Contacts of the strand formed by residues 583 - 592 (chain C) in PDB entry 1XKH
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 TYR 583 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163C ARG* 3.2 4.0 + - - -
579C LEU* 3.7 13.4 + - + -
580C ASN* 3.4 18.3 + - + +
582C THR* 1.3 100.4 - - + +
584C SER* 1.3 70.8 + - - +
620C ILE* 3.4 23.1 - - + -
621C LYS 3.2 14.1 - - - -
622C GLY* 3.9 5.6 - - - -
624C TYR* 3.1 33.7 + + - -
631C THR* 4.7 3.1 - - - -
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Residues in contact with SER 584 (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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163C ARG* 2.5 55.6 + - - -
576C VAL* 4.3 7.2 - - - -
577C TYR 3.4 11.2 - - - -
578C ASP* 3.2 11.1 - - - -
579C LEU* 4.1 4.7 - - - +
583C TYR* 1.3 72.3 + - - +
585C VAL* 1.3 65.9 + - - +
620C ILE* 2.8 18.9 - - - +
621C LYS* 2.9 19.1 + - - -
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Residues in contact with VAL 585 (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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575C ALA 3.7 0.3 - - - +
576C VAL* 3.0 6.8 - - - +
577C TYR* 2.6 60.1 + - + +
579C LEU* 4.4 19.5 - - + -
584C SER* 1.3 81.8 - - - +
586C TYR* 1.3 62.9 + - - +
619C GLY 3.5 6.1 - - - +
620C ILE* 3.8 24.7 - - + -
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Residues in contact with TYR 586 (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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163C ARG 5.9 0.4 - - - +
165C THR 4.6 2.0 - - - +
166C PRO* 2.8 49.4 - - + -
167C GLN 3.9 9.4 - - - -
168C SER* 4.0 9.7 + - - -
575C ALA 3.1 13.0 - - - +
576C VAL* 4.4 7.9 - - + -
585C VAL* 1.3 76.1 - - - +
587C ALA* 1.3 63.6 + - - +
617C GLU* 3.6 25.9 - - + +
618C ILE* 3.3 9.1 - - - +
619C GLY* 2.8 71.2 + - - +
620C ILE* 3.9 3.8 - - - -
621C LYS* 4.6 24.0 - - + -
632C SER* 6.0 1.5 - - - -
633C LEU 5.1 0.2 - - - -
634C ALA* 2.9 25.8 - - + +
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Residues in contact with ALA 587 (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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166C PRO* 4.1 5.0 - - - +
574C GLY* 3.2 20.8 - - - -
575C ALA* 3.3 10.6 + - + +
586C TYR* 1.3 75.8 - - - +
588C SER* 1.3 65.6 + - - +
617C GLU 3.1 14.1 - - - +
618C ILE* 3.8 15.3 - - + -
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Residues in contact with SER 588 (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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166C PRO* 3.3 21.4 + - - -
167C GLN* 4.6 5.9 - - - +
572C TYR* 5.4 2.0 - - - -
573C VAL 3.3 10.8 - - - -
574C GLY* 4.6 2.2 - - - -
587C ALA* 1.3 78.0 - - - +
589C TYR* 1.3 60.8 + - - +
590C THR* 4.0 16.5 + - - +
615C ASN 3.2 4.2 + - - +
616C TYR* 3.7 4.3 - - - -
617C GLU* 2.8 49.7 + - - +
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Residues in contact with TYR 589 (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 43.5 - - + +
573C VAL* 2.9 33.1 + - + +
588C SER* 1.3 72.7 - - - +
590C THR* 1.3 62.0 + - - +
591C ASP* 4.4 3.8 + - + -
614C GLN* 3.4 38.9 + - + +
615C ASN 3.8 2.2 - - - -
616C TYR* 3.3 42.8 - + + -
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Residues in contact with THR 590 (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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167C GLN* 3.2 41.3 - - + +
252C ALA* 3.1 25.7 + - - +
571C PRO 4.3 2.2 - - - -
572C TYR* 3.8 17.0 - - + -
588C SER* 3.8 6.3 + - - +
589C TYR* 1.3 77.0 - - - +
591C ASP* 1.3 57.8 + - - +
614C GLN* 3.2 8.3 - - - +
615C ASN* 2.9 58.7 + - - +
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Residues in contact with ASP 591 (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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252C ALA* 3.5 5.9 + - - +
254C GLY* 3.1 20.6 + - - -
255C LEU 4.3 0.4 + - - +
569C PHE 4.1 3.1 - - - +
570C ILE* 3.2 24.3 - - + +
571C PRO* 3.5 38.6 + - + +
589C TYR* 4.4 2.6 + - + -
590C THR* 1.3 75.8 - - - +
592C ILE* 1.3 82.8 + - - +
593C PHE* 5.5 0.3 - - - +
612C GLU* 4.1 14.6 - - - +
613C GLY 3.0 20.1 - - - +
614C GLN* 3.0 21.2 - - + +
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Residues in contact with ILE 592 (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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252C ALA* 4.0 13.5 - - + -
253C THR* 4.0 19.1 - - + +
254C GLY* 3.7 5.8 - - - +
258C GLY 4.1 10.1 - - - +
260C GLY* 3.3 9.9 - - - +
261C SER 3.1 41.3 - - - +
262C LEU* 3.2 29.6 - - + +
570C ILE* 4.1 7.9 - - - -
591C ASP* 1.3 88.6 - - - +
593C PHE* 1.3 73.3 + - - +
612C GLU* 3.2 4.7 - - - +
613C GLY 2.9 29.0 + - - +
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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