Contacts of the helix formed by residues 15 - 29 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H ASN* 2.9 24.4 + - - +
14H THR* 1.3 80.8 - - - +
16H ARG* 1.3 61.6 + - - -
17H GLN 3.3 3.4 - - - -
18H ALA* 3.4 2.4 + - - -
19H ALA* 2.8 28.2 + - - +
1354H NAD 3.4 26.0 - - - -
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Residues in contact with ARG 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H THR 3.7 2.2 + - - +
15H GLY* 1.3 69.4 - - - -
17H GLN* 1.3 65.4 + - - +
19H ALA* 4.3 4.4 - - - +
20H SER* 3.2 23.7 + - - -
23H ARG* 5.4 0.2 + - - -
43H ILE* 6.4 2.2 - - + -
153H TYR* 3.3 26.2 - - + -
155H ASN* 2.7 53.0 + - - +
156H ASN* 3.2 28.3 + - - +
192H ALA* 3.9 22.4 - - + +
193H GLU* 4.7 9.0 + - + +
1354H NAD 2.9 43.3 + - - +
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Residues in contact with GLN 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H ARG* 1.3 78.7 - - - +
18H ALA* 1.3 63.2 + - - +
20H SER* 3.4 4.0 + - - -
21H LEU* 3.4 16.3 + - - +
78H PHE* 3.3 23.4 - - + -
80H ASN* 3.4 19.8 + - - +
111H SER* 2.7 27.1 + - - -
148H VAL* 5.0 0.7 - - - +
150H ALA* 3.6 24.2 - - + +
153H TYR* 2.9 34.9 + - + +
196H VAL* 3.7 28.7 - - + +
218H LEU* 5.5 2.9 - - - +
1354H NAD 3.2 19.5 + - - +
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Residues in contact with ALA 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H VAL* 3.8 25.8 - - + -
11H VAL 3.8 3.1 - - - +
12H ASN* 3.3 26.5 - - + +
13H ALA* 3.9 6.1 - - - +
15H GLY 3.4 2.3 + - - +
17H GLN* 1.3 78.4 - - - +
19H ALA* 1.3 66.5 + - - +
21H LEU* 2.8 6.2 + - - +
22H ILE* 2.8 26.0 + - - +
78H PHE* 4.1 14.3 - - + -
80H ASN* 5.3 2.7 - - + +
1354H NAD 4.5 0.8 + - - +
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Residues in contact with ALA 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H ALA 3.3 14.5 + - - +
14H THR 4.5 0.4 - - - +
15H GLY 2.8 23.4 + - - +
16H ARG* 4.3 4.5 - - - +
18H ALA* 1.3 73.1 - - - +
20H SER* 1.3 61.6 + - - +
22H ILE* 3.8 6.2 - - - +
23H ARG* 3.1 56.2 + - - +
43H ILE* 4.4 12.1 - - + -
47H LEU* 4.7 4.3 - - + -
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Residues in contact with SER 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H ARG 3.2 17.6 + - - -
17H GLN 3.4 6.3 - - - -
18H ALA 3.0 0.6 - - - -
19H ALA* 1.3 80.5 - - - +
21H LEU* 1.3 59.7 + - - +
23H ARG* 3.9 11.4 - - - +
24H VAL* 3.3 23.6 + - - +
192H ALA 3.1 14.6 + - - -
193H GLU* 3.0 25.5 + - - +
196H VAL* 4.1 0.9 - - - -
197H GLY* 2.8 27.4 + - - -
198H PRO* 4.6 1.0 - - - +
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Residues in contact with LEU 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H ILE* 4.4 6.3 - - + -
10H VAL* 4.4 15.7 - - + -
17H GLN 3.4 7.4 + - - +
18H ALA* 2.8 12.6 + - - +
20H SER* 1.3 73.7 - - - +
22H ILE* 1.3 58.5 + - - +
24H VAL* 2.9 9.9 - - + +
25H ALA* 2.6 45.5 + - + +
32H VAL* 6.2 0.7 - - + -
78H PHE* 3.5 34.5 - - + -
197H GLY* 3.8 11.0 - - - +
200H LEU* 3.8 30.7 - - + -
201H LEU* 4.2 15.9 - - + +
204H PHE* 4.2 15.9 - - + -
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Residues in contact with ILE 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H VAL* 4.4 13.0 - - + -
13H ALA* 3.6 40.4 - - + +
18H ALA 2.8 20.2 + - - +
19H ALA 3.8 4.0 - - - +
21H LEU* 1.3 76.9 - - + +
23H ARG* 1.3 58.7 + - - +
25H ALA* 4.4 4.5 - - - -
26H ALA* 2.8 32.1 + - - +
32H VAL* 4.0 17.5 - - + -
34H ALA* 3.9 14.6 - - + -
47H LEU* 3.6 20.9 - - + -
50H ILE* 4.6 0.9 - - + -
53H VAL* 3.6 30.3 - - + -
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Residues in contact with ARG 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H ARG 5.4 0.4 + - - -
19H ALA* 3.1 46.3 + - - +
20H SER* 3.9 9.3 - - - +
22H ILE* 1.3 75.8 - - - +
24H VAL* 1.3 58.0 + - - +
26H ALA* 4.3 0.7 - - - +
27H ALA* 3.1 30.8 + - - +
43H ILE* 4.3 16.8 - - - +
46H GLU* 2.5 36.2 + - - +
47H LEU* 4.6 4.6 - - + +
50H ILE* 4.2 20.5 - - + +
193H GLU* 4.5 14.6 + - - +
709P PRO* 3.5 18.9 - - + +
710P LEU 4.3 5.6 - - - +
711P SER* 3.2 40.1 - - - +
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Residues in contact with VAL 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H SER 3.3 14.8 + - - +
21H LEU* 2.9 19.5 - - + +
23H ARG* 1.3 77.5 - - - +
25H ALA* 1.3 63.7 + - - +
27H ALA* 3.8 0.5 - - - +
28H VAL* 3.3 25.6 + - - +
197H GLY* 3.6 25.4 - - - +
198H PRO* 4.2 9.6 - - + -
201H LEU* 3.3 17.5 - - + -
700P PHE* 3.0 43.5 - - + -
709P PRO* 3.8 11.4 - - + +
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Residues in contact with ALA 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H ILE* 4.0 26.5 - - + -
21H LEU* 2.6 30.9 + - + +
22H ILE 3.8 2.0 - - - +
24H VAL* 1.3 73.5 - - - +
26H ALA* 1.3 65.8 + - - +
28H VAL* 3.3 5.7 + - - +
29H GLY 3.3 5.9 + - - -
30H HIS* 3.1 23.9 + - + +
32H VAL* 4.0 12.8 - - + -
201H LEU* 4.2 11.0 - - + -
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Residues in contact with ALA 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H ILE 2.8 19.3 + - - +
23H ARG 4.3 1.1 - - - +
25H ALA* 1.3 73.4 - - - +
27H ALA* 1.3 65.1 + - - +
29H GLY* 3.0 14.9 + - - -
30H HIS 3.6 14.7 - - - +
32H VAL* 4.4 2.2 - - + +
50H ILE* 3.5 30.1 - - + -
52H ASN* 4.4 13.5 - - + +
53H VAL* 3.8 15.3 - - + -
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Residues in contact with ALA 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H ARG 3.1 20.6 + - - +
24H VAL 3.8 3.6 - - - +
25H ALA 3.2 0.2 - - - -
26H ALA* 1.3 80.9 - - - +
28H VAL* 1.3 60.7 + - - +
29H GLY* 3.3 0.3 + - - -
50H ILE* 5.2 1.3 - - - +
706P VAL* 4.1 20.1 - - + +
707P VAL 5.0 1.1 - - - +
709P PRO* 3.7 28.3 - - + -
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Residues in contact with VAL 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H LYS* 3.8 24.8 - - + +
24H VAL 3.3 14.6 + - - +
25H ALA* 3.3 4.9 + - - +
27H ALA* 1.3 74.0 - - - +
29H GLY* 1.3 56.1 + - - +
30H HIS* 3.3 33.0 - - + +
201H LEU* 4.2 8.5 - - + -
700P PHE* 3.9 11.0 - - + -
704P HIS* 3.7 38.0 - - + +
706P VAL* 3.8 21.9 - - + +
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Residues in contact with GLY 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5H LYS* 3.3 20.7 - - - +
26H ALA 3.0 11.8 + - - -
27H ALA 3.2 1.2 + - - -
28H VAL* 1.3 79.9 - - - +
30H HIS* 1.3 64.8 + - - +
31H HIS* 3.9 7.6 + - - -
52H ASN* 4.3 10.4 - - - +
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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