Contacts of the strand formed by residues 15 - 22 (chain B) in PDB entry 3RR1
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 TRP 15 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ARG* 3.7 2.8 - - - +
11B LEU* 2.8 36.0 + - + +
13B PRO* 3.3 52.9 + - + +
14B ARG* 1.3 82.1 - - - +
16B MET* 1.3 60.0 + - - +
17B PHE* 4.3 15.3 - + + -
31B GLU* 3.8 16.4 - - - +
32B PRO 5.7 0.4 - - - -
34B ILE* 3.6 6.2 - - - +
287B PRO 4.1 6.7 + - - -
288B LEU* 3.6 36.7 - - + +
289B GLY* 3.6 21.5 - - - -
290B PRO* 4.4 1.1 - - + -
312B SER* 4.2 7.4 - - - -
322B GLU* 3.9 18.6 - - + -
323B LEU* 3.7 28.3 - - + -
326B TYR* 4.0 16.6 - + - -
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Residues in contact with MET 16 (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 THR* 4.2 12.1 - - + -
9B TYR 3.3 13.7 - - - +
10B ARG* 4.5 10.5 - - + +
15B TRP* 1.3 74.9 - - - +
17B PHE* 1.3 71.9 + - - +
31B GLU* 3.4 22.6 - - - +
32B PRO* 3.6 40.0 + - + +
34B ILE* 3.7 26.9 - - + +
38B ALA 4.8 0.2 - - - +
41B VAL* 3.9 9.9 - - + -
42B GLU* 3.8 51.1 - - - +
45B VAL* 4.2 9.2 - - + -
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Residues in contact with PHE 17 (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 THR* 3.5 2.4 - - - -
9B TYR* 2.8 40.3 + - + +
11B LEU* 3.6 29.6 - - + +
15B TRP* 4.3 10.5 - + + -
16B MET* 1.3 85.5 - - - +
18B LEU* 1.3 62.1 + - - +
29B TRP* 4.0 17.7 - + + -
30B GLY 3.5 3.6 - - - +
31B GLU* 3.8 26.2 - - - -
290B PRO* 3.7 24.2 - - + -
291B ILE* 3.7 22.0 - - + -
326B TYR* 3.7 28.3 - + + -
352B ILE* 4.4 5.2 - - + -
357B VAL* 3.8 15.9 - - + -
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Residues in contact with LEU 18 (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* 4.5 5.6 - - + -
7B THR 3.5 6.5 - - - +
8B THR* 4.4 7.6 - - + -
17B PHE* 1.3 78.4 - - - +
19B LYS* 1.3 62.9 - - - +
20B VAL* 3.7 26.5 - - + -
29B TRP* 3.3 11.5 - - - -
30B GLY 2.9 33.9 + - - +
32B PRO* 4.2 11.9 - - + -
45B VAL* 3.6 41.1 - - + -
85B GLY* 3.9 33.9 - - - +
86B ILE* 4.0 7.4 - - + +
89B ALA* 4.0 3.4 - - + -
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Residues in contact with LYS 19 (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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5B ARG 3.7 1.4 - - - +
6B LEU* 3.3 5.9 - - - +
7B THR* 2.9 47.4 + - - +
9B TYR* 3.4 23.2 + - + +
18B LEU* 1.3 76.2 - - - +
20B VAL* 1.3 59.1 + - - +
21B GLU* 2.9 39.7 + - + +
27B THR* 3.6 22.2 - - + -
28B GLY 3.4 3.6 - - - -
29B TRP* 3.6 36.3 - - + -
354B GLU* 3.4 24.4 + - - +
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Residues in contact with VAL 20 (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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3B ILE* 3.7 34.5 - - + -
5B ARG 3.5 3.1 - - - -
6B LEU* 3.8 17.5 - - + -
18B LEU* 3.7 15.3 - - + -
19B LYS* 1.3 71.8 - - - +
21B GLU* 1.3 63.9 + - - +
27B THR* 3.4 5.6 - - - +
28B GLY 2.8 38.7 + - - +
52B LEU* 5.7 0.9 - - + -
86B ILE* 4.9 7.2 - - + +
89B ALA* 3.5 26.7 - - + -
90B LEU* 4.7 5.8 - - + +
93B ILE* 3.8 20.8 - - + +
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Residues in contact with GLU 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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3B ILE* 3.5 7.4 - - - +
4B THR* 2.8 34.2 + - - +
5B ARG* 2.9 51.8 + - + +
7B THR* 4.1 1.7 + - - -
19B LYS* 2.9 42.6 + - + +
20B VAL* 1.3 75.1 - - - +
22B THR* 1.3 63.6 + - - +
26B VAL 4.3 3.1 - - - -
27B THR* 4.1 12.7 + - - +
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Residues in contact with THR 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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1B VAL* 3.9 12.4 - - + +
2B LYS 3.2 11.9 - - - +
3B ILE* 4.3 4.9 - - + -
4B THR* 3.8 8.7 + - - +
21B GLU* 1.3 79.6 - - - +
23B ASP* 1.3 59.4 + - - +
24B GLU 3.1 2.6 + - - -
25B GLY* 3.1 20.3 + - - -
26B VAL* 2.6 43.9 + - - +
27B THR* 5.3 0.2 + - - -
57B PRO* 3.9 20.6 - - + -
93B ILE* 3.8 25.1 - - + -
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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