Contacts of the strand formed by residues 838 - 845 (chain B) in PDB entry 4X52
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 VAL 838 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788B ALA* 4.0 7.2 - - + -
789B THR 3.3 7.4 - - - +
791B ARG* 4.5 4.5 + - - -
828B HIS* 4.5 8.1 - - + +
831B CYS* 3.6 28.7 - - + -
833B TYR* 3.5 23.1 - - + +
834B ASP 3.4 17.5 - - - +
835B ALA* 3.2 16.6 + - - +
836B LYS 3.6 0.2 - - - -
837B ASN* 1.3 77.8 - - - +
839B VAL* 1.3 73.4 + - - +
893B TYR* 3.2 44.0 + - + +
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Residues in contact with VAL 839 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787B TYR 4.1 0.3 - - - +
788B ALA* 3.4 3.5 - - - -
789B THR* 2.9 45.3 + - + +
790B SER 4.0 7.0 - - - +
791B ARG* 3.3 44.9 - - + +
794B VAL* 3.6 27.6 - - + -
838B VAL* 1.3 78.4 - - - +
840B MET* 1.3 59.2 + - - +
841B PHE* 4.3 3.1 - - + -
890B VAL* 4.0 11.2 - - + -
891B ILE 3.6 10.3 - - - +
892B GLU* 4.2 10.1 - - + -
893B TYR* 3.9 4.0 - - - -
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Residues in contact with MET 840 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747B PHE* 4.1 14.6 - - + -
751B MET* 4.1 6.7 - - + -
786B PHE* 3.6 44.0 - - + -
787B TYR 3.9 1.1 - - - -
788B ALA* 3.8 27.1 - - + -
824B ALA* 3.3 28.7 - - + +
827B SER* 4.1 2.0 - - - -
828B HIS* 4.0 6.3 - - + -
839B VAL* 1.3 71.9 - - - +
841B PHE* 1.3 63.2 + - - +
890B VAL* 3.5 1.6 - - - -
891B ILE* 2.7 48.2 + - + +
893B TYR* 3.6 31.1 - - + +
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Residues in contact with PHE 841 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762B ILE* 3.6 25.1 - - + -
786B PHE* 3.5 6.1 - - - -
787B TYR* 2.8 38.4 + - + +
789B THR* 3.7 23.8 - - + -
794B VAL* 3.8 29.8 - - + -
797B ILE* 3.5 43.5 - - + -
798B CYS* 4.1 2.7 - - - -
802B PHE* 3.8 29.6 - + + -
839B VAL* 4.3 3.6 - - + -
840B MET* 1.3 80.8 - - - +
842B VAL* 1.4 59.4 + - - +
843B ALA 4.0 0.2 - - - -
887B PRO* 4.2 1.6 - - + -
889B TYR 3.3 15.0 - - - -
890B VAL* 3.6 15.5 - - + -
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Residues in contact with VAL 842 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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743B VAL* 4.0 13.2 - - + -
746B HIS* 6.3 0.2 - - + -
784B LEU* 3.5 40.8 - - + -
785B LEU 3.5 4.0 - - - +
786B PHE* 3.8 16.2 - - + -
841B PHE* 1.4 71.4 - - - +
843B ALA* 1.3 62.2 + - - +
844B GLN* 5.5 0.9 - - - +
887B PRO* 4.1 1.6 - - - +
888B GLN* 2.8 26.1 + - + -
889B TYR* 2.8 37.6 + - + +
891B ILE* 3.6 31.0 - - + -
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Residues in contact with ALA 843 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783B LYS 3.3 1.7 - - - +
784B LEU* 3.5 3.8 - - - -
785B LEU* 2.8 36.5 + - - +
787B TYR* 5.7 0.7 - - + -
802B PHE* 3.8 16.2 - - + -
820B PHE* 3.8 29.6 - - + -
841B PHE* 4.0 1.1 - - + -
842B VAL* 1.3 76.1 - - - +
844B GLN* 1.4 61.4 + - - +
845B VAL* 3.8 4.4 + - + +
885B VAL* 3.8 6.1 - - + -
886B TYR 3.4 11.4 - - - +
888B GLN* 4.2 0.9 - - - +
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Residues in contact with GLN 844 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771B PHE* 3.3 26.0 - - + -
782B GLY* 3.5 32.9 + - - +
783B LYS 3.5 3.0 - - - -
784B LEU* 3.6 30.9 - - - +
842B VAL* 5.5 1.0 - - - +
843B ALA* 1.4 71.9 - - - +
845B VAL* 1.3 58.4 + - - +
885B VAL* 3.4 2.8 - - - +
886B TYR* 2.9 41.8 + - + +
888B GLN* 4.7 21.4 - - + +
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Residues in contact with VAL 845 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771B PHE* 4.5 0.2 - - - -
781B GLU 4.3 0.7 - - - +
782B GLY* 3.6 2.2 - - - -
783B LYS* 2.8 39.4 + - - +
785B LEU* 3.8 21.8 - - + -
820B PHE* 3.9 25.1 - - + -
843B ALA* 4.0 19.7 - - + +
844B GLN* 1.3 79.1 - - - +
846B LEU* 1.3 63.4 + - - +
847B VAL* 3.2 17.8 + - + -
879B ILE* 3.5 36.8 - - + -
884B GLN 3.4 4.9 - - - +
885B VAL* 4.1 5.4 - - + -
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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