Contacts of the strand formed by residues 599 - 607 (chain B) in PDB entry 1ZXE
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 PHE 599 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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594B ARG* 4.1 9.2 - - - -
595B TYR* 2.8 52.8 + + + +
596B ALA* 3.9 9.0 - - - +
597B SER 3.6 0.6 - - - -
598B ASP* 1.3 91.5 - - + +
600B GLU* 1.3 60.5 + - - +
601B GLU 3.9 2.0 + - - -
616B ALA* 4.0 15.7 - - + -
617B ARG 3.3 15.9 - - - -
618B ASN* 3.0 39.9 - - + -
625B TYR* 4.5 5.6 - + - -
627B ILE* 3.9 14.8 - - + -
662B TRP* 3.5 23.6 - + - -
787B GLN* 3.8 22.4 - - - -
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Residues in contact with GLU 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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599B PHE* 1.3 73.1 - - - +
601B GLU* 1.3 69.2 + - - +
602B ILE* 3.3 9.5 + - + +
616B ALA* 3.0 6.7 - - - -
617B ARG* 3.0 57.5 + - + +
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Residues in contact with GLU 601 (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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595B TYR* 2.7 41.4 + - + +
599B PHE 3.9 3.8 + - - -
600B GLU* 1.3 76.9 - - - +
602B ILE* 1.3 60.0 + - - +
603B ALA 4.7 4.5 - - - +
604B VAL* 5.2 3.1 - - - +
612B GLN* 3.7 5.7 - - - +
614B VAL* 3.4 29.1 - - + +
615B LYS 3.8 2.7 - - - -
616B ALA* 4.0 2.7 - - - +
629B LYS* 3.0 20.7 + - - -
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Residues in contact with ILE 602 (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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600B GLU* 3.7 19.3 - - + +
601B GLU* 1.3 75.1 - - - +
603B ALA* 1.3 65.1 + - + +
615B LYS* 2.9 32.7 + - + +
617B ARG* 4.3 9.0 - - + +
624B TYR* 3.2 41.5 - - + -
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Residues in contact with ALA 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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601B GLU* 3.9 3.9 - - - +
602B ILE* 1.3 86.7 - - + +
604B VAL* 1.3 69.5 + - - +
605B LEU* 5.5 3.1 - - + -
614B VAL* 3.1 8.6 - - - +
615B LYS* 2.8 36.0 + - + +
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Residues in contact with VAL 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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601B GLU* 5.2 2.9 - - - +
603B ALA* 1.3 81.4 - - - +
605B LEU* 1.3 65.6 + - - +
606B GLY 3.4 24.5 - - - +
607B GLN* 4.3 10.8 - - + +
612B GLN* 4.1 25.8 - - + +
613B VAL 3.9 4.3 - - - +
614B VAL* 4.2 7.9 - - + +
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Residues in contact with LEU 605 (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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498B GOL 4.1 18.2 - - - +
603B ALA* 5.3 3.4 - - + +
604B VAL* 1.3 78.6 - - - +
606B GLY* 1.3 55.7 + - - +
613B VAL* 2.6 30.9 + - + +
614B VAL 3.7 26.2 - - - +
615B LYS* 4.1 9.2 - - + +
626B ALA* 4.2 4.7 - - + -
790B TYR* 4.0 33.0 - - + +
791B CYS 5.8 0.7 - - - +
793B ASN* 6.1 5.2 - - + -
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Residues in contact with GLY 606 (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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604B VAL* 3.4 7.0 - - - +
605B LEU* 1.3 78.1 - - - +
607B GLN* 1.3 61.8 + - - +
612B GLN* 3.1 7.8 - - - +
613B VAL* 3.0 35.4 + - - +
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Residues in contact with GLN 607 (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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604B VAL* 4.3 10.3 - - + +
606B GLY* 1.3 76.3 - - - +
608B GLY* 1.3 69.8 + - - +
611B GLY 3.6 17.4 - - - +
612B GLN* 3.3 26.5 + - - +
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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