Contacts of the strand formed by residues 952 - 959 (chain B) in PDB entry 3H44
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 HIS 952 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771B LEU* 3.4 37.0 + - + -
772B PRO 3.2 26.2 - - - -
773B ASP* 2.7 28.2 + - - -
775B GLY 4.2 0.2 - - - -
794B TYR 3.5 0.2 - - - +
795B TYR* 3.2 6.3 - - - +
796B GLN* 2.9 57.4 + - + +
797B THR 4.2 4.6 + - - -
943B MET* 4.0 5.9 + - + -
950B ARG* 3.0 37.8 + - - -
951B ARG* 1.3 71.9 - - - +
953B LYS* 1.3 60.8 + - - +
1005B PHE* 6.2 3.6 - + - -
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Residues in contact with LYS 953 (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 LEU* 4.0 3.2 - - - +
775B GLY 3.2 15.8 + - - +
776B TRP* 3.1 45.6 - - + +
777B PHE* 3.0 26.3 + - - -
793B ILE* 3.8 9.0 - - - -
794B TYR 3.2 5.2 - - - +
795B TYR* 3.4 35.8 + - + -
860B GLU* 2.8 23.9 + - - -
864B GLU* 4.0 15.6 + - - +
951B ARG* 3.4 18.9 - - + +
952B HIS* 1.3 75.5 - - - +
954B VAL* 1.3 64.3 + - - +
955B SER* 3.5 10.1 - - - +
986B LEU* 4.8 3.8 - - - +
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Residues in contact with VAL 954 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686B LEU* 4.5 11.6 - - + +
689B LEU* 4.8 3.6 - - + -
690B MET* 3.8 29.4 - - + -
771B LEU* 3.1 32.1 - - + -
777B PHE* 3.3 25.1 - - + +
792B GLU 4.2 0.2 - - - +
793B ILE* 3.7 1.2 - - - +
794B TYR* 2.7 46.2 + - + +
953B LYS* 1.3 72.3 - - - +
955B SER* 1.3 71.3 + - - +
992B ILE* 4.4 10.3 - - + -
998B PHE* 4.8 1.6 - - + -
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Residues in contact with SER 955 (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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776B TRP* 2.8 28.4 + - - -
777B PHE 2.9 5.9 + - - +
778B VAL* 3.2 4.8 - - - +
779B TYR* 3.0 25.1 + - - +
792B GLU 3.4 8.7 - - - -
793B ILE* 4.4 2.2 - - - +
860B GLU* 2.9 25.7 + - - -
953B LYS* 3.5 7.6 - - - -
954B VAL* 1.3 80.3 + - - +
956B VAL* 1.3 64.8 + - - +
957B HIS* 3.7 10.8 - - - -
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Residues in contact with VAL 956 (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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682B ALA* 3.6 34.6 - - + +
685B TYR* 3.7 29.4 - - + -
686B LEU* 3.7 34.1 - - + +
689B LEU* 4.2 11.4 - - + -
779B TYR* 3.5 11.7 - - + +
790B GLY 3.9 0.2 - - - +
791B ILE* 3.2 9.4 - - - +
792B GLU* 2.9 30.4 + - + +
955B SER* 1.3 76.6 - - - +
957B HIS* 1.3 63.5 + - - +
958B VAL* 3.9 3.5 + - + -
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Residues in contact with HIS 957 (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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776B TRP* 5.2 1.0 - - - -
778B VAL* 4.0 22.6 - - + +
779B TYR 3.1 7.9 + - - -
780B GLN* 3.3 18.1 - - + +
781B GLN 3.0 26.0 + - - +
790B GLY 3.7 4.0 - - - -
791B ILE* 3.7 10.7 - - + +
856B PRO* 3.3 28.6 - - + +
857B HIS* 4.4 7.4 + - + -
860B GLU* 2.8 44.7 + - + +
955B SER* 3.7 10.3 - - - -
956B VAL* 1.3 75.9 - - - +
958B VAL* 1.3 62.7 + - - +
959B LEU* 3.8 6.1 + - + +
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Residues in contact with VAL 958 (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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678B PRO* 3.8 11.9 - - + +
681B HIS* 3.9 18.6 - - + +
682B ALA* 3.6 37.9 - - + +
685B TYR* 4.1 11.0 - - + -
781B GLN* 3.2 9.9 - - + +
782B ARG 4.1 2.2 - - - -
783B ASN* 3.7 32.5 - - + +
789B SER* 3.2 6.9 - - - -
790B GLY 2.7 43.0 + - - +
856B PRO* 4.4 0.3 - - - +
956B VAL* 4.3 0.9 - - + -
957B HIS* 1.3 74.9 - - - +
959B LEU* 1.3 62.1 + - - +
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Residues in contact with LEU 959 (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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780B GLN* 4.0 27.6 - - - +
781B GLN 2.7 19.6 + - - +
782B ARG* 3.4 11.9 - - + +
783B ASN* 2.9 27.2 + - - +
788B ASN 4.4 0.7 - - - -
789B SER* 4.2 2.5 - - - -
856B PRO* 3.6 33.4 - - + -
957B HIS* 4.5 10.1 - - + +
958B VAL* 1.3 72.7 - - - +
960B ALA* 1.3 69.1 + - - +
963B MET* 4.2 11.0 - - + -
964B ASP* 3.5 42.8 - - - +
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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