Contacts of the strand formed by residues 607 - 612 (chain A) in PDB entry 2WSK
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 607 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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557A LEU* 4.0 21.1 - - + -
560A ARG* 3.7 31.2 - - + -
561A ILE* 3.8 38.6 - - + -
562A PRO* 4.2 1.6 - - + -
601A ILE 3.7 0.4 - - - +
602A LEU* 2.9 5.7 - - - +
603A LEU* 2.8 42.1 + - + +
604A SER* 4.7 2.2 - - - -
606A ARG* 1.3 119.2 - - + +
608A LEU* 1.3 61.5 + - - +
609A ILE* 5.6 2.9 - - + -
627A TRP* 3.8 0.9 - - - -
630A ILE* 4.4 2.0 - - + -
655A PHE 3.4 4.7 - - - +
656A GLN* 3.1 39.3 - - + -
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Residues in contact with LEU 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600A GLN* 3.2 38.8 - - + +
601A ILE 3.5 4.9 - - - +
602A LEU* 4.1 12.6 - - + -
607A PHE* 1.3 77.4 - - - +
609A ILE* 1.3 76.8 + - - +
610A ALA* 3.8 9.4 - - + +
622A LEU* 4.2 6.5 - - + -
623A PRO* 3.3 29.2 - - + -
627A TRP* 3.4 21.5 - - + -
654A VAL* 3.2 4.0 - - - +
655A PHE* 2.7 55.8 + - + -
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Residues in contact with ILE 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A PHE* 4.1 22.0 - - + -
501A THR* 4.9 1.1 - - + -
505A LEU* 3.6 35.4 - - + -
561A ILE* 6.0 1.8 - - + -
599A LEU 3.8 0.9 - - - +
600A GLN* 3.2 5.0 - - - -
601A ILE* 2.8 53.6 + - + +
603A LEU* 4.5 11.7 - - + -
607A PHE* 5.6 2.2 - - + -
608A LEU* 1.3 79.2 - - - +
610A ALA* 1.3 60.1 + - - +
611A ILE* 3.8 25.1 + - + +
652A LEU* 4.0 15.0 - - + -
653A CYS 3.7 3.6 - - - +
654A VAL* 3.9 16.6 - - + -
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Residues in contact with ALA 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599A LEU 3.8 3.1 - - - -
600A GLN* 4.5 6.1 - - + +
608A LEU* 3.8 9.5 - - + +
609A ILE* 1.3 72.3 - - - +
611A ILE* 1.3 61.2 + - - +
620A ILE* 4.7 7.0 - - + -
622A LEU* 5.7 0.9 - - + -
645A TRP* 3.5 29.4 - - + -
652A LEU* 3.1 29.5 - - - +
653A CYS 2.9 15.2 + - - +
655A PHE* 3.8 15.5 - - + -
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Residues in contact with ILE 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A PHE* 3.9 18.4 - - + -
404A TRP* 3.6 22.0 - - + -
414A PHE* 5.2 7.6 - - + -
597A LYS 4.5 1.3 - - - +
598A GLN* 3.1 21.1 - - - -
599A LEU* 2.8 42.7 + - + +
601A ILE* 4.8 7.9 - - + -
609A ILE* 3.8 15.7 - - + +
610A ALA* 1.3 73.9 - - - +
612A ASN* 1.3 63.3 + - - +
613A ALA* 3.8 10.1 - - + +
620A ILE* 3.4 10.5 - - - +
645A TRP* 4.2 0.4 - - - -
651A GLY 4.1 0.7 - - - -
652A LEU* 3.3 38.1 - - + -
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Residues in contact with ASN 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A LYS 4.1 0.9 - - - -
598A GLN* 3.5 10.2 - - - +
611A ILE* 1.3 74.1 - - - +
613A ALA* 1.3 55.8 + - - +
614A THR* 2.7 29.5 + - - +
616A GLU 3.2 16.8 - - - +
618A THR* 3.4 21.2 + - - +
620A ILE* 4.6 1.3 - - + -
645A TRP* 4.1 14.3 - - + -
647A GLY 3.3 10.0 - - - +
648A PRO 2.9 23.4 - - - +
649A ALA* 3.9 1.0 - - - -
650A HIS 3.1 19.2 + - - -
651A GLY 3.0 19.4 + - - +
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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