Contacts of the strand formed by residues 56 - 65 (chain B) in PDB entry 3JRS
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 ARG 56 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B LEU* 3.9 27.9 - - + +
53B GLY* 3.4 22.7 - - - +
54B ASN* 2.9 7.6 - - - +
55B GLY* 1.3 84.3 - - - +
57B CYS* 1.3 64.8 + - - +
146B ASN* 2.8 36.3 + - - +
174B VAL* 3.4 32.2 - - + +
175B VAL* 3.4 12.1 + - - +
176B ASP* 3.0 22.8 + - - +
177B VAL* 4.3 2.3 - - - +
183B GLU* 5.2 1.7 - - - +
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Residues in contact with CYS 57 (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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52B LEU* 4.0 2.9 - - - -
56B ARG* 1.3 76.3 - - - +
58B SER* 1.3 60.7 + - - +
173B TYR* 4.2 5.5 - - - -
174B VAL* 3.2 3.3 - - - -
175B VAL* 2.8 55.7 + - - +
177B VAL* 3.8 21.5 - - + +
183B GLU* 4.1 20.6 - - + +
186B THR* 4.4 10.1 - - - -
187B ARG* 4.3 26.2 - - + +
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Residues in contact with SER 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B TYR* 3.7 23.4 + - - +
52B LEU* 3.2 23.0 - - - +
57B CYS* 1.3 76.2 - - - +
59B SER* 1.3 65.9 + - - +
173B TYR* 3.1 20.9 - - - -
174B VAL* 4.2 1.1 - - - -
187B ARG* 3.4 19.8 + - - +
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Residues in contact with SER 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B HIS 5.8 0.2 - - - -
50B TYR* 4.9 1.2 - - - -
58B SER* 1.3 82.1 - - - +
60B LEU* 1.3 62.9 + - - +
61B LEU* 4.0 3.3 - - - +
172B SER* 3.1 25.7 - - - -
173B TYR* 3.2 24.4 + - - +
187B ARG* 2.9 24.9 + - - +
191B ASP* 2.9 30.6 + - - -
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Residues in contact with LEU 60 (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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32B LEU* 5.3 6.7 - - + -
44B ILE* 4.2 32.5 - - + -
48B HIS* 3.8 35.7 - - + +
59B SER* 1.3 79.2 + - - +
61B LEU* 1.3 80.4 + - - +
62B ALA* 6.1 0.4 - - + -
170B LEU* 4.0 15.7 - - + -
171B GLU 3.6 11.0 - - - +
172B SER* 3.9 4.5 - - - -
187B ARG* 5.0 0.8 - - - +
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Residues in contact with LEU 61 (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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59B SER* 4.0 4.0 - - - +
60B LEU* 1.3 85.7 - - - +
62B ALA* 1.4 59.5 + - - +
169B VAL 3.9 0.3 - - - +
170B LEU* 3.3 3.5 - - - -
171B GLU 2.8 41.9 + - - +
173B TYR* 4.2 12.3 - - + -
191B ASP* 3.2 53.2 - - + +
194B ILE* 3.9 13.2 - - + -
195B ARG* 3.7 37.5 - - + +
198B LEU* 4.2 14.5 - - + +
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Residues in contact with ALA 62 (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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30B SER* 3.8 19.9 + - - +
31B ASP* 5.6 0.2 - - - -
32B LEU* 3.6 26.5 - - + +
60B LEU* 6.1 0.4 - - + -
61B LEU* 1.4 73.4 - - - +
63B GLN* 1.3 54.7 + - - +
168B VAL* 4.5 2.2 - - + -
169B VAL 3.3 6.7 - - - -
170B LEU* 3.6 19.5 - - + -
195B ARG* 2.3 33.3 + - - +
198B LEU* 4.7 0.7 - - - -
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Residues in contact with GLN 63 (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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30B SER* 5.2 2.8 + - - -
62B ALA* 1.3 75.1 - - - +
64B ARG* 1.3 82.7 + - - +
65B ILE* 3.8 12.3 + - + +
168B VAL* 3.4 4.0 - - - -
169B VAL* 2.8 38.7 + - + +
195B ARG* 3.3 19.4 + - - +
198B LEU* 3.6 39.0 - - + +
199B GLN* 3.7 22.9 + - - +
202B ALA* 3.9 10.7 - - - +
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Residues in contact with ARG 64 (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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30B SER* 4.2 21.6 + - - +
31B ASP 3.1 24.5 + - - -
32B LEU* 4.3 2.0 - - - +
33B THR* 4.1 11.6 - - - +
36B GLU* 2.7 40.3 + - - +
63B GLN* 1.3 94.1 + - - +
65B ILE* 1.3 59.8 + - - +
66B HIS* 4.6 22.6 - - - +
166B TRP* 3.4 31.2 - - + +
167B THR 3.4 3.4 - - - +
168B VAL* 4.1 5.8 - - + -
206B GLU* 4.5 3.8 - - - +
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Residues in contact with ILE 65 (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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63B GLN* 3.8 13.0 - - + +
64B ARG* 1.3 80.0 - - - +
66B HIS* 1.3 64.1 + - - +
67B ALA* 3.1 8.0 + - + -
72B VAL* 3.8 19.5 - - + -
166B TRP* 3.6 2.5 - - - +
167B THR* 2.6 40.8 + - - +
169B VAL* 3.8 26.0 - - + -
198B LEU 4.6 0.2 - - - +
201B LEU* 3.9 19.5 - - + -
202B ALA* 3.7 25.8 - - + +
205B THR* 3.3 20.0 - - - +
206B GLU* 3.7 17.0 - - + -
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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