Contacts of the strand formed by residues 20 - 28 (chain B) in PDB entry 4OIP
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 TYR 20 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B ARG 5.2 0.9 - - - -
15B THR* 3.7 6.9 - - - +
16B GLN* 3.2 65.6 + - + +
17B GLY 4.0 2.6 - - - +
18B ARG 3.4 2.2 + - - -
19B GLU* 1.3 82.4 - - + +
21B GLY* 1.3 71.7 + - - +
22B GLU* 3.0 46.9 + - + +
198B ARG* 3.5 20.4 + - + +
199B ILE 3.5 14.8 - - - -
200B TRP* 3.4 46.9 - + + -
207B PRO* 3.4 10.8 - - - +
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Residues in contact with GLY 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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14B ARG 3.1 11.4 - - - -
15B THR* 4.2 6.3 - - - -
20B TYR* 1.3 84.5 - - - +
22B GLU* 1.3 68.1 + - - +
23B PHE* 4.0 8.0 - - - -
197B LEU 4.0 0.2 - - - +
198B ARG* 3.7 1.4 - - - -
199B ILE 3.3 28.6 + - - -
207B PRO* 3.6 11.1 - - - +
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Residues in contact with GLU 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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12B THR 3.7 0.7 - - - +
13B VAL* 3.5 4.0 - - - -
14B ARG* 2.5 83.0 + - + +
16B GLN* 5.3 2.3 + - - -
20B TYR* 3.0 40.7 + - + +
21B GLY* 1.3 72.3 - - - +
23B PHE* 1.3 65.7 + - - +
24B VAL 4.3 0.2 - - - -
196B THR* 4.7 8.8 - - + +
197B LEU 3.3 4.9 - - - +
198B ARG* 4.4 11.0 + - + +
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Residues in contact with PHE 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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225A PHE* 5.6 1.1 - - + -
11B PHE* 3.6 31.0 - + + -
12B THR 3.4 2.7 - - - -
13B VAL* 3.9 25.4 - - + -
15B THR* 5.3 1.1 - - + -
21B GLY* 4.0 18.4 - - - -
22B GLU* 1.3 77.8 - - - +
24B VAL* 1.3 63.7 + - - +
25B LEU 4.2 0.2 + - - -
195B LEU* 3.6 1.4 - - - +
196B THR* 3.2 2.8 - - - +
197B LEU* 2.6 59.0 + - + +
199B ILE* 3.6 29.2 - - + -
207B PRO* 3.8 7.2 - - + -
208B LEU* 3.6 44.2 - - + -
211B LEU* 3.9 15.0 - - + -
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Residues in contact with VAL 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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10B VAL 3.4 5.9 - - - +
11B PHE* 3.9 3.3 - - - -
12B THR* 2.9 47.0 + - + +
14B ARG* 3.9 31.0 - - - +
23B PHE* 1.3 77.0 - - - +
25B LEU* 1.3 62.1 + - - +
26B GLU* 3.9 19.5 - - + +
194B LYS* 3.6 29.6 - - + +
195B LEU 3.2 4.5 - - - +
196B THR* 3.8 17.7 - - + +
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Residues in contact with LEU 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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224A TYR* 3.8 27.6 - - + +
225A PHE* 3.9 22.7 - - + -
9B PRO* 3.7 26.9 - - + -
10B VAL 4.1 0.9 - - - -
11B PHE* 4.1 24.2 - - + -
23B PHE 4.2 0.6 - - - -
24B VAL* 1.3 71.6 - - - +
26B GLU* 1.3 60.2 + - - +
28B LEU* 3.8 34.9 - - + +
36B LEU* 3.9 15.7 - - + -
194B LYS* 3.9 1.0 - - - -
195B LEU* 2.7 44.9 + - + +
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Residues in contact with GLU 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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9B PRO* 3.5 3.2 - - - +
10B VAL* 3.3 33.0 + - + +
24B VAL* 3.9 12.3 - - + +
25B LEU* 1.3 76.4 - - - +
27B PRO* 1.3 74.4 - - + +
28B LEU 4.2 0.4 - - - +
184B THR* 3.8 15.2 + - + -
194B LYS* 3.3 49.5 + - + +
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Residues in contact with PRO 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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6B LEU* 5.5 6.2 - - + +
7B LYS 4.8 2.6 - - - +
8B ALA* 3.8 26.7 - - + -
9B PRO* 3.4 19.6 - - - +
10B VAL* 5.8 0.7 - - + -
26B GLU* 1.3 88.1 - - + +
28B LEU* 1.3 61.7 + - - +
184B THR* 4.4 7.9 - - + -
185B ARG 5.9 0.4 - - - -
186B LEU* 4.3 28.9 - - + -
192B LEU* 3.8 27.1 - - + -
193B ASP 3.7 2.9 - - - +
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Residues in contact with LEU 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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221A HIS* 3.9 26.7 - - + +
224A TYR* 4.3 2.2 - - + -
6B LEU* 5.5 2.5 - - - -
9B PRO* 4.0 11.2 - - + -
25B LEU* 3.8 46.7 - - + +
27B PRO* 1.3 80.9 - - - +
29B GLU* 1.3 66.2 + - - +
32B PHE* 3.8 25.8 - - + +
33B GLY* 4.3 1.6 - - - -
36B LEU* 4.0 5.4 - - + -
192B LEU* 3.4 11.0 - - - +
193B ASP* 2.8 39.4 + - + +
195B LEU* 4.2 15.5 - - + -
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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