
36C ARG* 1.3 66.7 + - - +
38C ALA* 3.1 2.9 + - - +
39C GLN* 2.9 45.5 + - - +
220C THR* 3.8 17.5 - - + -
221C GLU* 4.2 24.7 - - + +
224C ALA 3.6 21.3 - - - +
226C GLY* 3.9 8.7 - - - +
227C GLY* 3.6 24.5 - - - +
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Residues in contact with ARG 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4490 A 5.6 0.2 + - - -
7510 U 5.9 1.5 + - - -
13480 A 2.9 38.3 + - - +
13490 G 3.6 42.1 + - - +
29C ASP 5.3 1.8 + - - -
32C GLY* 2.8 31.9 + - - +
33C LYS* 3.5 27.7 - - - +
35C VAL* 1.3 76.0 - - - +
37C ALA* 1.3 57.4 + - - +
39C GLN* 3.5 13.5 + - - +
40C ALA* 3.0 28.9 + - - +
100C LEU* 4.2 15.3 - - + -
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Residues in contact with ALA 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6760 C 4.2 0.9 - - - +
33C LYS* 3.0 17.0 + - + +
34C ALA 3.6 4.9 - - - +
35C VAL 3.1 0.4 - - - -
36C ARG* 1.3 74.8 - - - +
38C ALA* 1.3 64.7 + - - +
40C ALA 3.9 0.3 - - - -
41C ASN* 2.9 35.2 + - - +
100C LEU* 4.1 31.9 - - + +
101C ASP 5.0 0.7 - - - +
102C LEU* 4.1 21.3 - - + -
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Residues in contact with ALA 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6750 U 2.6 22.7 + - - +
6760 C 3.5 34.1 + - - -
34C ALA 3.1 11.3 + - - +
35C VAL 3.1 6.7 + - - +
37C ALA* 1.3 77.4 - - - +
39C GLN* 1.3 62.6 + - - +
41C ASN 3.5 6.1 + - - -
42C ARG* 3.3 4.5 + - - -
219C ASN* 6.4 0.2 - - - -
221C GLU* 3.4 26.9 - - + +
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Residues in contact with GLN 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4490 A 5.4 5.8 + - + +
13060 U 6.1 0.2 - - - -
13070 A 3.0 39.7 + - - +
35C VAL* 2.9 36.3 + - - +
36C ARG* 3.8 11.0 - - - +
38C ALA* 1.3 79.2 - - - +
40C ALA* 1.3 59.2 + - - +
42C ARG* 3.5 31.8 + - - +
43C LYS* 3.0 37.2 + - - +
221C GLU* 3.8 9.9 - - - +
226C GLY* 4.6 2.4 + - - -
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Residues in contact with ALA 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4490 A 4.0 22.9 - - - +
36C ARG 3.0 17.2 + - - +
37C ALA 3.3 2.0 + - - +
39C GLN* 1.3 77.0 - - - +
41C ASN* 1.3 66.1 + - - +
43C LYS* 3.2 21.3 + - - +
98C ARG 3.5 19.5 - - - +
100C LEU* 3.6 29.6 - - + -
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Residues in contact with ASN 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6740 A 4.2 2.6 + - - -
6750 U 3.4 32.4 - - - +
6760 C 2.9 21.0 + - - +
37C ALA* 2.9 24.7 + - - +
38C ALA 3.5 0.2 + - - -
39C GLN 3.3 0.6 - - - -
40C ALA* 1.3 76.1 - - - +
42C ARG* 1.3 56.8 + - - +
43C LYS 3.4 3.4 + - - +
99C SER* 3.2 15.5 - - - +
100C LEU 3.0 41.6 + - - +
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Residues in contact with ARG 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4480 G 5.9 0.2 - - - +
4490 A 4.4 4.6 + - - -
6740 A 4.1 10.5 + - - +
6750 U 2.8 60.4 + - - +
13070 A 6.1 2.4 - - - -
38C ALA 3.3 5.4 + - - +
39C GLN* 3.5 30.1 + - - +
41C ASN* 1.3 76.9 - - - +
43C LYS* 1.3 72.2 + - + +
44C GLN* 3.6 9.0 + - - +
221C GLU* 2.9 37.8 + - - -
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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