Contacts of the helix formed by residues 490 - 499 (chain B) in PDB entry 4L6V
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 TRP 490 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257B PHE* 3.3 65.1 - + + +
258B LEU 3.4 10.6 - - - +
259B GLY* 3.9 7.6 - - - -
486B THR* 5.6 5.2 - - - -
488B ALA 2.3 21.1 + - - -
489B ALA* 1.3 87.6 - - + +
491B LEU* 1.3 85.9 + - + +
492B PRO* 3.5 3.4 - - - -
494B TRP* 3.3 25.6 + + + +
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Residues in contact with LEU 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B LEU* 4.0 28.7 - - + -
483B ALA 4.7 3.4 - - - +
484B SER* 3.3 38.6 - - - +
486B THR* 5.4 3.6 - - - +
488B ALA* 2.8 19.5 + - - +
490B TRP* 1.3 97.9 - - + +
492B PRO* 1.3 68.5 - - + +
494B TRP* 3.2 6.6 + - + -
495B LEU* 2.9 59.2 + - + +
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Residues in contact with PRO 492 (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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258B LEU 5.2 0.7 - - - +
488B ALA* 3.9 23.8 - - + -
489B ALA 4.6 2.7 - - - +
490B TRP* 3.5 4.5 - - - +
491B LEU* 1.3 94.5 - - + +
493B GLY* 1.3 60.0 + - - +
495B LEU* 4.3 7.2 - - + +
496B ASP* 3.4 22.7 + - - +
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Residues in contact with GLY 493 (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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258B LEU 3.9 6.3 + - - -
259B GLY 3.5 22.9 - - - -
260B GLY* 3.6 4.3 - - - -
261B PHE 4.9 0.3 + - - -
490B TRP 3.7 3.0 + - - -
491B LEU 3.3 0.4 - - - -
492B PRO* 1.3 78.3 - - - +
494B TRP* 1.3 59.4 + - - +
496B ASP* 3.6 5.1 + - - +
497B ALA* 3.0 27.4 + - - +
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Residues in contact with TRP 494 (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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259B GLY* 4.2 1.9 - - - -
260B GLY* 4.4 14.4 - - - +
353B LEU* 4.4 27.6 - - + -
465B SER* 2.8 30.1 + - - -
476B LEU* 4.8 8.6 - - + +
490B TRP* 3.3 23.4 + + + +
491B LEU* 3.2 9.5 + - + +
493B GLY* 1.3 76.7 - - - +
495B LEU* 1.3 73.2 + - + +
497B ALA* 3.0 8.7 + - + +
498B ILE* 2.9 38.9 + - + +
505B LEU* 4.4 12.3 - - + -
506B PHE* 3.8 30.5 - + - -
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Residues in contact with LEU 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B SER 4.7 0.4 - - - +
466B GLY* 4.0 22.0 - - - +
476B LEU* 3.9 25.8 - - + +
484B SER* 6.2 1.6 - - - -
491B LEU* 2.9 46.9 + - + +
492B PRO* 4.3 5.8 - - + +
494B TRP* 1.3 84.4 - - + +
496B ASP* 1.3 61.6 + - - +
498B ILE* 3.7 4.3 - - - -
499B ASN* 2.9 35.8 + - - +
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Residues in contact with ASP 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 PRO 3.4 17.8 + - - +
493B GLY* 3.8 5.8 - - - +
494B TRP 3.1 0.2 - - - -
495B LEU* 1.3 80.2 - - - +
497B ALA* 1.3 62.1 + - - +
499B ASN* 4.0 1.6 - - - -
500B SER* 3.3 24.9 + - - -
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Residues in contact with ALA 497 (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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260B GLY* 4.0 18.2 - - - -
261B PHE* 4.5 9.0 - - + +
493B GLY 3.0 17.8 + - - +
494B TRP* 3.0 8.9 + - + +
496B ASP* 1.3 77.8 - - - +
498B ILE* 1.3 57.9 + - - +
500B SER* 2.8 14.0 + - - -
503B ASN* 2.5 34.9 + - - +
505B LEU* 4.3 10.3 - - + -
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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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462B GLN 4.1 0.2 - - - +
465B SER* 3.9 16.6 - - - +
466B GLY 3.6 18.4 - - - +
467B LYS* 3.9 44.5 + - + +
494B TRP* 2.9 25.5 + - + +
495B LEU* 3.3 18.6 - - - +
497B ALA* 1.3 77.2 - - - +
499B ASN* 1.3 62.4 + - - +
500B SER 3.3 5.5 + - - +
503B ASN* 4.9 0.3 - - - +
505B LEU* 3.7 27.8 - - + +
506B PHE* 3.3 33.9 - - + -
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Residues in contact with ASN 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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466B GLY 2.9 28.0 + - - +
467B LYS* 3.4 9.3 - - - +
468B ALA* 3.3 22.4 + - - +
469B LEU* 4.7 1.7 + - - +
495B LEU* 2.9 29.6 + - - +
496B ASP* 4.0 2.9 - - - +
497B ALA 3.3 0.2 - - - -
498B ILE* 1.3 77.2 - - - +
500B SER* 1.3 60.7 + - - +
501B GLY 3.8 2.5 + - - -
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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