Contacts of the strand formed by residues 363 - 367 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B SER 4.2 1.6 - - - +
316B PHE* 3.4 39.5 - - + -
328B CYS* 4.0 15.0 - - + -
329B VAL 3.1 13.5 - - - +
330B GLU* 4.3 3.4 - - + -
331B ILE* 3.5 13.9 - - - +
354B SER* 4.2 2.4 - - - -
355B SER* 3.5 37.9 + - - +
359B LEU* 4.0 27.6 - - + +
361B GLY 5.2 0.9 + - - -
362B LYS* 1.3 90.6 + - + +
364B TRP* 1.3 63.5 + - - +
365B ARG* 3.8 21.1 - - + -
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Residues in contact with TRP 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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313B LEU* 5.1 1.3 - - + -
327B THR 3.7 0.2 - - - +
328B CYS* 3.5 3.6 - - - -
329B VAL* 2.8 62.8 + - + -
330B GLU 3.7 18.2 - - - -
331B ILE* 3.6 13.0 - - + +
332B PRO* 3.8 11.7 - - + -
335B ILE* 3.4 33.9 - - + -
337B GLY* 2.9 27.4 + - - -
340B VAL* 3.8 23.6 - - + +
341B ARG* 4.6 4.7 - - + -
352B ILE* 3.9 27.8 - - + -
353B ALA 3.2 13.9 - - - +
354B SER* 4.9 4.7 - - - -
363B ILE* 1.3 78.1 - - - +
365B ARG* 1.3 64.0 + - - +
366B ILE* 4.1 3.1 - - + -
385B LEU* 4.8 8.7 - - + -
389B LEU* 3.9 22.2 - - + -
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Residues in contact with ARG 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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17B MET 3.8 2.9 - - - +
19B PRO* 3.8 23.4 - - + +
99B PHE* 5.9 0.8 - - - -
149B THR* 3.0 45.8 + - - -
150B SER* 3.8 20.6 + - - +
326B VAL* 4.3 3.8 - - + -
327B THR 3.4 3.8 - - - +
328B CYS* 4.0 10.1 - - - -
352B ILE* 3.9 0.9 - - - +
353B ALA* 2.7 49.1 + - + +
354B SER 3.1 25.6 + - - -
355B SER* 3.5 12.9 + - - +
356B PHE* 5.7 0.6 - - - +
363B ILE* 3.8 14.1 - - + -
364B TRP* 1.3 76.2 - - - +
366B ILE* 1.3 64.1 + - - +
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Residues in contact with ILE 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B MET* 3.4 22.9 - - + +
19B PRO* 4.9 0.2 - - - -
304B LEU* 3.9 25.0 - - + +
308B ILE* 4.4 9.2 - - + -
326B VAL* 3.6 1.0 - - - -
327B THR* 2.8 44.7 + - - +
329B VAL* 4.1 21.5 - - + -
352B ILE* 3.9 22.7 - - + -
364B TRP* 5.0 2.5 - - + -
365B ARG* 1.3 75.5 - - - +
367B GLY* 1.3 68.4 + - - +
368B THR* 3.9 0.5 + - - +
381B VAL* 4.3 20.2 - - + -
385B LEU* 4.2 22.0 - - + -
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Residues in contact with GLY 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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17B MET* 2.8 35.3 + - - +
18B THR 3.4 24.0 - - - -
19B PRO* 4.0 6.9 - - - -
22B VAL* 5.9 0.2 - - - -
325B VAL 3.4 9.4 - - - -
326B VAL* 4.4 2.2 - - - -
365B ARG 3.9 0.6 + - - -
366B ILE* 1.3 73.6 - - - +
368B THR* 1.3 66.0 + - - +
369B MET* 3.8 3.6 - - - -
372B SER* 5.4 0.3 - - - -
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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
------------------------------------------------------------
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