Contacts of the helix formed by residues 498 - 508 (chain B) in PDB entry 4D2Y
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 ASN 498 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477B SER* 4.4 1.2 + - - -
481B ARG* 3.0 49.2 + - - +
482B TYR 2.6 31.1 + - - +
484B GLY 4.1 0.7 - - - +
495B ASP* 2.8 29.5 + - - +
497B ALA* 1.3 79.4 - - - +
499B VAL* 1.3 53.2 + - - +
500B GLN 3.3 2.5 - - - -
501B PHE* 3.4 10.4 + - + +
502B THR* 2.6 45.1 + - - +
520B LEU* 3.9 13.9 - - + -
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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
----------------------------------------------------------
484B GLY 3.4 16.9 - - - +
485B TYR 4.3 0.4 - - - +
486B LYS* 4.1 27.4 - - + +
492B THR* 3.8 28.7 - - + +
495B ASP 3.8 0.6 + - - -
496B PRO* 3.3 20.5 + - + +
497B ALA 3.5 1.0 - - - -
498B ASN* 1.3 76.4 - - - +
500B GLN* 1.3 57.7 + - - +
502B THR* 3.3 2.4 + - - -
503B GLU* 3.0 48.4 + - + +
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Residues in contact with GLN 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B ALA 5.1 1.6 + - - +
498B ASN 3.3 0.6 - - - -
499B VAL* 1.3 79.8 - - - +
501B PHE* 1.3 64.5 + - - +
503B GLU* 3.3 14.9 + - - +
504B ILE* 3.1 28.4 + - + +
711B TRP* 3.3 41.6 + - + +
712B ASN* 5.1 2.4 + - - -
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Residues in contact with PHE 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B TRP* 3.6 38.8 - - + -
476B ASN* 3.3 40.6 - - - -
477B SER 5.7 1.1 - - - -
497B ALA 5.7 0.2 + - - -
498B ASN* 3.4 13.0 + - + +
499B VAL 3.4 0.4 - - - -
500B GLN* 1.3 79.2 - - - +
502B THR* 1.3 61.7 + - - +
504B ILE* 3.3 10.1 + - + +
505B CYS* 3.0 42.9 + - - -
520B LEU* 3.6 27.1 - - + -
521B PRO 4.0 2.7 - - - -
523B LEU* 3.9 16.6 - - + -
711B TRP* 4.0 23.2 - + + -
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Residues in contact with THR 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B ALA* 3.3 16.5 - - + -
484B GLY 2.9 36.3 + - - +
485B TYR* 3.7 27.6 - - + -
498B ASN 2.6 28.5 + - - -
499B VAL 3.6 0.7 - - - -
501B PHE* 1.3 74.2 - - - +
503B GLU* 1.3 62.5 + - + +
505B CYS* 3.3 3.9 + - - +
506B ILE* 3.0 26.5 + - + +
510B TRP* 4.1 7.9 - - + -
520B LEU* 3.6 12.6 - - - +
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Residues in contact with GLU 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B GLY 5.7 1.1 - - - +
486B LYS* 4.7 8.2 - - - +
499B VAL* 3.0 36.7 + - + +
500B GLN* 3.3 14.5 + - + +
502B THR* 1.3 77.1 - - + +
504B ILE* 1.3 56.1 + - + +
506B ILE* 3.4 11.8 + - + +
507B GLN* 2.9 31.1 + - - +
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Residues in contact with ILE 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B TRP* 4.6 8.3 - - + -
500B GLN* 3.1 20.1 + - + +
501B PHE* 3.6 9.9 - - + +
502B THR 3.3 0.2 - - - -
503B GLU* 1.3 76.6 - - + +
505B CYS* 1.3 52.8 + - - +
507B GLN* 3.1 14.8 + - - +
508B GLN* 2.8 49.3 + - + +
523B LEU* 3.6 25.4 - - + -
711B TRP* 3.6 55.0 - - + -
716B TRP* 5.7 1.8 - - + -
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Residues in contact with CYS 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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501B PHE* 3.0 52.8 + - - +
502B THR* 3.3 8.5 + - - +
504B ILE* 1.3 77.1 - - - +
506B ILE* 1.3 62.4 + - - +
508B GLN* 3.0 12.5 + - - -
509B GLY 3.1 0.9 + - - -
510B TRP* 2.9 28.8 + - + +
520B LEU* 4.5 1.6 - - - -
521B PRO* 3.7 32.1 - - + -
523B LEU* 4.6 2.9 - - - -
533B LEU* 3.5 14.4 - - + +
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Residues in contact with ILE 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B TYR* 4.3 9.4 - - + -
502B THR* 3.0 30.5 + - + +
503B GLU* 3.6 14.1 - - + +
505B CYS* 1.3 74.7 - - - +
507B GLN* 1.3 58.7 - - - +
509B GLY* 2.9 20.4 + - - -
510B TRP* 3.6 32.6 + - + +
511B LYS* 5.6 0.3 + - - -
512B ALA* 4.2 16.4 - - + -
514B ARG* 4.8 7.4 - - - +
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Residues in contact with GLN 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B GLU 2.9 17.1 + - - +
504B ILE* 3.4 15.1 - - - +
506B ILE* 1.3 78.5 - - - +
508B GLN* 1.3 75.2 + - - +
509B GLY* 3.0 4.4 + - - -
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Residues in contact with GLN 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B ILE* 2.8 33.2 + - + +
505B CYS* 3.0 7.8 + - - +
507B GLN* 1.3 99.4 + - - +
509B GLY* 1.3 54.8 + - - +
523B LEU* 4.4 15.5 - - + -
531B PRO* 4.7 8.1 - - - +
533B LEU* 3.3 24.1 - - + +
716B TRP* 3.8 35.7 - - + -
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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