Contacts of the strand formed by residues 648 - 653 (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 ARG 648 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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629E TYR* 3.3 11.1 - - - -
630E LEU 3.0 26.0 + - - +
645E ASP* 3.5 35.9 + - - +
646E GLY 2.9 21.6 + - - -
647E SER* 1.3 81.0 + - - +
649E TRP* 1.3 66.1 + - - +
650E HIS* 3.5 30.4 - - + +
647F SER* 3.7 23.1 - - - +
648F ARG* 4.5 25.8 - - + +
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Residues in contact with TRP 649 (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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600E ALA* 5.4 5.8 + - + +
604E LEU* 3.5 33.2 - - + -
606E ARG* 4.1 19.1 - - - -
607E GLN* 4.5 2.0 - - - -
627E GLN* 3.7 12.6 - - + +
628E PHE* 3.3 42.4 - - - -
629E TYR* 3.7 25.5 - + + +
648E ARG* 1.3 83.1 - - - +
650E HIS* 1.3 69.2 + - - +
598F ASP* 5.6 0.4 - - - +
599F PRO* 3.5 49.6 - - + -
600F ALA* 3.5 30.0 - - + +
629F TYR* 5.5 2.9 - + - -
647F SER* 5.0 5.5 + - - +
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Residues in contact with HIS 650 (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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627E GLN* 3.2 7.4 - - - +
628E PHE* 2.7 57.5 + + + +
630E LEU* 3.5 28.7 - - + +
644E LEU* 3.9 27.8 - - + +
645E ASP* 2.9 30.4 + - + -
648E ARG* 3.5 28.4 + - + +
649E TRP* 1.3 78.9 + - - +
651E LYS* 1.3 62.2 + - - +
652E GLN* 4.1 2.5 - - + -
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Residues in contact with LYS 651 (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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625E ASP* 4.2 24.6 + - - +
626E VAL 3.7 3.6 - - - +
627E GLN* 4.1 33.4 - - + +
650E HIS* 1.3 73.6 - - - +
652E GLN* 1.3 74.8 + - - +
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Residues in contact with GLN 652 (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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625E ASP* 3.6 4.3 - - - +
626E VAL* 3.0 32.5 + - + -
628E PHE* 3.6 25.4 - - + -
642E ASP* 4.2 0.2 - - - +
644E LEU* 3.8 11.1 - - - +
650E HIS* 4.1 2.4 - - + -
651E LYS* 1.3 86.6 + - - +
653E GLN* 1.3 66.2 + - - +
654E HIS* 2.7 39.3 + - + +
660E PRO* 3.7 2.6 - - - +
662E TYR* 2.6 29.4 + - - -
2004E MPO 3.6 30.1 - - - +
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Residues in contact with GLN 653 (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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623E ALA* 3.6 18.1 + - - +
624E GLY 3.2 20.9 - - - -
625E ASP* 3.7 14.5 - - - +
651E LYS* 6.2 0.2 - - - +
652E GLN* 1.3 81.2 - - - +
654E HIS* 1.3 74.0 + - - +
655E GLY* 4.9 1.4 - - - +
2004E MPO 3.6 20.9 + - - +
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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