Contacts of the helix formed by residues 492 - 505 (chain B) in PDB entry 3II5
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 GLN 492 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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490B THR* 2.9 24.1 + - - +
491B PRO* 1.3 89.2 - - - +
493B GLN* 1.3 62.1 + - + +
495B GLN* 3.3 5.1 + - - +
496B ALA* 2.9 26.9 + - - +
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Residues in contact with GLN 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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467B PHE* 5.8 13.6 - - + -
484B LEU* 3.6 33.0 - - + +
486B VAL* 3.5 27.7 - - - +
488B ALA 4.5 1.4 - - - +
489B PRO* 3.4 8.4 - - + +
490B THR* 2.8 45.6 + - - +
492B GLN* 1.3 75.1 - - + +
494B LEU* 1.3 65.4 + - - +
495B GLN 2.9 1.7 + - - -
496B ALA* 3.0 7.9 + - - +
497B PHE* 2.8 26.5 + - - +
524B LEU* 4.4 2.1 - - - +
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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
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489B PRO* 4.7 10.2 - - + +
490B THR 2.8 19.7 + - - +
491B PRO* 4.1 12.1 - - + -
493B GLN* 1.3 73.4 - - - +
495B GLN* 1.3 60.3 + - - +
497B PHE* 3.6 8.6 - - + +
498B LYS* 3.3 58.4 + - + +
524B LEU* 4.4 21.5 - - + +
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Residues in contact with GLN 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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491B PRO 3.3 19.9 + - - +
492B GLN* 3.3 6.7 + - - +
493B GLN 2.9 0.8 - - - -
494B LEU* 1.3 81.8 - - - +
496B ALA* 1.3 66.2 + - - +
498B LYS* 3.4 16.5 + - - +
499B ASN* 2.9 58.5 + - - +
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Residues in contact with ALA 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 GLN 2.9 14.1 + - - +
493B GLN* 3.5 10.1 - - - +
495B GLN* 1.3 74.9 - - - +
497B PHE* 1.3 65.0 + - - +
499B ASN* 2.9 12.3 + - - +
500B GLU* 2.8 26.2 + - - +
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Residues in contact with PHE 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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493B GLN 2.8 16.3 + - - +
494B LEU* 3.6 7.2 - - + +
496B ALA* 1.3 78.5 - - - +
498B LYS* 1.3 79.7 + - + +
499B ASN 3.1 0.3 + - - -
500B GLU* 3.1 6.0 + - - +
501B VAL* 3.1 32.8 + - + +
518B TYR* 4.0 19.5 - + + -
519B SER 3.6 18.8 - - - -
520B THR* 4.4 12.3 - - - -
524B LEU* 3.6 44.0 - - + -
525B ALA 3.6 21.1 - - - -
526B ILE* 3.9 18.6 - - + -
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Residues in contact with LYS 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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494B LEU* 3.3 50.7 + - - +
495B GLN* 4.0 18.7 + - - +
496B ALA 3.4 0.2 - - - -
497B PHE* 1.3 93.1 - - + +
499B ASN* 1.3 60.9 + - - +
501B VAL* 4.2 4.6 - - - +
502B GLY* 3.1 20.5 + - - -
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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 GLN* 2.9 50.4 + - - +
496B ALA* 2.9 14.3 + - - +
498B LYS* 1.3 76.1 - - - +
500B GLU* 1.3 64.6 + - - +
502B GLY* 3.4 2.4 + - - -
503B VAL* 3.1 28.3 + - + +
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Residues in contact with GLU 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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1B 831 2.9 49.1 + - + -
482B LYS* 2.7 35.3 + - - -
496B ALA 2.8 14.9 + - - +
497B PHE* 3.7 8.2 - - - +
499B ASN* 1.3 71.8 - - - +
501B VAL* 1.3 56.1 + - - +
503B VAL* 2.8 27.7 + - - +
504B LEU* 2.8 17.7 + - + +
526B ILE* 3.3 20.9 - - + +
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Residues in contact with VAL 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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497B PHE* 3.1 33.2 + - + +
498B LYS* 4.2 5.2 - - - +
500B GLU* 1.3 77.8 - - - +
502B GLY* 1.3 62.8 + - - +
503B VAL 3.0 1.2 + - - -
504B LEU* 3.2 7.3 + - - +
505B ARG* 3.0 35.1 + - - +
515B PHE* 4.3 13.6 - - + -
518B TYR* 4.0 31.2 - - + -
526B ILE* 3.9 28.0 - - + -
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Residues in contact with GLY 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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447A ASP* 4.8 0.2 - - - +
498B LYS 3.1 18.1 + - - -
499B ASN 3.8 2.2 - - - -
500B GLU 3.2 0.4 - - - -
501B VAL* 1.3 78.3 - - - +
503B VAL* 1.3 59.4 + - - +
505B ARG* 3.5 18.5 - - - +
506B LYS* 3.2 30.3 - - - +
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Residues in contact with VAL 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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1B 831 4.5 21.5 - - + -
499B ASN* 3.1 16.4 - - + +
500B GLU* 2.8 12.4 + - - +
502B GLY* 1.3 78.4 - - - +
504B LEU* 1.3 64.2 + - + +
505B ARG 3.2 1.6 - - - -
506B LYS* 3.1 23.7 + - - +
507B THR* 3.6 7.7 - - + +
571B ILE* 3.6 32.0 - - + +
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Residues in contact with LEU 504 (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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508A ARG* 3.8 2.4 + - - -
1B 831 3.6 67.8 - - + +
500B GLU* 2.8 23.3 + - + +
501B VAL* 3.9 4.3 - - - +
503B VAL* 1.3 76.7 - - - +
505B ARG* 1.3 56.3 + - - +
506B LYS 3.1 0.4 - - - -
507B THR* 2.6 36.3 + - - +
513B LEU* 4.9 9.6 - - + +
515B PHE* 3.8 29.5 - - + +
526B ILE* 4.1 23.8 - - + -
528B THR* 4.8 4.0 - - + -
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Residues in contact with ARG 505 (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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447A ASP* 3.1 29.3 + - - +
449A TRP* 3.2 24.4 - - - -
508A ARG* 3.4 12.0 + - - +
726A PO4 3.3 31.4 + - - +
448B ASP* 4.5 14.8 + - - +
449B TRP* 3.6 25.5 - - + +
501B VAL* 3.0 31.4 + - - +
502B GLY* 3.5 20.9 - - - +
504B LEU* 1.3 72.0 - - - +
506B LYS* 1.3 54.5 + - - +
507B THR 3.1 5.6 - - - -
515B PHE* 4.0 17.9 - - + -
518B TYR* 4.9 6.5 + - - -
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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