Contacts of the strand formed by residues 363 - 370 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ARG* 3.0 51.4 + - + -
14A GLN* 3.8 25.1 - - - +
32A HIS* 3.9 25.4 - - + +
33A SER* 3.6 2.2 - - - -
359A ASN* 3.4 0.7 - - - +
360A SER 3.0 23.4 + - - +
361A ASN* 3.6 12.1 - - + +
362A GLU* 1.3 83.6 - - - +
364A TYR* 1.3 61.4 + - - +
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Residues in contact with TYR 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ARG* 3.1 16.0 - - - +
33A SER* 3.1 12.5 + - - -
34A PHE 3.0 33.1 + - - +
35A ARG* 3.4 49.1 + - + -
57A SER* 3.4 34.1 - - - -
312A TRP* 5.3 4.2 + - - +
314A ARG* 5.2 3.5 + - - -
341A ALA* 6.0 1.8 - - + -
357A GLU* 4.2 13.2 - - + -
358A ILE 3.3 7.2 - - - +
359A ASN* 3.4 29.2 + - + -
362A GLU* 2.5 37.3 + - - -
363A VAL* 1.3 78.0 - - - +
365A SER* 1.3 60.1 + - - +
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Residues in contact with SER 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLU* 2.5 37.1 + - - -
11A PHE 3.2 16.4 - - - -
13A ARG* 3.0 25.9 + - - +
34A PHE 4.0 2.3 - - - +
357A GLU* 3.2 7.1 - - - +
358A ILE* 2.9 39.0 + - - +
364A TYR* 1.3 73.8 - - - +
366A LEU* 1.3 65.8 + - - +
367A VAL 4.1 0.2 - - - -
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Residues in contact with LEU 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLU* 4.0 1.2 - - - -
10A LEU* 3.2 20.6 + - - +
11A PHE* 3.2 40.3 + - + +
34A PHE* 3.7 19.1 - - + +
35A ARG 4.5 1.1 - - - +
37A PRO* 3.9 23.6 - - + -
50A ALA* 3.7 30.3 - - + -
355A LEU* 3.9 10.1 - - + -
356A HIS 3.0 10.8 - - - +
357A GLU* 3.5 31.9 - - + -
365A SER* 1.3 76.6 - - - +
367A VAL* 1.3 63.9 + - - +
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Residues in contact with VAL 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ARG* 3.8 33.9 - - + +
8A VAL 3.3 11.9 - - - +
9A GLU* 4.1 12.1 - - + -
354A CYS 3.7 0.5 - - - +
355A LEU* 3.4 5.5 - - - +
356A HIS* 2.7 74.9 + - + +
358A ILE* 3.9 26.2 - - + -
365A SER 4.1 0.2 - - - -
366A LEU* 1.3 78.5 - - - +
368A PHE* 1.3 59.7 + - - +
369A ALA* 5.1 0.9 - - + +
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Residues in contact with PHE 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ARG* 3.7 1.4 - - - -
8A VAL* 2.9 37.8 + - + +
10A LEU* 3.6 28.4 - - + +
39A LEU* 4.0 20.9 - - + -
46A MET* 3.0 34.8 - - + -
73A ASP 4.1 1.3 - - - -
74A GLY* 4.0 14.4 - - - -
77A TRP* 4.0 11.2 - + - -
353A TYR* 3.2 36.1 - + + -
354A CYS 3.7 2.7 - - - -
355A LEU* 4.2 5.4 - - + -
366A LEU 4.0 0.6 + - - -
367A VAL* 1.3 71.8 - - - +
369A ALA* 1.3 59.9 + - - +
370A ARG* 4.0 30.0 + - + +
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Residues in contact with ALA 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A SER 3.3 10.3 - - - +
7A ARG* 3.8 14.1 - - + -
333A VAL* 5.3 2.5 - - + +
353A TYR* 3.3 9.4 - - - +
354A CYS* 2.8 40.5 + - + +
356A HIS* 5.0 11.2 - - + +
367A VAL* 4.0 0.6 - - + -
368A PHE* 1.3 76.6 - - - +
370A ARG* 1.3 62.5 + - - +
371A LEU* 3.6 18.5 + - + +
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Residues in contact with ARG 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A SER* 3.3 4.5 - - - -
6A SER* 2.7 48.2 + - - +
73A ASP* 2.8 35.0 + - - +
74A GLY* 3.4 22.4 + - - -
75A GLU* 3.6 25.2 + - - +
352A LEU 3.9 4.9 - - - +
353A TYR* 3.7 25.6 + - + -
368A PHE* 4.0 11.3 - - + +
369A ALA* 1.3 72.1 - - - +
371A LEU* 1.3 59.5 + - - +
372A VAL* 2.8 25.2 + - + +
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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