Contacts of the helix formed by residues 495 - 503 (chain B) in PDB entry 4S15
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 TYR 495 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316B ARG* 4.2 26.2 + - - +
317B GLU* 3.6 38.3 + - + -
491B PHE* 2.8 50.9 + + + +
492B LYS 3.5 3.1 - - - -
494B ILE* 1.3 105.4 - - + +
496B PRO* 1.3 65.0 - - - +
497B ASP 3.3 2.5 - - - -
498B ILE* 3.2 26.6 + - + -
499B VAL* 3.3 14.7 + - - +
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Residues in contact with PRO 496 (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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492B LYS* 3.1 26.9 - - + +
493B ALA* 4.0 7.0 - - - +
494B ILE 3.3 9.6 - - - +
495B TYR* 1.3 90.0 - - - +
497B ASP* 1.3 69.1 + - - +
499B VAL* 3.4 3.3 + - - +
500B ARG* 2.9 30.0 + - - +
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Residues in contact with ASP 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ASN* 5.8 1.6 + - - +
314A LYS* 5.7 2.9 - - - +
495B TYR 3.3 0.6 - - - -
496B PRO* 1.3 83.5 - - - +
498B ILE* 1.3 63.7 + - + +
500B ARG* 3.7 28.4 + - - +
501B LEU* 2.9 42.3 + - + +
502B HIS* 5.0 0.4 - - - -
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Residues in contact with ILE 498 (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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317B GLU* 4.1 30.7 - - + +
321B GLN* 4.9 2.9 - - + -
491B PHE* 4.2 11.2 - - + -
495B TYR* 3.2 28.9 + - + +
497B ASP* 1.3 79.5 - - + +
499B VAL* 1.3 57.7 + - - +
502B HIS* 2.9 50.6 + - + +
503B PHE* 3.5 21.8 + - + -
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Residues in contact with VAL 499 (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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488B LEU* 5.0 2.7 - - + -
491B PHE* 3.8 27.1 - - + -
492B LYS* 4.0 37.5 - - + -
495B TYR 3.3 12.6 + - - +
496B PRO 3.8 6.1 - - - +
498B ILE* 1.3 78.2 - - - +
500B ARG* 1.3 65.3 + - - +
503B PHE* 3.3 41.1 + - + +
508B LYS* 3.4 25.9 - - + +
512B THR* 4.9 8.7 - - + +
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Residues in contact with ARG 500 (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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310A ASN* 5.3 5.1 + - - -
311A TYR* 5.1 1.4 + - - -
326A LYS* 5.4 5.0 + - - -
382A ASP* 3.7 15.4 + - - +
496B PRO 2.9 17.2 + - - +
497B ASP* 3.7 23.9 + - - +
499B VAL* 1.3 78.0 - - - +
501B LEU* 1.3 100.4 + - - +
503B PHE 5.1 0.5 - - - +
508B LYS* 2.8 32.1 + - - +
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Residues in contact with LEU 501 (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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310A ASN* 5.4 1.6 - - - +
311A TYR* 4.8 3.1 - - + -
314A LYS* 3.4 37.5 - - - +
322A LEU* 3.4 37.4 - - + +
325A ILE* 3.4 14.3 - - - +
326A LYS* 5.6 1.6 + - - +
382A ASP* 3.4 20.9 - - - +
497B ASP* 2.9 23.4 + - + +
500B ARG* 1.3 121.5 - - - +
502B HIS* 1.3 73.5 + - + +
503B PHE 3.8 1.6 - - - -
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Residues in contact with HIS 502 (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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314A LYS* 5.0 4.2 + - + +
318A VAL* 3.3 49.3 - - + +
321A GLN* 2.6 22.9 + - + +
322A LEU* 4.0 14.1 + - + -
325A ILE* 3.4 12.0 - - - +
321B GLN* 2.9 39.3 + - + +
497B ASP 4.3 0.9 - - - -
498B ILE* 2.9 38.7 + - + +
501B LEU* 1.3 96.8 + - + +
503B PHE* 1.3 67.5 + - - +
504B PRO* 3.9 0.7 - - - +
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Residues in contact with PHE 503 (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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325A ILE* 4.1 7.0 - - - +
320B TRP* 4.0 21.8 - + + -
321B GLN* 3.7 26.2 - - + -
324B ALA* 3.8 13.5 - - + -
488B LEU* 4.0 14.1 - - + -
491B PHE* 3.6 22.0 - + - -
498B ILE* 3.7 25.4 - - + -
499B VAL* 3.3 30.5 + - + +
501B LEU 4.9 0.9 - - - -
502B HIS* 1.3 82.3 + - - +
504B PRO* 1.3 70.5 - - + +
505B PRO* 3.5 4.5 - - - +
507B TYR* 3.6 32.1 - + + -
508B LYS* 3.7 20.0 + - + +
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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