Contacts of the strand formed by residues 599 - 604 (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 HIS 599 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545B TRP* 5.8 0.2 - - - +
593B ASP* 3.8 18.0 - - - +
595B GLN 4.8 0.7 + - - -
596B GLY 2.5 33.2 + - - +
597B GLY* 2.8 27.2 + - - -
598B GLY* 1.3 79.0 - - - -
600B SER* 1.3 62.4 - - - +
601B TYR* 4.0 22.5 + - + -
610B LYS* 3.7 38.6 + - + +
611B LEU 3.1 12.1 - - - +
612B GLU* 4.6 5.3 - - + +
613B ASN* 3.4 13.6 + - - +
618B SER* 4.3 12.8 + - - -
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Residues in contact with SER 600 (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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543B PHE* 3.7 26.6 - - - -
545B TRP* 3.9 13.6 - - - +
591B VAL* 4.2 5.0 - - - +
593B ASP* 4.1 11.0 + - - -
599B HIS* 1.3 75.1 - - - +
601B TYR* 1.3 64.1 + - - +
602B PHE* 3.3 7.5 - - - -
611B LEU* 2.8 45.4 + - - +
613B ASN* 3.8 12.8 - - - -
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Residues in contact with TYR 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591B VAL* 3.3 26.7 - - - +
592B VAL 3.3 4.9 + - - +
593B ASP* 2.6 41.6 - - + +
596B GLY* 4.7 5.9 + - - -
599B HIS* 4.0 22.7 + - + -
600B SER* 1.3 72.3 - - - +
602B PHE* 1.3 59.8 + - - +
603B PHE* 4.2 5.9 - - + -
608B TYR* 3.7 22.4 - + + -
609B LEU 3.1 7.9 - - - +
610B LYS* 3.6 37.8 + - + -
611B LEU 4.4 0.9 - - - +
627B ASP* 4.9 5.6 - - - -
628B TRP* 3.3 33.4 - + + -
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Residues in contact with PHE 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B PHE* 4.3 16.6 - + - -
554B PHE* 4.1 15.7 - + - -
581B TRP* 4.4 11.0 - + - -
584B ILE* 3.6 38.8 - - + -
588B LEU* 3.9 15.0 - - + -
590B ALA 4.0 1.6 - - - -
591B VAL* 3.4 33.2 - - + -
600B SER* 3.3 28.0 - - - -
601B TYR* 1.3 75.8 - - - +
603B PHE* 1.3 62.4 + - - +
607B TYR 3.9 1.0 - - - +
608B TYR* 3.1 3.4 - - - -
609B LEU* 2.5 55.9 + - + +
611B LEU* 3.7 25.4 - - + -
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Residues in contact with PHE 603 (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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449B ILE* 3.8 33.7 - - + -
588B LEU* 3.7 5.6 - - - +
589B ASP* 3.1 18.8 + - + -
590B ALA* 2.9 35.0 + - + +
591B VAL* 4.1 15.0 - - - -
592B VAL 4.5 9.2 - - - -
601B TYR* 4.4 10.8 - - + -
602B PHE* 1.3 74.4 - - - +
604B LYS* 1.3 63.2 + - - +
607B TYR 4.1 2.5 - - - -
608B TYR* 3.9 4.7 - - + -
624B ILE* 3.5 31.0 - - + -
628B TRP* 3.2 64.2 - + - -
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Residues in contact with LYS 604 (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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585B PRO* 4.4 22.9 - - + -
586B ASP 4.4 7.4 - - - +
587B ASN* 2.9 26.2 + - - +
588B LEU* 3.5 33.0 - - + +
589B ASP* 3.9 13.5 + - - +
603B PHE* 1.3 75.2 - - - +
605B GLY* 1.3 83.0 + - - +
606B ALA* 2.6 20.1 + - - -
607B TYR* 3.0 23.4 + - - +
609B LEU* 5.2 7.0 - - + -
624B ILE* 5.9 0.6 - - - +
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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