Contacts of the strand formed by residues 503 - 507 (chain B) in PDB entry 1GXD
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 ALA 503 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452B ILE* 3.4 33.7 - - + -
484B TRP* 5.4 2.2 - - - +
495B TYR 3.9 3.4 - - - -
496B GLU* 5.4 0.7 - - - +
501B GLU 4.4 0.2 + - - -
502B LYS* 1.3 68.4 - - - +
504B VAL* 1.3 59.6 + - - +
505B PHE* 3.9 7.7 + - + -
513B ILE* 3.5 1.1 - - - +
514B TYR* 2.2 69.3 + - + +
515B SER* 4.3 1.9 - - - +
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Residues in contact with VAL 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B VAL* 3.2 6.1 - - - +
495B TYR* 2.5 94.3 + - + +
497B ALA* 4.3 13.2 - - + -
500B GLU* 6.0 1.1 - - - +
502B LYS* 4.2 8.5 - - + +
503B ALA* 1.3 75.7 - - - +
505B PHE* 1.3 65.9 + - - +
511B TYR* 6.1 1.6 - - + -
512B TRP 4.1 0.9 - - - -
513B ILE* 3.9 32.3 - - + +
562B TYR* 6.2 0.2 - - + -
564B GLU* 4.3 11.4 - - - +
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Residues in contact with PHE 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B ILE* 4.8 0.7 - - + -
459B PHE* 3.4 25.8 - + - -
484B TRP* 3.6 37.9 - + - -
487B LEU* 3.3 24.5 - - + -
491B ILE* 3.4 26.5 - - + -
493B ALA 3.5 13.2 - - - -
494B VAL* 3.4 20.9 - - + -
495B TYR* 4.3 0.7 + - - -
503B ALA* 4.5 12.1 - - + -
504B VAL* 1.3 84.6 - - - +
506B PHE* 1.3 70.2 + - - +
511B TYR* 4.2 2.9 - - - +
512B TRP* 2.6 46.5 + - + +
514B TYR* 4.1 12.8 - + + -
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Residues in contact with PHE 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B ILE* 3.4 7.1 - - - +
492B ASP* 2.8 24.0 + - + -
493B ALA* 2.8 36.4 + - + +
495B TYR* 2.8 47.8 - + - -
505B PHE* 1.3 76.0 - - - +
507B ALA* 1.3 64.4 + - - +
510B GLU 4.3 3.6 - - - -
511B TYR* 4.4 2.5 - - + +
512B TRP* 5.0 0.9 - - - +
527B LEU* 3.1 44.4 - - + -
530B LEU* 3.9 15.3 - - + -
539B VAL* 3.6 37.2 - - + -
542B ALA* 4.5 0.7 - - + -
553B ILE* 4.0 12.1 - - + -
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Residues in contact with ALA 507 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B LEU* 4.3 1.8 - - + -
488B PRO* 4.2 17.4 - - + +
489B GLU 5.8 0.2 - - - +
490B LYS 5.0 1.1 - - - +
491B ILE* 3.9 17.7 - - + +
492B ASP* 3.9 7.1 - - - +
506B PHE* 1.3 78.8 - - - +
508B GLY* 1.3 63.8 + - - +
509B ASN 3.4 0.5 + - - -
510B GLU* 3.2 24.6 + - - +
512B TRP* 3.8 27.9 - - + -
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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
------------------------------------------------------------
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