Contacts of the strand formed by residues 707 - 713 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462G PRO* 4.2 26.0 - - + +
643H LEU 3.0 6.9 + - - -
644H ARG* 3.1 29.7 - - + +
645H THR 2.6 33.8 + - - -
705H PRO* 3.3 4.0 - - - +
706H ARG* 1.3 80.0 - - - +
708H PHE* 1.3 59.6 + - - +
709H ASN* 3.6 30.1 - - - +
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Residues in contact with PHE 708 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138G GLY 4.1 8.7 - - - -
140G ALA* 4.0 22.7 - - + -
144G ARG* 4.6 11.4 + - - +
645H THR* 3.7 6.7 - - - -
647H ILE* 3.7 19.1 - - + -
665H GLU* 3.2 37.5 - - + -
668H TYR* 3.8 19.1 - + - -
669H VAL* 3.7 12.6 - - + -
704H ARG* 4.8 1.8 - - + -
705H PRO* 3.6 36.6 - - + +
706H ARG 4.2 0.2 - - - -
707H ILE* 1.3 75.2 - - - +
709H ASN* 1.3 62.0 + - - +
710H VAL* 3.6 27.5 + - + +
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Residues in contact with ASN 709 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644H ARG* 3.3 24.4 - - - +
645H THR 2.9 9.7 + - - -
646H ASP* 2.8 28.3 + - - +
647H ILE 2.6 36.0 + - - +
707H ILE* 3.6 15.7 - - - +
708H PHE* 1.3 72.9 - - - +
710H VAL* 1.3 57.7 + - - +
711H ALA* 5.6 0.7 - - - -
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Residues in contact with VAL 710 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647H ILE* 3.8 11.4 - - + -
661H ILE* 3.7 37.8 - - + +
664H ILE* 3.5 36.1 - - + -
665H GLU* 3.6 24.9 - - + +
708H PHE* 3.6 31.2 + - + +
709H ASN* 1.3 74.6 - - - +
711H ALA* 1.3 63.8 + - - +
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Residues in contact with ALA 711 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647H ILE* 3.0 13.3 + - - +
648H LEU* 3.1 18.9 - - + -
649H HIS* 3.0 24.4 + - - +
661H ILE* 4.7 2.2 - - - -
709H ASN 5.4 0.7 - - - +
710H VAL* 1.3 76.8 - - - +
712H LEU* 1.3 66.2 + - - +
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Residues in contact with LEU 712 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648H LEU* 3.9 8.0 - - - +
649H HIS 3.3 8.1 - - - +
651H ALA* 4.4 12.3 - - + -
654H SER* 4.3 14.8 - - - -
657H PRO* 3.7 37.0 - - + +
660H ASP* 4.6 3.8 - - + -
661H ILE* 3.5 20.2 - - + -
664H ILE* 3.6 31.6 - - + -
711H ALA* 1.3 76.9 - - - +
713H TRP* 1.3 66.9 + - - +
714H ASP* 3.5 10.7 + - + +
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Residues in contact with TRP 713 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413H VAL* 3.5 31.2 - - + +
416H GLU* 3.8 22.2 - - + -
417H LEU* 3.6 34.8 - - + -
420H ARG* 3.1 43.3 - - - +
648H LEU* 3.9 19.8 - - + +
649H HIS 2.7 19.4 + - - +
650H ASP* 3.4 36.6 - - + +
651H ALA 3.9 9.9 + - - -
652H GLY 3.7 11.1 - - - +
711H ALA 3.9 1.2 + - - -
712H LEU* 1.3 72.3 - - - +
714H ASP* 1.3 57.9 + - - +
715H GLN* 3.5 40.9 + - + +
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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