Contacts of the strand formed by residues 508 - 512 (chain D) 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 TRP 508 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D GLU* 3.0 27.2 + - - -
169D PHE* 6.0 1.6 - + - -
477D VAL* 5.2 0.4 - - - -
478D HIS 3.3 19.3 - - - +
480D GLY* 3.6 13.1 - - - -
493D SER* 3.1 46.0 - - - -
494D LEU* 4.9 0.7 - - - -
496D GLY* 4.7 0.4 - - - -
497D GLY* 3.4 24.3 - - - +
500D ILE* 4.0 25.4 - - + -
507D PHE* 1.3 74.0 - - - +
509D SER* 1.3 63.7 + - - +
510D HIS* 3.8 35.7 - + + -
530D PHE* 4.2 7.6 - + - -
534D SER* 4.5 1.6 - - - -
535D SER* 3.0 22.9 + - - -
536D HIS* 3.6 9.4 + - - +
588D MET* 3.9 33.8 - - + +
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Residues in contact with SER 509 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464D PHE* 3.3 31.5 - - - -
477D VAL* 3.6 7.9 - - - +
478D HIS 2.9 8.5 + - - +
479D TRP* 3.5 13.4 - - - +
480D GLY* 2.7 31.4 + - - -
508D TRP* 1.3 79.1 - - - +
510D HIS* 1.3 59.1 + - - +
536D HIS* 3.2 32.3 - - - -
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Residues in contact with HIS 510 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479D TRP* 4.1 7.0 - - - -
480D GLY* 4.4 5.6 - - - +
481D GLY 6.0 0.2 - - - -
493D SER* 4.3 6.7 + - - +
508D TRP* 3.8 26.7 - + + -
509D SER* 1.3 78.8 - - - +
511D ASP* 1.3 66.6 + - - +
512D ILE* 3.8 1.7 + - - +
527D TRP* 3.6 19.5 + + + +
530D PHE* 3.3 41.5 - + - -
531D GLY* 3.4 22.6 - - - -
534D SER* 2.9 25.2 + - - -
536D HIS 4.1 9.0 - - - -
537D SER* 4.5 0.5 - - - -
538D ARG* 3.6 20.8 + - - +
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Residues in contact with ASP 511 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479D TRP* 2.9 26.3 + - + +
481D GLY 5.4 2.5 + - - +
483D CYS* 4.4 7.1 - - - -
510D HIS* 1.3 75.7 - - - +
512D ILE* 1.3 65.1 + - - +
513D GLY 3.3 0.9 + - - -
514D GLY* 3.3 30.1 + - - +
515D PHE* 4.0 3.3 - - - -
527D TRP* 3.4 15.4 + - - -
538D ARG* 2.7 51.8 + - - +
540D HIS* 2.9 22.2 - - + +
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Residues in contact with ILE 512 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D LEU* 4.4 4.5 - - + -
510D HIS* 4.9 1.3 - - + +
511D ASP* 1.3 70.3 - - - +
513D GLY* 1.3 60.3 + - - +
514D GLY 3.2 0.7 - - - -
524D TYR* 4.2 11.2 - - + +
527D TRP* 4.0 4.9 - - - +
528D CYS* 3.4 44.4 - - + +
531D GLY* 4.2 19.7 - - - -
532D LEU* 3.5 31.2 - - + -
537D SER* 4.6 1.1 - - - -
538D ARG 2.8 29.1 + - - +
539D LEU* 3.8 28.8 - - + +
540D HIS 3.2 23.0 + - - +
546D ARG* 5.4 0.2 - - - -
559D VAL* 5.9 0.2 - - + -
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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
------------------------------------------------------------
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