Contacts of the strand formed by residues 810 - 819 (chain A) in PDB entry 3THW
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 THR 810 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807A THR* 3.0 45.0 + - - +
809A GLU* 1.3 88.4 + - - +
811A LEU* 1.3 71.3 + - - +
812A THR* 3.4 35.9 - - + +
829A HIS* 3.2 7.6 + - - -
833A LEU* 3.8 10.8 - - - +
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Residues in contact with LEU 811 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670A PRO* 5.3 4.0 - - + -
804A ALA* 3.5 30.1 - - + -
805A LEU 3.3 9.2 - - - +
806A THR* 5.1 0.2 - - + -
810A THR* 1.3 78.8 - - - +
812A THR* 1.3 61.7 + - - +
813A MET* 3.4 28.7 + - + +
826A PHE* 3.5 34.8 - - + -
829A HIS* 4.4 7.9 - - + -
830A VAL* 3.4 31.4 - - + -
833A LEU* 4.2 12.3 - - + +
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Residues in contact with THR 812 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804A ALA* 3.4 1.2 - - - -
805A LEU* 2.6 57.1 + - - +
807A THR* 4.4 2.6 + - - -
810A THR* 3.4 20.7 - - + +
811A LEU* 1.3 75.5 - - - +
813A MET* 1.3 62.1 + - - +
814A LEU* 5.7 2.5 - - - -
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Residues in contact with MET 813 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670A PRO* 4.4 7.2 - - + -
671A ASN 3.6 22.2 - - - +
672A MET* 3.4 28.9 - - + +
673A GLY* 4.2 11.2 - - - -
803A THR 4.0 5.4 - - - +
804A ALA* 3.7 19.5 - - - -
811A LEU* 3.4 35.4 - - + +
812A THR* 1.3 76.3 - - - +
814A LEU* 1.3 64.7 + - - +
815A TYR* 3.5 37.1 - - + +
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Residues in contact with LEU 814 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651A ILE* 4.5 8.1 - - - +
803A THR* 3.1 32.7 + - - +
804A ALA 4.3 18.4 - - - +
805A LEU* 4.2 23.3 - - + -
812A THR* 4.7 3.1 - - - +
813A MET* 1.3 73.3 - - - +
815A TYR* 1.3 71.7 + - - +
816A GLN* 3.0 18.0 + - + +
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Residues in contact with TYR 815 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649A ALA 5.9 4.0 - - - -
651A ILE* 3.7 32.0 - - + +
653A ASN* 3.0 21.8 + - - -
672A MET 3.9 20.0 + - - -
673A GLY 3.5 23.1 - - - -
674A GLY* 5.0 4.7 - - - -
802A VAL* 5.8 1.3 - - - -
803A THR 4.1 5.3 + - - +
813A MET* 3.2 32.3 - - + +
814A LEU* 1.3 78.6 - - - +
816A GLN* 1.3 57.7 + - - +
817A VAL* 5.7 0.4 - - - -
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Residues in contact with GLN 816 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651A ILE* 4.2 15.4 - - + +
652A PRO 5.2 2.9 + - - +
653A ASN* 3.3 4.9 - - - +
802A VAL* 3.3 5.6 - - - -
803A THR* 3.1 42.5 + - + +
814A LEU* 3.0 16.7 + - + +
815A TYR* 1.3 81.2 - - - +
817A VAL* 1.3 64.4 + - - +
818A LYS* 6.2 0.2 - - + -
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Residues in contact with VAL 817 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653A ASN* 2.8 24.1 + - + +
654A ASP 5.2 3.6 - - - +
667A ILE* 6.0 2.7 - - + -
678A TYR* 3.6 45.3 - - + +
800A LEU* 3.7 32.3 - - + -
801A HIS 3.6 8.1 - - - +
802A VAL* 4.5 13.9 - - + -
815A TYR 5.4 0.4 - - - +
816A GLN* 1.3 79.5 - - - +
818A LYS* 1.3 62.0 + - - +
819A LYS* 5.3 6.8 + - - +
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Residues in contact with LYS 818 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800A LEU* 3.6 5.5 - - - -
801A HIS* 3.0 57.4 + - + +
803A THR* 4.2 14.1 - - + -
816A GLN* 6.2 0.4 - - + -
817A VAL* 1.3 75.4 - - - +
819A LYS* 1.3 72.1 + - - +
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Residues in contact with LYS 819 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654A ASP* 4.9 19.6 + - - +
656A TYR* 5.1 12.5 - - - +
662A GLN* 4.5 17.7 - - - +
665A HIS* 6.2 0.2 - - - -
798A ASN* 4.8 10.5 - - - +
799A ASN 4.0 7.4 - - - +
800A LEU* 3.6 23.6 - - + +
801A HIS* 4.4 2.4 - - - -
817A VAL* 5.3 5.8 + - - +
818A LYS* 1.3 91.0 - - - +
820A GLY* 1.3 60.2 + - - +
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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