Contacts of the strand formed by residues 363 - 370 (chain B) in PDB entry 1MS4
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 363 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B ARG* 2.8 50.0 + - + +
14B GLN* 3.6 34.5 - - + +
32B HIS* 3.7 25.6 - - + +
33B SER* 3.5 3.1 - - - +
359B ASN* 3.4 0.6 - - - +
360B SER 2.9 21.8 + - - +
361B ASN* 3.6 10.5 - - + +
362B GLU* 1.3 83.3 - - - +
364B TYR* 1.3 55.9 + - - +
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Residues in contact with TYR 364 (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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13B ARG* 3.0 17.7 - - - +
33B SER* 3.0 10.9 + - - -
34B PHE 3.1 32.1 + - - +
35B ARG* 3.4 54.0 + - + -
57B SER* 3.5 33.4 - - - -
312B TRP* 5.5 3.5 + - - +
314B ARG* 5.4 2.1 + - - -
341B ALA* 5.9 2.0 - - + -
357B GLU* 4.1 13.7 - - + -
358B ILE 3.3 6.3 - - - +
359B ASN* 3.5 28.2 + - + -
362B GLU* 2.5 35.9 + - - -
363B VAL* 1.3 75.3 - - - +
365B SER* 1.3 58.7 + - - +
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Residues in contact with SER 365 (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 GLU* 2.7 36.2 + - - -
11B PHE 3.1 15.5 - - - -
13B ARG* 3.0 25.8 + - - +
34B PHE* 4.1 2.4 - - - +
357B GLU* 3.2 6.6 - - - +
358B ILE* 2.9 40.9 + - - +
364B TYR* 1.3 72.6 - - - +
366B LEU* 1.3 66.2 + - - +
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Residues in contact with LEU 366 (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 GLU* 3.8 1.9 - - - -
10B LEU* 3.1 21.0 + - - -
11B PHE* 3.0 38.7 + - + +
34B PHE* 3.6 20.6 - - + +
35B ARG 4.4 0.9 - - - +
37B PRO* 4.0 24.7 - - + -
50B ALA* 3.7 30.1 - - + -
355B LEU* 4.0 13.7 - - + -
356B HIS 3.0 10.8 - - - +
357B GLU* 3.5 26.9 - - + -
365B SER* 1.3 82.8 - - - +
367B VAL* 1.3 60.8 + - - +
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Residues in contact with VAL 367 (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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7B ARG* 3.7 37.5 - - + +
8B VAL 3.2 11.0 - - - +
9B GLU* 4.1 12.3 - - + -
354B CYS 3.7 0.7 - - - +
355B LEU* 3.4 7.0 - - - +
356B HIS* 2.8 76.0 + - + +
358B ILE* 3.9 23.1 - - + -
365B SER 4.0 0.2 - - - -
366B LEU* 1.3 75.1 - - - +
368B PHE* 1.3 61.9 + - - +
369B ALA 5.2 0.4 - - - +
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Residues in contact with PHE 368 (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 SER 4.4 0.2 - - - +
7B ARG* 3.5 1.5 - - - -
8B VAL* 2.7 42.7 + - + +
10B LEU* 3.7 25.3 - - + +
39B LEU* 4.0 19.3 - - + -
46B MET* 3.1 39.3 - - + -
73B ASP 4.0 4.0 - - - -
74B GLY* 4.0 22.2 - - - -
77B TRP* 4.0 10.3 - + - -
353B TYR* 3.3 30.3 - + + -
354B CYS 3.6 2.2 - - - -
355B LEU* 4.0 14.1 - - + -
366B LEU 4.3 0.4 + - - -
367B VAL* 1.3 72.3 - - - +
369B ALA* 1.3 60.6 + - - +
370B ARG* 4.3 14.7 + - + +
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Residues in contact with ALA 369 (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 SER* 6.4 0.2 - - - -
6B SER 3.4 11.2 - - - +
7B ARG* 3.9 13.0 - - + -
333B VAL* 5.3 2.2 - - + +
353B TYR* 3.1 10.7 - - - +
354B CYS* 2.7 43.6 + - + +
356B HIS* 5.1 10.8 - - + +
367B VAL* 4.0 0.4 - - + -
368B PHE* 1.3 75.2 - - - +
370B ARG* 1.3 63.5 + - - +
371B LEU* 4.0 19.7 - - + -
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Residues in contact with ARG 370 (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 SER* 3.2 19.4 - - - -
6B SER* 2.8 32.3 + - - +
8B VAL* 6.3 1.4 - - - +
73B ASP* 2.7 36.2 + - - +
74B GLY* 3.6 19.2 + - - -
75B GLU* 3.6 29.4 + - - +
352B LEU 3.8 5.2 - - - +
353B TYR* 3.6 24.2 + - + -
368B PHE* 4.4 12.3 - - + +
369B ALA* 1.3 73.0 - - - +
371B LEU* 1.3 59.1 + - - +
372B VAL* 2.9 24.0 + - + -
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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