Contacts of the helix formed by residues 20 - 32 (chain H) in PDB entry 5DSV
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 VAL 20 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H SER 4.6 0.4 - - - +
11H ALA* 3.6 33.0 - - - +
13H THR 4.0 6.7 - - - +
14H PHE* 3.7 29.8 - - + +
19H ARG* 1.3 70.2 - - - +
21H PHE* 1.3 66.9 + - - +
22H GLN 4.6 0.2 - - - +
23H VAL* 3.0 36.8 + - + +
24H GLU* 3.5 13.5 + - - +
123H THR 4.2 3.1 - - - +
80I LEU* 4.5 10.5 - - + -
129I ARG* 4.0 20.9 - - - +
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Residues in contact with PHE 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H SER* 4.1 10.8 - - - -
3H ILE* 3.6 36.8 - - + -
7H TYR 4.1 8.8 + - - -
8H ASP* 3.4 22.4 - - + -
13H THR 4.3 0.4 + - - -
15H SER* 3.4 37.5 - - - -
19H ARG* 3.3 50.8 + - + -
20H VAL* 1.3 73.9 - - - +
22H GLN* 1.3 57.9 + - - +
24H GLU* 2.9 15.3 + - - +
25H TYR* 2.9 59.9 + + + -
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Residues in contact with GLN 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H ASP* 3.2 23.7 - - - +
9H LEU 3.6 22.2 - - - -
10H SER 3.6 7.6 + - - +
11H ALA* 3.8 22.5 - - + +
20H VAL 3.2 0.2 - - - -
21H PHE* 1.3 79.4 - - - +
23H VAL* 1.3 58.8 + - - +
25H TYR* 3.9 6.2 - - - +
26H ALA* 3.3 18.5 + - - +
129H ARG* 4.2 5.5 - - - +
130H PRO* 4.0 7.3 - - + +
12N SER 3.6 14.3 + - - -
13N THR* 3.8 2.9 - - - +
14N PHE* 2.5 73.4 + - - +
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Residues in contact with VAL 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H ALA* 5.3 0.4 - - + -
20H VAL* 3.0 31.0 + - + +
22H GLN* 1.3 74.5 - - - +
24H GLU* 1.3 67.1 + - + +
25H TYR 3.1 1.3 - - - -
26H ALA* 2.9 8.0 + - + +
27H MET* 2.9 30.0 + - + +
123H THR* 4.0 24.9 - - - +
130H PRO* 4.1 9.9 - - + -
153H PRO* 4.4 5.4 - - + +
154H SER* 3.7 38.8 - - - +
129I ARG* 5.6 0.4 - - - +
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Residues in contact with GLU 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H ARG* 2.5 55.3 + - - +
20H VAL 3.5 10.3 + - - +
21H PHE* 2.9 19.3 + - - +
23H VAL* 1.3 77.2 - - + +
25H TYR* 1.3 62.3 + - + +
27H MET* 3.1 28.7 + - + +
28H LYS* 3.0 32.3 + - - +
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Residues in contact with TYR 25 (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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2H SER* 5.3 3.1 - - - -
3H ILE 3.4 12.0 + - - -
8H ASP* 3.0 48.2 + - + +
21H PHE* 2.9 36.3 + + + +
22H GLN* 3.9 9.4 - - - +
24H GLU* 1.3 77.7 - - + +
26H ALA* 1.3 65.5 + - - +
28H LYS* 3.0 22.0 + - - +
29H ALA* 3.1 9.7 + - - +
7N TYR* 4.4 1.7 + + - -
14N PHE* 3.8 19.5 - - + -
15N SER 3.4 17.3 - - - +
16N PRO* 3.4 50.4 - - + +
18N GLY* 3.5 12.3 - - - -
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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 GLN 3.3 9.1 + - - +
23H VAL* 2.9 12.2 + - - +
25H TYR* 1.3 77.5 - - - +
27H MET* 1.3 62.5 + - - +
29H ALA* 3.2 16.6 + - - +
30H VAL* 3.7 4.0 + - - +
130H PRO* 4.4 5.2 - - + -
131H PHE 3.6 16.2 - - - +
132H GLY* 4.0 2.6 - - - -
153H PRO* 3.8 15.3 - - + +
14N PHE* 3.3 34.7 - - + -
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Residues in contact with MET 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 VAL* 2.9 25.4 + - + +
24H GLU* 3.1 38.1 + - + +
26H ALA* 1.3 76.2 - - - +
28H LYS* 1.3 55.9 + - - +
30H VAL* 2.8 29.8 + - + +
31H GLU* 3.3 9.7 + - + +
152H ASP* 4.2 23.1 - - - +
153H PRO* 4.0 23.1 - - + -
154H SER* 4.8 4.5 - - - -
169H ARG* 5.2 8.8 + - - +
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Residues in contact with LYS 28 (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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24H GLU* 3.0 16.5 + - - +
25H TYR* 3.0 24.7 + - - +
27H MET* 1.3 72.7 - - - +
29H ALA* 1.3 62.9 + - - +
31H GLU* 3.7 21.0 - - + +
32H ASN* 3.5 30.2 + - - +
16N PRO* 3.3 29.0 + - - +
17N ASP* 4.2 11.2 - - - +
18N GLY* 4.1 2.5 - - - -
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Residues in contact with ALA 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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25H TYR 3.1 5.1 + - - -
26H ALA 3.3 12.3 - - - +
27H MET 3.2 0.4 - - - -
28H LYS* 1.3 76.2 - - - +
30H VAL* 1.3 63.2 + - - +
31H GLU 3.7 0.2 + - - -
32H ASN* 3.8 5.3 + - - +
33H SER* 3.8 9.4 + - - -
79H GLY* 3.7 13.9 - - - -
80H LEU* 5.0 7.1 - - + -
132H GLY* 3.9 12.8 - - - +
14N PHE* 4.0 17.9 - - + -
18N GLY* 3.3 24.4 - - - +
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Residues in contact with VAL 30 (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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26H ALA 3.9 8.3 - - - +
27H MET* 2.8 17.4 + - + +
29H ALA* 1.3 76.3 - - - +
31H GLU* 1.3 62.2 - - - +
33H SER* 3.0 22.3 + - - +
78H ALA* 3.8 23.6 - - + +
79H GLY* 3.8 5.8 - - - -
133H CYS* 3.8 11.7 - - - -
134H SER* 3.4 37.0 - - - +
153H PRO* 4.1 6.3 - - + -
166H GLY* 3.5 8.4 - - - +
169H ARG* 3.4 26.5 - - - +
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Residues in contact with GLU 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H MET* 3.8 5.6 - - - +
28H LYS* 3.7 33.2 - - + +
29H ALA 3.4 0.4 - - - -
30H VAL* 1.3 75.7 - - - +
32H ASN* 1.3 63.4 + - - +
33H SER 3.2 13.5 - - - +
166H GLY 3.6 17.8 - - - +
167H LYS* 3.2 23.8 - - - +
169H ARG* 4.0 27.3 + - - +
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Residues in contact with ASN 32 (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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28H LYS* 3.5 13.9 + - - +
29H ALA* 3.8 5.8 + - - +
30H VAL 3.3 0.6 - - - -
31H GLU* 1.3 80.7 - - - +
33H SER* 1.3 59.6 + - - +
167H LYS* 4.0 16.6 + - - +
17N ASP* 2.9 29.1 + - - +
18N GLY 4.9 4.0 + - - +
19N ARG* 5.0 7.1 - - - +
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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