Contacts of the helix formed by residues 594 - 603 (chain B) in PDB entry 1WSU
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 GLY 594 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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593B PHE* 1.3 91.7 - - - +
595B LEU* 1.3 66.1 - - - -
596B ALA* 3.3 3.6 - - - -
597B GLU* 2.7 21.1 + - - -
598B ALA 3.2 8.8 + - - -
613B LEU* 5.5 0.2 - - - -
627B ASP 4.0 16.6 - - - -
628B LYS* 4.3 4.8 - - - +
629B ARG* 6.0 0.9 - - - -
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Residues in contact with LEU 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594B GLY* 1.3 68.4 - - - -
596B ALA* 1.3 61.4 + - - +
598B ALA* 3.1 2.8 + - - +
599B ARG* 2.9 25.3 + - + +
606B ARG* 3.2 47.3 - - + +
609B VAL* 3.4 29.4 - - + -
610B LEU* 3.9 33.2 - - + +
613B LEU* 3.6 19.7 - - + -
627B ASP 4.9 0.4 + - - -
629B ARG* 5.2 3.4 - - - +
23F G 4.1 29.2 + - + +
24F U 4.1 5.6 - - - +
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Residues in contact with ALA 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594B GLY* 3.3 1.0 - - - -
595B LEU* 1.3 78.4 - - - +
597B GLU* 1.3 67.7 + - + +
599B ARG* 3.1 31.0 + - - +
600B ASP* 2.9 23.4 + - - +
606B ARG* 4.3 2.7 - - - +
22F G 3.8 12.1 - - - +
23F G 3.7 21.4 + - - +
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Residues in contact with GLU 597 (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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587B LEU* 4.0 13.8 - - + +
592B PRO 4.3 2.8 - - - +
593B PHE* 3.3 16.7 - - + +
594B GLY* 2.7 36.7 + - - +
595B LEU 3.3 0.4 - - - -
596B ALA* 1.3 81.1 - - + +
598B ALA* 1.3 57.5 + - - +
600B ASP* 3.3 10.0 + - - +
601B ALA* 2.9 29.1 + - - +
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Residues in contact with ALA 598 (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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584B ILE* 5.2 3.4 - - + -
587B LEU* 3.8 13.8 - - + +
593B PHE* 3.9 19.5 - - + -
594B GLY 3.2 9.8 + - - +
595B LEU 3.1 10.2 + - - +
597B GLU* 1.3 76.0 - - - +
599B ARG* 1.3 65.4 + - - +
601B ALA* 3.4 1.7 + - - +
602B LEU* 3.1 35.2 + - + +
609B VAL* 3.9 15.7 - - + -
613B LEU* 3.9 8.7 - - + -
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Residues in contact with ARG 599 (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 LEU* 2.9 13.2 + - + +
596B ALA* 3.4 20.4 + - - +
598B ALA* 1.3 77.1 - - - +
600B ASP* 1.3 87.0 + - - +
602B LEU 3.3 1.2 + - - -
603B GLY* 2.8 25.7 + - - -
604B SER 3.1 35.5 + - - +
605B SER* 3.6 14.4 - - - -
606B ARG* 4.0 7.2 - - + +
609B VAL* 3.8 17.2 - - + +
21F C 2.7 39.6 + - - +
22F G 2.9 41.2 + - - -
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Residues in contact with ASP 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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528A VAL* 5.9 0.2 - - - +
596B ALA* 2.9 18.2 + - - +
597B GLU* 3.6 11.1 - - - +
598B ALA 3.3 0.2 - - - -
599B ARG* 1.3 112.0 + - - +
601B ALA* 1.3 62.9 + - - +
603B GLY* 3.0 13.9 + - - +
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Residues in contact with ALA 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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528A VAL* 3.4 24.3 - - - +
583B VAL* 3.6 21.5 - - + +
584B ILE* 6.5 0.2 - - + -
587B LEU* 4.2 24.2 - - + -
597B GLU 2.9 17.0 + - - +
598B ALA 3.8 4.5 - - - +
599B ARG 3.4 0.2 - - - -
600B ASP* 1.3 76.4 - - - +
602B LEU* 1.3 57.5 + - + +
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Residues in contact with LEU 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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528A VAL* 4.2 6.0 - - - +
531B TRP* 3.2 41.8 - - + -
532B GLN* 4.8 0.9 + - - -
572B TRP* 5.5 3.6 - - + -
580B ALA* 4.0 24.5 - - + +
583B VAL* 3.8 28.3 - - + -
584B ILE* 4.7 10.5 - - + -
598B ALA 3.1 21.9 + - - +
599B ARG 4.0 2.0 - - - +
601B ALA* 1.3 76.0 - - + +
603B GLY* 1.3 64.6 + - - +
604B SER* 3.3 9.1 + - - +
609B VAL* 4.0 19.5 - - + -
612B LEU* 3.9 25.4 - - + -
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Residues in contact with GLY 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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528A VAL* 4.8 7.3 - - - +
532B GLN* 4.3 6.2 + - - -
599B ARG* 2.8 8.4 + - - -
600B ASP* 3.0 11.9 + - - -
601B ALA 3.4 0.2 - - - -
602B LEU* 1.3 79.1 - - - +
604B SER* 1.3 60.2 + - - +
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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