Contacts of the strand formed by residues 224 - 232 (chain C) in PDB entry 3OYP
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 224 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ARG* 3.7 24.0 - - - +
16A CYS* 3.6 19.1 - - - +
19A THR* 3.8 17.7 - - + +
20A SER* 3.5 33.2 - - - +
25A ASP* 5.3 1.8 - - + +
36A LEU* 3.2 6.0 - - - -
37A SER* 2.7 41.4 + - - +
65A ALA* 4.4 3.6 - - + -
222C SER 3.6 4.0 - - - +
223C VAL* 1.3 79.2 - - - +
225C ILE* 1.3 78.5 + - - +
226C VAL* 3.5 5.6 + - + +
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Residues in contact with ILE 225 (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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10A THR* 3.6 9.8 + - + +
11A ARG* 3.5 12.3 + - - -
25A ASP* 4.4 15.8 - - - +
29A VAL* 4.1 22.7 - - + -
34A GLN* 3.2 39.0 - - + +
35A VAL 3.5 4.9 - - - +
36A LEU* 3.5 18.6 - - + -
52A CYS* 5.9 0.4 - - - -
64A LEU* 4.2 17.2 - - + +
65A ALA 5.2 5.3 + - - +
88A PRO* 4.6 12.6 - - + -
223C VAL 4.5 0.2 + - - -
224C VAL* 1.3 82.3 - - - +
226C VAL* 1.3 58.0 + - - +
227C GLY 3.4 18.6 - - - +
228C ARG* 6.1 1.3 - - - +
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Residues in contact with VAL 226 (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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9A GLN* 3.6 10.6 - - - +
10A THR* 3.0 23.7 + - - -
11A ARG* 3.4 19.7 + - + +
12A GLY 5.1 1.3 - - - +
16A CYS* 3.8 24.9 - - + -
35A VAL* 2.7 37.2 + - + +
36A LEU 4.3 0.2 - - - -
37A SER* 3.7 31.9 - - - -
42A SER* 4.5 2.9 - - - +
109A ARG* 5.1 2.0 - - - +
224C VAL* 4.0 5.6 - - + +
225C ILE* 1.3 75.5 - - - +
227C GLY* 1.3 56.0 + - - +
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Residues in contact with GLY 227 (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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8A GLN 3.2 14.6 - - - -
9A GLN* 4.0 2.5 - - - -
10A THR* 3.1 11.4 + - - -
35A VAL* 2.7 41.8 + - - +
225C ILE* 3.4 10.8 - - - +
226C VAL* 1.3 80.7 - - - +
228C ARG* 1.3 57.1 + - - +
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Residues in contact with ARG 228 (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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7A SER* 3.4 3.5 - - - -
8A GLN* 2.9 67.1 + - - +
10A THR* 3.9 18.5 - - - +
28A GLN* 3.2 46.6 + - - +
29A VAL* 3.8 0.6 - - - +
30A ASP* 3.1 66.6 + - - +
31A GLY* 4.6 0.7 - - - -
33A VAL 3.4 9.9 - - - +
34A GLN* 3.7 9.6 - - - +
35A VAL* 4.1 2.1 - - - +
225C ILE* 6.1 1.0 - - - +
227C GLY* 1.3 74.4 - - - +
229C ILE* 1.3 65.1 + - - +
230C ILE* 3.7 17.6 - - + +
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Residues in contact with ILE 229 (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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5A ALA* 3.9 13.0 - - + -
6A TYR 3.4 12.6 - - - +
7A SER* 4.1 10.5 - - - -
31A GLY* 4.7 0.2 - - - -
32A GLU* 3.4 7.6 + - - +
33A VAL* 2.8 44.1 + - + +
35A VAL* 4.0 18.2 - - + -
44A LEU* 4.0 13.0 - - + -
107A VAL* 4.2 7.6 - - + -
108A THR 3.4 24.0 - - - +
109A ARG 3.6 13.9 - - - +
111A ALA* 4.2 6.1 - - + +
228C ARG* 1.3 79.4 - - - +
230C ILE* 1.3 65.0 + - - +
231C LEU* 3.8 19.3 - - + +
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Residues in contact with ILE 230 (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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4A THR 4.0 0.2 - - - +
5A ALA* 3.2 5.4 - - - -
6A TYR* 2.9 73.0 + - + +
8A GLN* 3.3 33.4 - - + +
30A ASP* 4.9 2.9 - - - +
31A GLY* 4.1 14.4 - - - +
32A GLU* 3.5 2.7 - - - -
92A ARG* 3.3 32.8 - - - +
228C ARG* 3.7 20.0 - - + +
229C ILE* 1.3 74.1 - - - +
231C LEU* 1.3 68.6 + - - +
232C SER* 6.0 0.7 - - - -
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Residues in contact with LEU 231 (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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3A ILE* 5.1 4.5 - - + -
4A THR 3.5 4.3 - - - +
5A ALA* 3.7 18.8 - - + -
6A TYR* 6.3 0.2 - - - -
32A GLU* 2.7 29.3 + - + +
33A VAL* 4.3 12.3 - - + -
92A ARG* 4.6 2.3 + - - -
94A MET* 3.9 25.8 - - + -
107A VAL* 4.4 13.5 - - + -
144A LEU* 3.7 30.1 - - + -
148A GLY 6.0 0.2 - - - +
229C ILE* 3.8 20.9 - - + +
230C ILE* 1.3 89.2 - - - +
232C SER* 1.3 64.0 + - - +
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Residues in contact with SER 232 (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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2A PRO 4.0 6.8 - - - +
3A ILE* 3.5 13.2 - - - +
4A THR* 2.7 59.3 + - - +
6A TYR* 5.9 3.6 - - - -
230C ILE* 6.0 0.7 - - - -
231C LEU* 1.3 78.0 - - - +
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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