Contacts of the helix formed by residues 493 - 502 (chain B) in PDB entry 4XK8
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 493 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257B ILE* 3.6 35.7 - - + +
258B LEU 3.2 17.8 - - - +
259B GLY* 4.6 4.3 - - - +
488B ALA 6.2 0.2 - - - -
489B GLY* 3.7 12.9 + - - -
492B ILE* 1.3 114.7 - - + +
494B LEU* 1.3 99.0 + - + +
495B PRO 3.3 3.3 - - - -
497B TRP* 3.0 35.1 + + + +
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Residues in contact with LEU 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B LEU* 3.9 35.0 - - + -
485B ALA 4.0 3.6 - - - +
486B LEU* 3.3 43.7 - - + +
489B GLY* 3.2 23.1 - - - +
490B ARG* 3.7 4.5 - - + +
493B TRP* 1.3 95.4 - - + +
495B PRO* 1.3 70.3 - - + +
497B TRP* 4.2 14.6 - - + -
498B LEU* 2.9 41.4 + - + +
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Residues in contact with PRO 495 (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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490B ARG 3.2 26.7 - - - +
491B ASN* 5.0 2.7 - - - -
492B ILE 3.8 13.0 - - - +
493B TRP 3.5 3.6 - - - -
494B LEU* 1.3 88.2 - - - +
496B GLY* 1.3 58.2 + - - +
498B LEU* 3.9 1.7 - - + +
499B ASN* 2.9 31.2 + - - +
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Residues in contact with GLY 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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258B LEU 3.9 13.3 + - - -
259B GLY 4.0 6.5 - - - -
260B GLY* 3.5 10.4 - - - -
493B TRP 3.4 3.6 + - - -
495B PRO* 1.3 79.1 - - - +
497B TRP* 1.3 57.5 + - - +
499B ASN* 3.4 9.2 + - - +
500B ALA* 2.9 29.6 + - - +
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Residues in contact with TRP 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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259B GLY* 5.0 3.1 - - - -
260B GLY* 3.9 16.6 - - - +
355B LEU* 4.2 19.1 - - + -
467B HIS* 3.0 29.4 + + + +
478B LEU* 4.5 4.4 - - + +
493B TRP* 3.0 28.2 + + + +
494B LEU* 4.1 15.0 - - + +
496B GLY* 1.3 75.7 - - - +
498B LEU* 1.3 69.6 + - + +
500B ALA* 3.0 4.9 + - - +
501B ILE* 2.9 40.8 + - + +
508B LEU* 3.8 24.9 - - + -
509B PHE* 3.8 31.4 - + - -
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Residues in contact with LEU 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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467B HIS 3.8 8.5 - - - +
468B GLY* 3.5 36.8 - - - +
478B LEU* 4.2 11.7 - - + +
486B LEU* 3.9 26.9 - - + -
494B LEU* 2.9 34.4 + - + +
495B PRO* 4.1 1.3 - - + +
497B TRP* 1.3 81.7 - - + +
499B ASN* 1.3 62.5 + - - +
501B ILE* 3.9 2.9 - - + -
502B ASN* 3.0 32.9 + - - +
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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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495B PRO 2.9 19.7 + - - +
496B GLY* 3.5 9.3 + - - +
498B LEU* 1.3 79.3 - - - +
500B ALA* 1.3 60.6 + - - +
502B ASN* 4.1 2.0 - - - +
503B GLU* 3.5 24.1 + - - +
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Residues in contact with ALA 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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260B GLY* 3.7 18.4 - - - -
261B PHE* 3.7 16.4 - - + +
496B GLY 2.9 17.3 + - - +
497B TRP 3.0 4.5 + - - +
499B ASN* 1.3 75.4 - - - +
501B ILE* 1.3 63.2 + - - +
502B ASN 3.2 2.2 - - - -
503B GLU* 3.3 12.4 + - - -
506B ASN* 3.4 22.9 + - - +
508B LEU* 3.6 17.8 - - + +
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Residues in contact with ILE 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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464B GLN 4.4 2.0 - - - +
467B HIS* 3.6 36.1 - - + +
468B GLY 3.5 12.3 - - - +
469B LYS* 4.0 24.5 + - + +
497B TRP* 2.9 22.2 + - + +
498B LEU* 3.6 9.6 - - - +
500B ALA* 1.3 76.9 - - - +
502B ASN* 1.3 78.6 + - - +
503B GLU 3.4 1.9 + - - -
504B ASN* 4.9 1.7 + - - -
508B LEU* 3.7 19.4 - - + +
509B PHE* 3.6 44.2 - - + -
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Residues in contact with ASN 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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468B GLY 2.6 23.6 + - - -
469B LYS* 3.2 7.7 - - - +
470B THR* 2.8 42.4 + - - +
471B THR* 4.8 1.2 + - - -
498B LEU* 3.0 27.9 + - - +
499B ASN* 4.1 3.8 - - - +
500B ALA 3.2 0.6 - - - -
501B ILE* 1.3 84.3 - - - +
503B GLU* 1.3 56.9 + - - +
504B ASN* 3.5 17.5 + - - +
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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