Contacts of the helix formed by residues 32 - 37 (chain C) 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 32 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 4.0 21.5 - - + -
27C MET 3.2 19.6 + - - +
28C ARG* 3.7 17.6 + - + +
30C ALA 3.8 0.6 - - - -
31C GLY* 1.3 76.0 - - - +
33C ILE* 1.3 71.4 + - + +
35C ARG* 3.4 1.4 + - - +
36C LEU* 3.2 36.5 + - + +
93C LEU* 4.5 0.9 - - + -
95C LEU* 4.4 11.7 - - + -
287C VAL* 4.0 16.1 - - + +
290C MET* 3.7 32.3 - - + -
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Residues in contact with ILE 33 (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* 3.4 29.2 - - + -
28C ARG* 5.7 3.6 - - + +
32C VAL* 1.3 81.9 - - + +
34C GLU* 1.3 70.3 + - + +
36C LEU* 3.2 3.6 + - - +
37C GLU* 2.8 58.8 + - + +
43C ILE* 3.6 20.8 - - + +
45C ASP* 4.1 28.0 - - + +
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Residues in contact with GLU 34 (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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28C ARG 4.4 4.9 - - - +
31C GLY* 3.3 26.5 - - - +
32C VAL 3.4 0.2 - - - -
33C ILE* 1.3 94.9 + - + +
35C ARG* 1.3 64.7 + - - +
37C GLU* 3.8 13.8 - - - +
38C ARG* 3.1 28.3 + - - +
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Residues in contact with ARG 35 (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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30C ALA 5.7 0.8 + - - -
31C GLY 3.0 17.3 + - - +
32C VAL 3.6 4.9 - - - +
33C ILE 3.3 0.2 - - - -
34C GLU* 1.3 78.6 - - - +
36C LEU* 1.3 62.2 + - + +
38C ARG* 3.4 44.4 - - - +
39C LEU* 3.5 13.3 - - - +
252C HIS* 5.6 1.2 - - - -
287C VAL* 4.0 33.0 - - + +
288C ALA* 3.7 30.2 + - - +
290C MET* 6.1 0.2 - - + -
291C GLY* 4.2 8.8 - - - +
296C GLU* 2.9 39.9 + - - +
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Residues in contact with LEU 36 (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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4C ILE* 4.1 13.9 - - + -
32C VAL* 3.2 25.3 + - + +
33C ILE 3.2 4.1 + - - +
35C ARG* 1.3 77.7 - - + +
37C GLU* 1.3 64.7 + - - +
38C ARG 3.1 2.0 - - - -
39C LEU* 3.0 17.9 + - + +
41C TYR* 3.3 29.0 + - + -
43C ILE* 4.3 20.4 - - + -
93C LEU* 3.7 29.6 - - + -
290C MET* 4.2 13.5 - - + +
291C GLY* 4.6 2.0 - - - +
294C PHE* 3.6 35.4 - - + -
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Residues in contact with GLU 37 (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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33C ILE* 2.8 48.3 + - + +
34C GLU* 3.8 12.6 - - - +
36C LEU* 1.3 72.9 - - - +
38C ARG* 1.3 54.6 + - - +
40C HIS* 2.6 30.5 + - - -
41C TYR 3.7 10.3 + - - +
43C ILE* 3.2 21.2 - - + +
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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