Contacts of the helix formed by residues 20 - 32 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A SER 4.6 0.7 - - - +
11A ALA* 3.7 33.2 - - - +
13A THR 4.0 6.7 - - - +
14A PHE* 3.6 30.3 - - + +
19A ARG* 1.3 71.8 - - - +
21A PHE* 1.3 64.6 + - - +
22A GLN 4.6 0.2 - - - +
23A VAL* 3.0 37.3 + - + +
24A GLU* 3.5 13.0 + - - +
123A THR 4.3 2.7 - - - +
80B LEU* 4.5 11.9 - - + +
129B ARG* 4.0 20.6 - - - +
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Residues in contact with PHE 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 6.0 0.2 - - - -
3A ILE* 3.6 42.6 - - + -
7A TYR 3.9 10.1 + - - +
8A ASP* 3.5 21.3 - - + -
13A THR 4.3 0.2 + - - -
15A SER* 3.4 36.1 - - - -
19A ARG* 3.3 51.5 + - + -
20A VAL* 1.3 73.7 - - - +
22A GLN* 1.3 58.1 + - - +
24A GLU* 2.9 30.4 + - - +
25A TYR* 2.9 44.5 + + + -
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Residues in contact with GLN 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ASP* 3.2 23.8 + - - +
9A LEU 3.6 22.7 - - - -
10A SER 3.6 7.4 + - - +
11A ALA* 3.8 22.4 - - + +
21A PHE* 1.3 79.4 - - - +
23A VAL* 1.3 58.3 + - - +
25A TYR* 3.9 6.2 - - - +
26A ALA* 3.3 18.9 + - - +
129A ARG* 4.2 4.8 - - - +
130A PRO* 4.0 6.7 - - + +
12G SER 3.7 14.1 + - - -
13G THR* 3.7 2.5 - - - +
14G PHE* 2.4 75.2 + - - +
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Residues in contact with VAL 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ALA* 5.3 0.7 - - + -
20A VAL* 3.0 30.7 + - + +
22A GLN* 1.3 75.0 - - - +
24A GLU* 1.3 67.0 + - + +
25A TYR 3.0 1.8 - - - -
26A ALA* 2.9 8.4 + - - +
27A MET* 2.9 29.5 + - + +
123A THR* 4.0 24.5 - - - +
130A PRO* 4.2 9.9 - - + -
153A PRO* 4.4 5.6 - - + +
154A SER* 3.7 39.0 - - - +
129B ARG* 5.5 0.4 - - - +
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Residues in contact with GLU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ARG* 2.5 56.1 + - - +
20A VAL 3.5 10.7 + - - +
21A PHE* 2.9 20.0 + - - +
23A VAL* 1.3 78.1 - - + +
25A TYR* 1.3 61.8 + - + +
27A MET* 3.1 29.4 + - + +
28A LYS* 3.0 32.1 + - - +
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Residues in contact with TYR 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 5.3 2.4 - - - -
3A ILE 3.4 12.0 + - - -
8A ASP* 3.0 48.2 + - + +
21A PHE* 2.9 35.4 + + + +
22A GLN* 3.9 13.0 - - - +
24A GLU* 1.3 78.6 - - + +
26A ALA* 1.3 59.1 + - - +
28A LYS* 3.0 25.0 + - - +
29A ALA 3.1 9.2 + - - -
7G TYR* 4.3 0.9 - + - -
14G PHE* 3.8 14.4 - - + -
15G SER 3.3 17.9 - - - +
16G PRO* 3.3 52.5 - - + +
18G GLY* 3.4 13.4 - - - -
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Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLN 3.3 9.3 + - - +
23A VAL* 2.9 11.6 + - - +
25A TYR* 1.3 77.4 - - - +
27A MET* 1.3 63.9 + - - +
29A ALA* 3.2 16.6 + - - +
30A VAL* 3.7 4.2 + - - +
130A PRO* 4.4 5.6 - - + -
131A PHE 3.6 15.7 - - - +
132A GLY* 3.9 2.9 - - - -
153A PRO* 3.8 15.2 - - + +
14G PHE* 3.3 34.9 - - + -
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Residues in contact with MET 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A VAL* 2.9 25.0 + - + +
24A GLU* 3.1 37.9 + - + +
26A ALA* 1.3 75.7 - - - +
28A LYS* 1.3 57.2 + - - +
30A VAL* 2.8 28.8 + - + +
31A GLU* 3.3 10.0 + - - +
152A ASP* 4.2 23.6 - - + +
153A PRO* 4.0 23.1 - - + -
154A SER* 4.8 4.9 - - - -
169A ARG* 5.2 8.2 + - - +
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Residues in contact with LYS 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLU* 3.0 16.7 + - - +
25A TYR* 3.0 24.4 + - - +
27A MET* 1.3 72.2 - - - +
29A ALA* 1.3 62.0 + - - +
30A VAL 3.3 0.2 - - - -
31A GLU* 3.6 21.2 + - + +
32A ASN* 3.5 28.4 + - - +
16G PRO* 3.2 28.7 + - - +
17G ASP* 3.8 14.7 - - + +
18G GLY* 4.1 2.5 - - - -
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A TYR 3.1 4.9 + - - -
26A ALA 3.3 13.2 - - - +
27A MET 3.1 0.6 - - - -
28A LYS* 1.3 75.9 - - - +
30A VAL* 1.3 62.6 + - - +
32A ASN* 3.8 5.1 + - - +
33A SER* 3.8 9.7 + - - -
79A GLY* 3.7 13.6 - - - -
80A LEU* 4.6 7.5 + - + -
132A GLY* 3.9 12.8 - - - +
14G PHE* 4.1 17.0 - - + -
18G GLY* 3.3 24.0 - - - +
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ALA 3.9 8.5 - - - +
27A MET* 2.8 16.5 + - - +
29A ALA* 1.3 75.0 - - - +
31A GLU* 1.3 63.1 + - - +
33A SER* 3.0 21.7 + - - +
78A ALA* 3.8 24.0 - - + +
79A GLY* 3.8 6.5 - - - -
133A CYS* 3.8 12.3 - - - -
134A SER* 3.4 37.2 - - - +
153A PRO* 4.1 5.8 - - + -
166A GLY* 3.5 7.8 - - - +
169A ARG* 3.4 25.1 - - - +
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Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A MET* 3.3 5.4 + - - +
28A LYS* 3.8 34.5 - - + +
29A ALA 3.4 0.4 - - - -
30A VAL* 1.3 77.2 - - - +
32A ASN* 1.3 65.7 + - - +
33A SER 3.1 10.1 - - - +
166A GLY 3.6 16.7 - - - +
167A LYS* 3.2 23.3 - - - +
169A ARG* 4.0 27.1 + - - +
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Residues in contact with ASN 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LYS* 3.5 13.9 + - - +
29A ALA* 4.3 5.2 - - - +
30A VAL 3.2 0.6 - - - -
31A GLU* 1.3 80.9 - - - +
33A SER* 1.3 57.9 + - - +
167A LYS* 4.0 17.4 + - - +
17G ASP* 3.0 27.7 + - - +
18G GLY 5.0 4.4 + - - +
19G ARG* 5.1 7.5 - - - +
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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