Contacts of the strand formed by residues 707 - 712 (chain F) in PDB entry 2W3S
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 ILE 707 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462E PRO* 3.7 30.7 - - + -
643F LEU 2.9 4.9 + - - -
644F ARG* 3.6 34.8 - - + +
645F THR 2.8 31.7 + - - +
705F PRO* 3.7 2.6 - - - +
706F ARG* 1.3 77.3 - - - +
708F PHE* 1.3 57.6 + - - +
709F ASN* 3.5 27.8 - - - +
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Residues in contact with PHE 708 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138E GLY 4.4 6.5 - - - -
140E ALA* 3.9 23.1 - - + -
144E ARG* 5.0 5.6 + - - +
645F THR* 3.6 7.2 - - - -
647F ILE* 3.9 15.3 - - + -
665F GLU* 3.6 49.9 - - + +
668F TYR* 3.8 19.5 - + + -
669F VAL* 4.1 14.4 - - + -
704F ARG* 5.0 2.0 - - + -
705F PRO* 3.9 30.9 + - + +
706F ARG 4.1 0.4 + - - -
707F ILE* 1.3 75.0 - - - +
709F ASN* 1.3 66.6 + - - +
710F VAL* 3.8 20.6 + - + +
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Residues in contact with ASN 709 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644F ARG* 4.0 6.9 - - - +
645F THR 2.7 9.9 + - - -
646F ASP* 2.9 28.7 + - + +
647F ILE* 2.5 37.0 + - - +
707F ILE* 3.5 25.1 - - - +
708F PHE* 1.3 75.7 + - - +
710F VAL* 1.3 57.3 - - - +
711F ALA* 5.7 0.4 - - - -
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Residues in contact with VAL 710 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647F ILE* 3.4 14.8 - - + +
661F ILE* 3.5 33.5 - - + +
664F ILE* 3.4 30.1 - - + -
665F GLU* 4.0 22.2 - - + +
708F PHE* 3.8 30.0 + - + +
709F ASN* 1.3 77.5 - - - +
711F ALA* 1.3 68.7 + - - +
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Residues in contact with ALA 711 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647F ILE 2.7 10.6 + - - +
648F LEU* 3.2 16.2 - - + -
649F HIS* 2.8 30.3 + - - +
661F ILE* 4.3 3.6 - - - -
709F ASN 5.7 0.4 - - - -
710F VAL* 1.3 79.8 - - - +
712F LEU* 1.3 59.7 + - - +
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Residues in contact with LEU 712 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648F LEU* 3.7 10.4 - - - +
649F HIS 3.1 8.7 - - - +
651F ALA* 3.8 24.5 - - + +
654F SER* 4.4 11.7 - - - +
657F PRO* 4.0 37.7 - - + +
660F ASP* 4.5 4.9 - - + -
661F ILE* 3.8 15.2 - - + +
664F ILE* 3.7 29.2 - - + -
711F ALA* 1.3 75.4 - - - +
713F TRP* 1.3 61.5 + - - +
714F ASP* 3.3 11.6 + - + +
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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
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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