Contacts of the strand formed by residues 698 - 704 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666F ASN* 4.5 6.3 - - - +
693F LEU* 5.0 0.7 - - - -
697F HIS* 1.3 79.2 + - - +
699F ALA* 1.3 62.1 + - - +
700F VAL* 3.9 15.6 + - + +
715F LYS* 3.3 34.6 + - - +
716F ALA 3.4 11.7 - - - +
717F ALA* 3.9 22.6 - - + +
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Residues in contact with ALA 699 (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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666F ASN 3.5 28.9 - - - +
668F LEU* 3.5 19.7 - - - +
690F LEU* 3.8 29.2 - - + -
693F LEU* 4.3 4.9 - - + +
697F HIS 4.3 0.2 - - - -
698F GLU* 1.3 71.1 - - - +
700F VAL* 1.3 62.6 + - - +
716F ALA 3.0 30.7 + - - +
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Residues in contact with VAL 700 (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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613F ASN* 5.6 3.1 + - - -
668F LEU* 3.9 9.7 + - - +
698F GLU* 3.9 22.1 + - + +
699F ALA* 1.3 76.6 - - - +
701F CYS* 1.3 67.9 + - - +
702F GLU* 4.4 10.1 - - + -
713F THR* 3.8 26.0 - - + -
714F LEU 3.8 2.2 - - - -
715F LYS* 4.0 25.6 - - + +
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Residues in contact with CYS 701 (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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668F LEU* 2.9 43.3 - - + +
670F ALA* 3.5 33.9 - - - -
688F PHE* 3.5 18.5 - - + -
700F VAL* 1.3 73.4 - - - +
702F GLU* 1.3 65.6 + - - +
703F VAL* 4.1 3.5 + - - -
712F PHE 3.9 0.7 - - - +
713F THR* 3.5 3.6 - - - +
714F LEU* 2.9 31.7 + - - +
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Residues in contact with GLU 702 (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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571F PRO 4.5 1.6 - - - +
572F TYR* 5.9 0.3 - - - -
575F ARG* 3.5 43.4 + - + +
579F ARG* 4.4 10.0 + - - -
700F VAL* 4.4 8.0 - - + +
701F CYS* 1.3 79.8 - - - +
703F VAL* 1.3 62.7 + - - +
704F PRO* 3.6 7.8 - - - +
710F VAL* 3.4 30.8 - - + +
712F PHE 3.6 3.8 - - - -
713F THR* 3.9 20.0 + - + +
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Residues in contact with VAL 703 (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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571F PRO* 4.8 4.3 - - + -
575F ARG* 5.1 0.2 - - - -
670F ALA* 4.2 13.5 - - + -
682F TRP* 4.2 10.8 - - + +
683F HIS* 3.9 31.2 - - + +
686F THR* 4.6 3.8 - - + +
688F PHE* 3.8 35.4 - - + -
701F CYS* 4.5 0.2 - - - -
702F GLU* 1.3 74.8 - - - +
704F PRO* 1.3 69.0 - - + +
710F VAL* 3.6 2.5 - - - -
711F ILE* 2.7 35.0 + - + +
712F PHE* 2.8 27.7 + - + +
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Residues in contact with PRO 704 (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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571F PRO* 3.1 26.7 - - + +
574F TYR* 4.2 6.1 - - + +
575F ARG* 3.9 27.3 - - + +
682F TRP* 3.2 28.5 - - + +
683F HIS* 5.1 1.9 + - - -
702F GLU 3.6 6.7 - - - +
703F VAL* 1.3 96.3 - - + +
705F ALA* 1.3 64.3 + - - +
708F GLY* 3.7 21.1 - - - +
709F SER 3.1 8.5 - - - +
710F VAL* 4.3 0.4 - - - -
711F ILE* 3.9 3.0 - - - +
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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
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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