Contacts of the strand formed by residues 829 - 834 (chain B) in PDB entry 2HRC
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 ASN 829 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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748B PHE* 4.0 5.3 - - + -
752B LYS* 3.7 21.3 - - - +
755B GLU* 2.7 42.7 + - - +
756B VAL* 3.4 13.0 - - + -
757B VAL* 2.9 26.0 + - - +
827B ARG 3.5 1.5 - - - -
828B LYS* 1.3 78.3 - - - +
830B ILE* 1.3 62.2 + - - +
863B GLU* 3.2 20.6 + - - +
864B ASN* 3.0 40.8 + - - +
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Residues in contact with ILE 830 (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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748B PHE* 3.3 6.7 - - - -
756B VAL* 4.3 0.2 - - - -
757B VAL* 3.4 13.0 - - + +
759B LEU* 3.9 26.5 - - + -
819B ILE* 4.1 25.8 - - + +
822B LEU* 3.9 25.1 - - + -
823B CYS* 4.2 7.2 - - - -
827B ARG 3.8 21.1 - - - +
828B LYS 4.4 0.4 - - - -
829B ASN* 1.3 81.1 - - - +
831B LEU* 1.3 64.7 + - - +
832B LEU* 4.1 15.0 - - + -
862B VAL* 4.8 0.4 - - + -
864B ASN 2.8 9.3 + - - -
865B ILE* 3.2 16.8 - - + +
866B ARG 2.9 25.1 + - - +
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Residues in contact with LEU 831 (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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741B ILE* 3.8 36.1 - - + +
744B GLU* 3.4 31.9 - - + -
745B LEU* 3.9 19.3 - - + -
748B PHE* 4.1 6.7 - - + -
756B VAL* 3.8 15.9 - - + +
757B VAL 2.9 10.3 + - - +
758B ILE* 3.5 9.4 - - + +
759B LEU 2.8 26.4 + - - -
830B ILE* 1.3 75.1 - - - +
832B LEU* 1.3 62.1 + - - +
833B VAL* 3.8 13.8 + - + -
866B ARG 3.4 11.4 - - - +
868B ALA* 3.7 12.6 - - - +
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Residues in contact with LEU 832 (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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759B LEU* 3.5 29.4 - - + +
761B SER* 5.6 1.8 - - - -
815B THR* 4.5 8.1 - - + -
819B ILE* 3.8 29.4 - - + -
830B ILE* 4.1 6.3 - - + -
831B LEU* 1.3 72.9 - - - +
833B VAL* 1.3 62.1 + - - +
834B PRO* 3.7 2.5 - - - +
848B LEU* 4.3 31.2 - - + +
849B ASP* 6.0 0.2 - - - +
853B SER* 3.8 22.0 - - - +
865B ILE* 4.3 9.6 - - + -
866B ARG 2.8 17.0 + - - +
867B ARG* 3.4 14.1 - - + -
868B ALA 2.9 26.2 + - - -
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Residues in contact with VAL 833 (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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737B PHE* 4.8 6.7 - - + -
741B ILE* 3.9 28.0 - - + -
758B ILE* 3.7 25.6 - - + -
759B LEU 2.9 10.7 + - - +
760B PHE* 3.3 28.2 - - + -
761B SER* 2.9 24.0 + - - +
831B LEU* 4.0 11.2 - - + -
832B LEU* 1.3 80.0 - - - +
834B PRO* 1.3 76.0 - - + +
835B ILE* 3.0 8.5 + - + +
868B ALA* 4.3 9.0 - - + -
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Residues in contact with PRO 834 (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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737B PHE* 3.5 18.2 - - - -
761B SER* 3.3 12.3 - - - +
802B GLN* 5.5 1.6 - - - +
832B LEU 3.7 7.0 - - - +
833B VAL* 1.3 85.7 - - + +
835B ILE* 1.3 58.6 + - - +
836B ALA 3.7 2.0 - - - +
837B PHE* 4.4 12.7 - - + +
841B HIS* 5.9 0.4 - - + -
844B THR* 3.6 31.0 - - + -
848B LEU* 3.8 19.1 - - + -
867B ARG* 4.0 13.7 - - + +
868B ALA* 4.3 9.4 - - + +
870B SER* 5.2 6.1 - - - +
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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