Contacts of the strand formed by residues 698 - 704 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666E ASN* 4.5 6.2 - - - +
693E LEU* 4.8 1.3 - - - -
697E HIS* 1.3 78.8 - - - +
699E ALA* 1.3 69.0 + - - +
700E VAL* 4.1 11.2 + - + +
715E LYS* 3.0 37.2 + - - +
716E ALA 3.3 15.0 - - - +
717E ALA* 4.1 17.2 - - + +
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Residues in contact with ALA 699 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666E ASN* 3.3 28.5 - - - +
667E THR 3.9 1.8 - - - -
668E LEU* 3.8 25.6 - - + +
690E LEU* 4.0 14.6 - - + -
693E LEU* 4.8 3.0 - - + +
698E GLU* 1.3 72.7 - - - +
700E VAL* 1.3 61.9 + - - +
714E LEU 3.8 1.0 - - - +
715E LYS* 3.5 3.5 - - - -
716E ALA* 3.0 32.9 + - - +
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Residues in contact with VAL 700 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613E ASN* 5.7 2.6 + - - -
668E LEU* 3.9 10.1 + - - +
698E GLU* 4.1 18.3 + - + +
699E ALA* 1.3 76.9 - - - +
701E CYS* 1.3 67.8 + - - +
702E GLU* 4.3 9.2 - - + -
713E THR* 3.7 25.8 - - + -
714E LEU 3.7 3.1 - - - -
715E LYS* 4.2 22.2 - - + -
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Residues in contact with CYS 701 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668E LEU* 3.0 43.1 - - + +
670E ALA* 3.5 33.0 - - - -
688E PHE* 3.6 16.2 - - + -
700E VAL* 1.3 72.2 - - - +
702E GLU* 1.3 66.3 + - - +
703E VAL* 4.4 4.4 - - - +
712E PHE 3.7 1.4 - - - +
713E THR* 3.3 3.9 - - - +
714E LEU* 2.9 35.4 + - + +
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Residues in contact with GLU 702 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571E PRO 4.5 2.3 - - - +
572E TYR* 6.0 0.2 - - - -
575E ARG* 2.9 47.3 + - + +
579E ARG* 3.9 9.2 + - - -
700E VAL* 4.5 8.5 - - + -
701E CYS* 1.3 79.9 - - - +
703E VAL* 1.3 63.0 + - - +
704E PRO* 3.6 7.3 - - - +
710E VAL* 3.4 36.7 - - + +
712E PHE 3.6 3.6 - - - -
713E THR* 3.9 19.1 + - + +
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Residues in contact with VAL 703 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571E PRO* 4.8 4.0 - - + -
670E ALA* 4.2 12.1 - - + -
682E TRP* 4.1 20.2 - - + +
683E HIS* 4.0 23.6 - - + -
686E THR* 4.7 3.4 - - + +
688E PHE* 3.8 35.2 - - + -
701E CYS* 4.4 1.1 - - - -
702E GLU* 1.3 75.0 - - - +
704E PRO* 1.3 74.3 - - + +
710E VAL* 3.6 2.6 - - - -
711E ILE* 2.8 26.6 + - + +
712E PHE* 2.8 28.4 + - + +
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Residues in contact with PRO 704 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571E PRO 3.3 24.7 - - - +
574E TYR* 4.2 13.9 - - + -
575E ARG* 4.0 28.9 - - + +
682E TRP* 3.2 23.1 - - + +
683E HIS* 5.4 1.9 + - - -
702E GLU 3.6 5.4 - - - +
703E VAL* 1.3 95.0 - - + +
705E ALA* 1.3 66.1 + - - +
708E GLY* 3.9 16.4 - - - +
709E SER 3.1 12.6 - - - +
710E VAL* 4.1 0.9 - - + -
711E ILE* 4.2 2.9 - - - +
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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