Contacts of the strand formed by residues 363 - 367 (chain A) in PDB entry 3ISL
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 ILE 363 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A SER 4.2 1.6 - - - +
316A PHE* 3.4 37.0 - - + -
328A CYS* 4.1 15.3 - - + -
329A VAL 3.2 13.7 - - - +
330A GLU* 4.3 2.5 - - + -
331A ILE* 3.6 14.4 - - - +
354A SER* 4.2 2.4 - - - -
355A SER* 3.2 41.2 + - - +
359A LEU* 3.7 33.6 + - + +
361A GLY 5.3 0.7 + - - -
362A LYS* 1.3 87.4 + - + +
364A TRP* 1.3 62.8 + - - +
365A ARG* 3.8 21.8 - - + -
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Residues in contact with TRP 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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313A LEU* 4.9 1.1 - - + -
327A THR 3.8 0.2 - - - +
328A CYS* 3.4 3.8 - - - -
329A VAL* 2.8 59.7 + - + +
330A GLU 3.9 7.0 - - - -
331A ILE* 3.6 35.7 - - + -
332A PRO* 3.7 21.8 - - + -
335A ILE* 4.6 0.2 - - + -
337A GLY* 3.0 31.9 + - - -
340A VAL* 3.7 32.8 - - + +
341A ARG* 4.4 3.3 - - + +
352A ILE* 3.7 28.7 - - + -
353A ALA 3.4 13.5 - - - +
354A SER* 4.6 7.6 - - - -
363A ILE* 1.3 76.0 - - - +
365A ARG* 1.3 63.0 + - - +
366A ILE* 4.1 4.0 - - + -
385A LEU* 4.7 7.2 - - + -
389A LEU* 3.8 26.9 - - + -
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Residues in contact with ARG 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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17A MET 3.9 0.7 - - - +
19A PRO* 3.8 23.1 - - + +
98A ARG* 3.7 25.6 - - - +
149A THR* 3.1 47.8 + - - -
150A SER* 3.9 14.4 + - - +
326A VAL* 4.2 5.2 - - + -
327A THR 3.5 4.0 - - - -
328A CYS* 4.1 8.7 - - - -
353A ALA* 2.9 45.8 + - + +
354A SER 3.0 25.3 + - - -
355A SER* 3.7 10.1 + - - +
356A PHE* 6.2 0.6 - - - -
363A ILE* 3.8 16.4 - - + -
364A TRP* 1.3 76.5 - - - +
366A ILE* 1.3 63.8 + - - +
367A GLY 3.8 0.8 + - - -
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Residues in contact with ILE 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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17A MET* 3.4 23.8 - - + +
304A LEU* 3.8 29.9 - - + +
308A ILE* 4.2 15.9 - - + -
326A VAL* 3.5 2.4 - - - -
327A THR* 2.8 42.9 + - - +
329A VAL* 4.0 22.2 - - + -
352A ILE* 4.0 22.2 - - + -
364A TRP* 5.0 2.2 - - + -
365A ARG* 1.3 77.9 - - - +
367A GLY* 1.3 68.5 + - - +
368A THR* 5.0 0.7 + - - +
381A VAL* 4.4 13.5 - - + -
385A LEU* 4.3 13.7 - - + -
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Residues in contact with GLY 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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17A MET* 2.9 34.8 + - - +
18A THR 3.2 26.2 - - - -
19A PRO* 3.9 7.1 - - - +
325A VAL 3.4 9.4 - - - -
326A VAL* 4.5 1.6 - - - -
365A ARG 3.8 0.4 + - - -
366A ILE* 1.3 73.3 - - - +
368A THR* 1.3 64.8 + - - +
369A MET* 3.8 4.0 - - - -
372A SER* 5.4 0.8 - - - -
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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