Contacts of the strand formed by residues 634 - 637 (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 ARG 634 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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633D GLY* 1.3 70.8 - - - -
635D TRP* 1.3 60.8 + - - +
636D THR* 4.0 0.9 + - - -
643D GLU* 3.6 28.7 + - + +
644D LEU* 3.3 13.8 - - - +
645D ASP* 2.6 43.7 + - - +
663D VAL 4.4 0.2 - - - +
665D ASP* 3.2 28.2 + - + +
692D ASN* 3.1 37.0 + - + +
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Residues in contact with TRP 635 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595D PHE* 3.8 18.6 - + - -
609D MET* 4.2 7.6 - - + -
615D MET* 3.9 14.6 - - + -
630D LEU* 3.4 37.1 - - + +
631D PRO* 3.0 49.3 + - + -
632D GLU 3.9 8.9 + - - -
633D GLY* 3.6 14.1 - - - -
634D ARG* 1.3 74.1 - - - +
636D THR* 1.3 62.1 + - - +
642D ASP 3.8 0.2 - - - +
643D GLU* 3.0 7.4 - - - +
644D LEU 2.7 38.0 + - - -
646D GLY* 4.3 0.2 - - - -
662D TYR* 3.5 41.4 - - + -
663D VAL 3.4 14.6 - - - +
664D ARG* 3.3 35.9 - - + -
665D ASP 5.6 0.7 - - - -
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Residues in contact with THR 636 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634D ARG 4.3 0.5 + - - -
635D TRP* 1.3 74.0 - - - +
637D HIS* 1.3 70.6 + - - +
638D LEU 3.1 0.9 + - - -
641D ASN* 3.6 31.4 - - - +
642D ASP 3.2 3.1 - - - +
643D GLU* 3.3 18.1 + - + +
662D TYR* 3.4 4.3 - - - -
663D VAL* 2.8 34.5 + - - +
691D PHE* 3.6 29.2 - - + +
692D ASN* 3.7 12.6 + - - -
739D ARG* 5.1 0.4 - - + -
740D ASN* 3.7 12.8 - - - +
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Residues in contact with HIS 637 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636D THR* 1.3 71.7 - - - +
638D LEU* 1.3 67.0 + - - +
639D TRP* 2.9 55.5 + + - -
640D HIS* 3.2 31.9 + + + -
641D ASN* 2.9 22.0 + - - +
642D ASP* 2.8 33.9 + - - +
654D HIS* 4.7 4.3 - + - -
658D SER* 4.2 0.4 + - - -
659D LEU 3.1 24.1 + - - -
660D PRO* 4.6 1.1 - - + -
661D VAL 3.4 14.5 + - - -
662D TYR* 3.2 26.6 - + + -
739D ARG* 4.2 0.9 + - - -
2003D MPO 5.7 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
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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