Contacts of the strand formed by residues 698 - 704 (chain B) in PDB entry 1XSK
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 GLU 698 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666B ASN* 5.2 2.2 - - - +
693B LEU* 5.0 0.2 - - - -
697B HIS* 1.3 77.6 + - - +
699B ALA* 1.3 61.0 + - - +
700B VAL* 3.8 13.9 + - + +
715B LYS* 3.3 38.5 - - + +
716B ALA 3.5 4.5 - - - +
717B ALA* 3.9 25.5 - - + +
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Residues in contact with ALA 699 (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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666B ASN* 3.6 27.4 - - - +
668B LEU* 3.6 27.7 - - + +
690B LEU* 3.9 17.3 - - + -
693B LEU* 4.5 4.6 - - + +
697B HIS 4.2 0.8 - - - -
698B GLU* 1.3 71.5 - - - +
700B VAL* 1.3 61.2 + - - +
715B LYS* 3.3 3.8 - - - +
716B ALA 2.8 34.4 + - - +
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Residues in contact with VAL 700 (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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613B ASN* 5.8 1.7 + - - -
668B LEU* 4.0 9.6 + - - +
698B GLU* 3.8 17.4 + - + +
699B ALA* 1.3 78.0 - - - +
701B CYS* 1.3 67.1 - - - +
702B GLU* 4.3 9.4 - - + -
713B THR* 3.6 27.8 - - + -
714B LEU 3.3 4.9 - - - +
715B LYS* 3.8 23.6 - - + -
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Residues in contact with CYS 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668B LEU* 3.0 41.7 - - + +
670B ALA* 3.4 34.1 - - - -
688B PHE* 3.7 13.9 - - - -
700B VAL* 1.3 72.4 - - - +
702B GLU* 1.3 64.3 + - - +
703B VAL* 3.7 6.0 + - - +
712B PHE 3.7 0.2 - - - +
713B THR* 3.4 1.7 - - - -
714B LEU* 2.8 40.1 + - + +
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Residues in contact with GLU 702 (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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571B PRO 4.4 0.9 - - - +
575B ARG* 3.0 56.0 + - + +
579B ARG* 4.2 10.2 + - - -
700B VAL* 4.4 7.9 - - + -
701B CYS* 1.3 77.4 - - - +
703B VAL* 1.3 61.4 + - - +
704B PRO* 3.2 9.7 - - - +
710B VAL* 3.6 22.3 - - + +
712B PHE 3.4 4.0 - - - -
713B THR* 3.9 23.3 + - + +
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Residues in contact with VAL 703 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B PRO* 4.8 3.4 - - + -
670B ALA* 4.2 12.8 - - + -
682B TRP* 4.1 9.4 - - + +
683B HIS* 3.9 37.2 - - + +
686B THR* 4.7 3.6 - - + +
688B PHE* 3.6 37.2 - - + -
701B CYS* 4.4 2.2 - - - +
702B GLU* 1.3 71.6 - - - +
704B PRO* 1.3 71.1 - - + +
710B VAL* 3.9 0.9 - - - -
711B ILE* 3.0 27.5 + - - +
712B PHE* 2.7 27.6 + - + +
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Residues in contact with PRO 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B PRO* 3.0 28.7 - - + +
574B TYR* 4.2 13.0 - - + -
575B ARG* 3.9 27.1 - - + +
682B TRP* 3.3 21.6 - - + +
683B HIS* 5.3 2.1 + - - -
702B GLU 3.2 7.2 - - - +
703B VAL* 1.3 93.0 - - + +
705B ALA* 1.3 63.4 + - - +
708B GLY* 3.6 19.7 - - - +
709B SER 3.4 7.4 - - - +
710B VAL* 4.5 0.7 - - - -
711B ILE* 3.9 6.0 - - - +
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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
------------------------------------------------------------
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