Contacts of the strand formed by residues 697 - 704 (chain C) 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 HIS 697 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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666C ASN* 3.0 29.9 + - + +
693C LEU* 3.5 6.2 - - + +
694C GLN* 3.1 46.5 + - + +
695C ASP 3.6 10.7 + - - -
696C GLY* 1.3 81.8 + - - +
698C GLU* 1.3 62.6 + - - +
717C ALA* 3.4 3.2 - - - +
718C ARG 3.0 25.3 + - - +
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Residues in contact with GLU 698 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666C ASN* 4.8 4.2 - - - +
693C LEU* 4.8 0.9 - - - -
697C HIS* 1.3 78.6 + - - +
699C ALA* 1.3 65.6 + - - +
700C VAL* 3.8 18.7 + - - +
715C LYS* 3.1 38.5 + - + +
716C ALA 3.6 3.4 - - - +
717C ALA* 3.6 25.6 - - + +
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Residues in contact with ALA 699 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666C ASN* 3.6 25.4 - - - +
668C LEU* 3.9 23.2 - - + +
690C LEU* 3.9 21.1 - - + -
693C LEU* 4.4 4.1 - - + +
697C HIS 4.3 0.2 - - - -
698C GLU* 1.3 73.3 - - - +
700C VAL* 1.3 61.3 + - - +
714C LEU 4.0 0.5 - - - +
715C LYS* 3.4 4.7 - - - +
716C ALA* 3.0 33.2 + - + +
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Residues in contact with VAL 700 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613C ASN* 5.5 4.2 + - - -
668C LEU* 3.7 11.4 + - - +
698C GLU* 3.8 30.3 + - - +
699C ALA* 1.3 79.3 - - - +
701C CYS* 1.3 70.0 + - - +
702C GLU* 4.6 8.7 - - + -
713C THR* 4.0 22.9 - - + -
714C LEU 3.7 4.0 - - - +
715C LYS* 4.2 12.8 - - + -
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Residues in contact with CYS 701 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668C LEU* 3.1 41.7 - - + +
670C ALA* 3.5 35.2 - - - -
688C PHE* 3.9 15.3 - - + -
700C VAL* 1.3 75.2 - - - +
702C GLU* 1.3 69.4 + - - +
703C VAL* 4.2 1.3 + - - +
712C PHE 4.0 0.2 - - - +
713C THR* 3.4 4.2 - - - +
714C LEU* 3.0 30.6 + - + +
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Residues in contact with GLU 702 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571C PRO 4.4 2.1 - - - +
575C ARG* 3.2 50.3 + - + +
579C ARG* 5.0 3.3 + - - -
700C VAL* 4.6 8.7 - - + -
701C CYS* 1.3 81.3 - - - +
703C VAL* 1.3 64.2 + - - +
704C PRO* 3.5 8.1 - - - +
710C VAL* 3.3 31.6 - - + +
712C PHE 3.5 3.8 - - - -
713C THR* 4.0 21.1 + - + +
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Residues in contact with VAL 703 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571C PRO* 4.7 4.9 - - + -
575C ARG* 5.5 0.4 - - - -
670C ALA* 4.2 13.9 - - + -
682C TRP* 4.1 11.0 - - + +
683C HIS* 4.0 31.4 - - + +
686C THR* 4.5 3.6 - - + +
688C PHE* 3.8 32.8 - - + -
701C CYS* 4.5 1.8 - - - +
702C GLU* 1.3 74.8 - - - +
704C PRO* 1.3 69.0 - - + +
710C VAL* 3.7 2.0 - - - -
711C ILE* 2.8 34.3 + - - +
712C PHE* 2.8 29.2 + - + +
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Residues in contact with PRO 704 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571C PRO* 3.3 25.4 - - + +
574C TYR* 4.2 8.3 - - + -
575C ARG* 4.0 24.5 - - + +
682C TRP* 3.3 33.7 - - + +
683C HIS* 4.9 2.4 + - - -
702C GLU 3.5 5.8 - - - +
703C VAL* 1.3 96.7 - - + +
705C ALA* 1.3 66.0 + - - +
708C GLY* 4.0 11.9 - - - +
709C SER 3.3 13.0 - - - +
710C VAL* 4.4 0.9 - - - -
711C ILE* 3.7 8.1 - - - +
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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