Contacts of the helix formed by residues 20 - 29 (chain B) in PDB entry 5CEV
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B MET 3.3 18.6 - - - +
12B ASP* 3.5 18.2 - - + -
15B GLN* 3.9 15.0 - - + +
17B ARG 4.8 0.9 - - - +
18B ARG 3.7 0.6 - - - -
19B GLY* 1.3 72.6 - - - +
21B ASP* 1.3 56.4 + - - +
22B MET 3.0 1.1 - - - -
23B GLY 3.0 10.5 + - - -
97B GLY 3.0 27.0 + - - -
98B ASP* 3.7 19.5 - - + +
271B GLU* 3.7 35.2 - - - +
272B VAL 3.5 19.0 - - - +
273B ASN* 3.5 13.9 - - + +
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Residues in contact with ASP 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PRO* 3.3 49.7 - - + +
11B MET 4.0 1.1 - - - -
12B ASP* 3.4 23.6 - - + +
18B ARG* 5.3 0.7 - - - +
19B GLY* 3.2 24.3 + - - -
20B VAL* 1.3 80.8 - - - +
22B MET* 1.3 67.2 + - - +
23B GLY 3.2 0.9 - - - -
24B PRO* 3.4 6.6 - - - +
25B SER 5.4 0.3 + - - -
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Residues in contact with MET 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLY* 2.8 15.0 + - - +
21B ASP* 1.3 91.2 - - - +
23B GLY* 1.3 63.6 + - - +
24B PRO* 3.5 0.9 - - - -
25B SER* 3.4 7.1 + - - +
26B ALA* 3.1 22.0 + - - +
274B PRO* 3.6 18.3 - - + +
275B ILE* 3.2 39.3 - - + -
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Residues in contact with GLY 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B VAL 3.0 8.2 + - - -
22B MET* 1.3 77.2 - - - +
24B PRO* 1.3 66.8 - - - +
26B ALA* 3.1 13.0 + - - +
27B MET* 3.1 18.0 + - - +
96B GLY 3.4 12.1 - - - -
272B VAL* 3.2 31.7 + - - -
274B PRO* 4.4 0.7 - - - -
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Residues in contact with PRO 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLY* 4.0 8.3 - - - -
9B VAL 3.6 19.3 - - - +
10B PRO* 3.9 2.9 - - + -
21B ASP 3.4 15.0 - - - +
22B MET 3.6 0.4 - - - -
23B GLY* 1.3 87.5 - - - +
25B SER* 1.3 57.6 + - - +
27B MET* 3.4 4.3 + - + +
28B ARG* 3.0 46.2 + - - +
48B ASP* 4.3 6.3 - - - +
95B LEU* 3.2 40.8 - - + +
96B GLY 3.5 10.5 - - - +
97B GLY 3.8 1.8 - - - +
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Residues in contact with SER 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B MET* 3.4 6.8 + - - +
23B GLY 3.3 0.4 - - - -
24B PRO* 1.3 77.4 - - - +
26B ALA* 1.3 60.6 + - - +
28B ARG* 3.5 24.1 + - - +
29B TYR* 2.8 60.6 + - - -
48B ASP* 4.7 3.6 + - - -
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Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B MET 3.1 4.0 + - - +
23B GLY* 3.1 9.9 + - - +
25B SER* 1.3 76.8 - - - +
27B MET* 1.3 53.9 + - - +
29B TYR* 3.4 8.4 + - - -
30B ALA* 2.8 27.2 + - - +
272B VAL* 4.5 1.6 - - + -
274B PRO* 3.5 30.3 - - + -
280B ASN* 3.1 33.0 + - - +
283B ALA* 3.6 8.5 - - + -
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Residues in contact with MET 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLY 3.1 16.0 + - - +
24B PRO 3.7 5.2 - - - +
26B ALA* 1.3 76.0 - - - +
28B ARG* 1.3 65.5 + - - +
30B ALA* 3.0 14.5 + - - +
31B GLY 3.2 7.4 + - - -
32B VAL* 3.3 11.4 + - + -
95B LEU* 3.9 24.9 - - + -
96B GLY 3.2 27.1 - - - +
269B PHE* 3.7 17.9 - - - +
272B VAL* 3.8 13.9 - - + -
283B ALA* 4.0 26.2 - - + +
286B ALA* 3.9 11.7 - - + -
287B VAL* 3.5 7.0 - - + +
290B MET* 3.7 25.1 - - + -
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Residues in contact with ARG 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 4.4 5.9 - - + +
8B GLY* 3.8 9.1 - - - +
24B PRO* 3.0 26.4 + - - +
25B SER* 3.5 30.8 + - - +
27B MET* 1.3 74.7 - - - +
29B TYR* 1.3 68.1 + - + +
31B GLY* 3.0 19.4 + - - -
32B VAL* 3.8 18.7 + - + +
33B ILE* 5.2 4.6 + - + +
34B GLU* 4.3 4.5 - - - +
45B ASP* 2.8 42.3 + - - +
47B GLY* 3.3 15.9 + - - -
48B ASP* 2.8 34.9 + - - -
95B LEU* 4.8 4.9 - - + -
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Residues in contact with TYR 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B SER* 2.8 45.1 + - - +
26B ALA* 3.5 9.2 - - - +
28B ARG* 1.3 79.9 - - + +
30B ALA* 1.3 58.1 + - - +
31B GLY* 3.0 9.0 + - - -
280B ASN* 4.4 6.4 + - - +
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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