Contacts of the helix formed by residues 20 - 29 (chain C) in PDB entry 4CEV
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C MET 3.6 1.1 - - - +
12C ASP* 3.3 29.2 - - + -
15C GLN* 3.3 25.4 - - - +
17C ARG 3.6 2.7 - - - +
18C ARG 3.5 0.4 - - - -
19C GLY* 1.3 75.7 - - - +
21C ASP* 1.3 57.9 + - - +
22C MET 3.1 1.1 - - - -
23C GLY 3.3 6.2 + - - -
97C GLY 2.9 31.9 + - - -
98C ASP* 3.5 25.4 - - + +
239C GLY* 6.2 0.9 - - - +
271C GLU* 3.8 20.4 - - - +
272C VAL 3.5 18.2 - - - +
273C ASN* 3.5 15.2 - - + +
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Residues in contact with ASP 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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10C PRO* 3.2 53.3 - - + +
11C MET 4.0 2.0 - - - +
12C ASP* 3.2 21.0 - - + +
19C GLY* 3.1 25.5 + - - -
20C VAL* 1.3 79.6 - - - +
22C MET* 1.3 67.5 + - - +
23C GLY 3.2 1.6 - - - -
24C PRO* 3.4 7.1 - - - +
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Residues in contact with MET 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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19C GLY* 2.8 13.6 + - - +
21C ASP* 1.3 90.3 - - - +
23C GLY* 1.3 63.0 + - - +
24C PRO* 3.4 2.0 - - - -
25C SER* 3.5 8.1 + - - +
26C ALA* 3.0 22.9 + - - +
274C PRO* 3.7 15.0 - - + -
275C ILE* 3.3 39.5 - - + -
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Residues in contact with GLY 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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20C VAL 3.3 4.8 + - - -
21C ASP 3.2 1.0 - - - -
22C MET* 1.3 77.9 - - - +
24C PRO* 1.3 68.4 - - - +
26C ALA* 3.2 1.3 + - - +
27C MET* 3.0 30.2 + - - +
96C GLY 3.5 11.2 - - - -
272C VAL* 3.4 31.8 + - - -
274C PRO* 4.0 1.5 - - - +
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Residues in contact with PRO 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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8C GLY* 4.0 8.3 - - - -
9C VAL 3.8 17.7 - - - +
10C PRO* 4.0 4.0 - - + -
21C ASP 3.4 14.8 - - - +
22C MET 3.6 0.9 - - - -
23C GLY* 1.3 89.0 - - - +
25C SER* 1.3 57.4 + - - +
27C MET* 3.4 3.6 + - - +
28C ARG* 3.1 48.2 + - - +
48C ASP* 4.3 5.6 - - - +
95C LEU* 3.3 39.1 - - + +
96C GLY 3.4 12.3 - - - +
97C GLY 3.9 1.6 - - - +
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Residues in contact with SER 25 (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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22C MET* 3.5 9.4 + - - +
23C GLY 3.3 0.2 - - - -
24C PRO* 1.3 78.5 - - - +
26C ALA* 1.3 61.3 + - - +
28C ARG* 3.9 20.4 + - - +
29C TYR* 2.8 60.9 + - - -
48C ASP* 4.9 3.3 + - - -
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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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22C MET 3.0 18.8 + - - +
23C GLY* 3.7 4.9 - - - +
25C SER* 1.3 75.2 - - - +
27C MET* 1.3 52.3 + - - +
29C TYR* 3.3 8.8 + - - +
30C ALA* 2.7 29.5 + - - +
272C VAL* 4.6 0.9 - - + -
274C PRO* 3.4 19.1 - - + -
280C ASN* 3.2 35.4 - - - +
283C ALA* 3.8 7.9 - - + -
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Residues in contact with MET 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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23C GLY 3.0 19.4 + - - +
24C PRO 3.7 3.6 - - - +
26C ALA* 1.3 75.2 - - - +
28C ARG* 1.3 64.3 + - - +
30C ALA* 3.2 12.5 + - - -
31C GLY 3.3 7.8 + - - -
32C VAL* 3.3 12.1 + - + +
95C LEU* 3.7 32.5 - - + -
96C GLY 3.2 26.9 - - - +
269C PHE* 3.7 15.5 - - - +
272C VAL* 4.1 12.6 - - + -
283C ALA* 4.1 23.1 - - + +
286C ALA* 3.8 11.7 - - + -
287C VAL* 3.4 10.6 - - + +
290C MET* 3.6 26.0 - - + -
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Residues in contact with ARG 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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6C ILE* 4.4 5.6 - - + +
8C GLY* 3.8 8.0 - - - +
24C PRO* 3.1 33.2 + - - +
25C SER* 3.5 22.9 + - - +
27C MET* 1.3 75.4 - - - +
29C TYR* 1.3 67.7 + - + +
31C GLY* 2.8 21.3 + - - -
32C VAL* 3.8 17.6 + - + +
33C ILE* 5.2 4.6 + - + +
34C GLU* 4.4 3.5 - - - +
45C ASP* 2.9 42.7 + - - +
47C GLY* 3.1 14.6 + - - -
48C ASP* 2.8 37.7 + - - -
95C LEU* 4.8 4.5 - - + -
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Residues in contact with TYR 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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25C SER* 2.8 41.8 + - - +
26C ALA* 3.6 9.0 - - - +
28C ARG* 1.3 78.5 - - + +
30C ALA* 1.3 60.6 + - - +
31C GLY* 3.0 6.9 + - - -
280C ASN* 4.6 5.2 - - - +
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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