Contacts of the helix formed by residues 15 - 29 (chain C) in PDB entry 2VUT
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 15 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ASN* 2.9 17.9 + - - +
14C THR* 1.3 80.5 + - - +
16C ARG* 1.3 61.1 + - - -
17C GLN 3.2 3.1 + - - -
18C ALA 3.4 2.2 + - - -
19C ALA* 2.9 30.4 + - - +
1355C NAD 3.4 29.6 - - - -
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Residues in contact with ARG 16 (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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14C THR 3.8 1.3 + - - +
15C GLY* 1.3 72.6 - - - -
17C GLN* 1.3 62.1 + - - +
19C ALA* 4.3 3.7 - - - +
20C SER* 3.2 23.4 + - - -
23C ARG* 5.5 0.3 + - - -
153C TYR* 3.5 18.5 - - + -
155C ASN* 2.9 54.3 + - - +
156C ASN* 3.5 24.4 + - - +
192C ALA* 4.1 20.7 - - + +
193C GLU* 4.8 12.8 + - + +
1355C NAD 3.0 46.8 + - - +
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Residues in contact with GLN 17 (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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16C ARG* 1.3 74.9 - - - +
18C ALA* 1.3 65.0 + - - +
20C SER* 3.3 12.1 + - - -
21C LEU 3.3 9.0 + - - -
78C PHE* 3.5 20.2 - - + -
80C ASN* 3.3 28.9 + - - +
111C SER* 2.8 31.9 + - - -
148C VAL* 5.0 1.7 - - - +
150C ALA* 3.9 16.2 - - - +
153C TYR* 2.6 34.4 + - + +
196C VAL* 3.7 27.7 - - + +
218C LEU* 5.5 3.0 - - - +
1355C NAD 3.0 17.4 + - - -
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Residues in contact with ALA 18 (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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10C VAL* 3.4 28.0 - - + -
11C VAL 3.6 3.8 - - - +
12C ASN* 3.5 24.7 - - + +
13C ALA* 3.8 6.3 - - - -
15C GLY 3.4 2.2 + - - +
17C GLN* 1.3 79.0 - - - +
19C ALA* 1.3 58.6 + - - +
21C LEU* 3.2 3.3 + - - +
22C ILE* 2.8 34.9 + - + +
78C PHE* 3.8 12.5 - - + -
80C ASN* 4.9 4.2 - - + +
1355C NAD 4.6 0.6 + - - -
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Residues in contact with ALA 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ALA 3.4 13.6 + - - +
14C THR 4.7 0.2 - - - +
15C GLY 2.9 20.6 + - - +
16C ARG* 4.3 4.3 - - - +
18C ALA* 1.3 72.9 - - - +
20C SER* 1.3 68.5 + - - +
22C ILE* 4.1 5.8 - - - +
23C ARG* 3.1 51.1 + - - +
43C ILE* 4.3 13.5 - - + -
47C LEU* 4.6 4.9 - - + -
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Residues in contact with SER 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ARG 3.2 13.8 + - - -
17C GLN 3.6 4.5 - - - -
18C ALA 3.2 1.0 - - - -
19C ALA* 1.3 82.3 - - - +
21C LEU* 1.3 62.7 + - - +
23C ARG* 3.4 12.5 + - - +
24C VAL* 3.2 24.1 + - - +
192C ALA 3.2 19.3 + - - -
193C GLU* 2.9 23.9 + - - -
196C VAL* 3.9 1.3 + - - -
197C GLY* 2.8 27.2 + - - -
198C PRO* 4.4 1.7 - - - +
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Residues in contact with LEU 21 (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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8C ILE* 4.3 14.6 - - + -
10C VAL* 4.1 14.1 - - + -
17C GLN 3.3 8.5 + - - +
18C ALA 3.2 7.5 + - - +
20C SER* 1.3 79.7 - - - +
22C ILE* 1.3 53.6 + - - +
24C VAL* 3.2 1.2 + - - +
25C ALA* 2.6 48.4 + - + +
78C PHE* 3.5 39.0 - - + -
197C GLY* 3.8 16.2 - - - +
200C LEU* 4.1 28.9 - - + -
201C LEU* 4.3 12.3 - - + +
204C PHE* 4.4 6.7 - - + -
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Residues in contact with ILE 22 (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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10C VAL* 4.7 10.8 - - + -
13C ALA* 3.7 39.0 - - + +
18C ALA* 2.8 27.0 + - + +
19C ALA* 4.1 4.3 - - - +
21C LEU* 1.3 70.5 - - + +
23C ARG* 1.3 66.7 + - - +
25C ALA* 4.5 4.5 - - - +
26C ALA* 3.0 24.1 + - - +
32C VAL* 4.0 18.4 - - + -
34C ALA* 4.1 14.6 - - + -
47C LEU* 4.4 17.9 - - + -
50C ILE* 4.8 1.6 - - + -
53C VAL* 3.6 32.8 - - + -
55C LEU* 5.5 0.2 - - + -
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Residues in contact with ARG 23 (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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16C ARG 5.5 0.4 + - - -
19C ALA* 3.1 49.6 + - - +
20C SER* 3.8 9.3 - - - +
22C ILE* 1.3 75.5 - - - +
24C VAL* 1.3 63.7 + - + +
26C ALA* 4.4 1.0 - - - +
27C ALA* 3.1 27.2 + - - +
43C ILE* 4.0 18.2 - - - +
46C GLU* 3.4 26.0 + - - +
47C LEU* 4.8 10.1 - - + +
50C ILE* 4.8 12.9 - - + +
193C GLU* 3.7 28.7 + - - +
709K PRO* 3.5 19.4 - - + +
710K LEU 4.4 5.2 - - - -
711K SER* 3.1 41.8 + - - +
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Residues in contact with VAL 24 (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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20C SER* 3.2 13.0 + - - +
21C LEU* 3.2 6.7 + - + +
23C ARG* 1.3 77.2 - - + +
25C ALA* 1.3 66.8 + - - +
27C ALA* 3.3 2.4 + - - +
28C VAL* 3.0 27.4 + - + +
197C GLY* 3.9 26.2 - - - +
198C PRO* 4.0 9.2 - - + -
201C LEU* 3.5 31.0 - - + -
700K PHE* 4.0 27.6 - - + -
708K ARG* 5.9 1.6 - - + -
709K PRO* 4.1 13.0 - - + +
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Residues in contact with ALA 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 3.8 29.2 - - + -
21C LEU* 2.6 28.8 + - + +
24C VAL* 1.3 73.4 - - - +
26C ALA* 1.3 63.8 + - - +
28C VAL* 3.1 12.8 - - - +
29C GLY 3.1 0.2 + - - -
30C HIS* 3.0 27.6 + - + -
32C VAL* 4.1 11.4 - - + -
201C LEU* 3.9 12.1 - - + -
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Residues in contact with ALA 26 (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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55A LEU 5.6 0.9 - - - +
56A PHE* 5.1 0.7 - - - -
22C ILE 3.0 19.5 + - - +
23C ARG 4.4 0.7 - - - +
25C ALA* 1.3 75.9 - - - +
27C ALA* 1.3 62.9 + - - +
29C GLY 3.1 5.4 + - - -
30C HIS 3.6 12.6 - - - +
32C VAL* 4.3 3.7 - - + +
50C ILE* 3.6 30.5 - - + -
52C ASN* 2.9 27.5 + - + +
53C VAL* 3.8 14.6 - - + -
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Residues in contact with ALA 27 (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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55A LEU 4.8 4.8 - - - +
56A PHE* 3.9 9.2 - - - -
57A GLN 5.5 0.3 + - - -
23C ARG 3.1 20.6 + - - +
24C VAL 3.7 2.7 - - - +
25C ALA 3.2 0.2 - - - -
26C ALA* 1.3 80.4 - - - +
28C VAL* 1.3 61.1 + - + +
29C GLY 3.5 0.2 + - - -
50C ILE* 5.3 1.7 - - - +
706K VAL* 3.5 25.5 - - + +
707K VAL 5.1 0.7 - - - +
709K PRO* 3.9 25.1 - - + -
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Residues in contact with VAL 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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56A PHE* 3.6 4.0 - - - -
69A THR* 3.3 22.0 + - - +
5C LYS* 3.8 13.4 - - + -
24C VAL* 3.0 17.6 + - + +
25C ALA* 3.1 15.3 - - - +
27C ALA* 1.3 76.3 - - - +
29C GLY* 1.3 55.5 + - - +
30C HIS* 3.3 25.4 - - + +
201C LEU* 4.4 9.0 - - + -
205C LYS* 6.2 0.9 - - - +
700K PHE* 3.8 17.3 - - + -
704K HIS* 3.7 36.9 - - + +
706K VAL* 4.0 14.1 - - + +
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Residues in contact with GLY 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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33A ARG* 5.1 6.1 + - - -
56A PHE* 3.3 24.3 - - - -
69A THR* 4.3 0.2 - - - -
5C LYS* 3.8 16.3 - - - +
26C ALA 3.1 10.2 + - - -
27C ALA 3.2 0.8 + - - -
28C VAL* 1.3 80.3 - - - +
30C HIS* 1.3 65.3 + - - +
31C HIS* 3.7 9.4 + - - -
52C ASN* 4.1 8.4 + - - -
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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