Contacts of the strand formed by residues 776 - 782 (chain A) 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 TRP 776 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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774A ARG 5.3 0.7 - - - +
775A GLY* 1.3 74.8 - - - +
777A PHE* 1.3 77.2 + - - +
778A VAL* 3.6 16.4 - - + +
860A GLU* 3.8 28.3 - - + -
951A ARG* 6.4 0.7 - - - -
953A LYS* 3.1 46.5 - - + +
955A SER* 3.3 18.4 + - - -
957A HIS* 5.3 0.9 - + - -
986A LEU* 4.0 28.7 - - + -
987A PRO* 3.3 44.4 - - + -
988A GLN 4.9 1.2 - - - +
989A PRO* 3.7 25.7 - - + -
990A GLU* 3.0 29.3 + - - +
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Residues in contact with PHE 777 (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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771A LEU* 4.3 12.1 - - + -
772A PRO* 3.6 40.2 - - + -
775A GLY* 4.5 1.6 - - - -
776A TRP* 1.3 95.3 + - - +
778A VAL* 1.3 63.1 + - - +
953A LYS 2.9 11.0 + - - -
954A VAL* 3.4 7.1 - - + -
955A SER 3.0 23.7 + - - -
990A GLU* 3.2 46.7 - - + +
992A ILE* 3.5 20.0 - - + -
998A PHE* 3.6 29.6 - + + -
1002A LEU* 4.7 9.0 - - + -
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Residues in contact with VAL 778 (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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776A TRP* 3.6 24.9 - - + +
777A PHE* 1.3 80.6 - - - +
779A TYR* 1.3 68.4 + - - +
780A GLN* 4.5 6.5 - - + -
955A SER* 3.3 10.1 - - - +
957A HIS* 4.0 31.0 - - + +
989A PRO* 3.7 22.2 - - + -
990A GLU 3.2 4.4 + - - -
991A VAL* 3.4 22.2 - - + +
992A ILE* 2.6 32.6 + - - -
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Residues in contact with TYR 779 (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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685A TYR* 3.9 36.2 - + + -
689A LEU* 3.7 26.2 - - + -
778A VAL* 1.3 73.5 - - - +
780A GLN* 1.3 66.1 + - - +
781A GLN* 3.2 42.4 + - + -
955A SER 2.9 9.0 + - - +
956A VAL* 3.3 8.0 - - + -
957A HIS* 2.8 25.5 + - - +
992A ILE* 3.7 32.6 - - + +
993A GLN 5.1 7.2 - - - -
995A MET* 4.4 25.8 - - + +
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Residues in contact with GLN 780 (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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778A VAL* 4.2 7.7 + - + -
779A TYR* 1.3 85.3 - - - +
781A GLN* 1.3 73.5 + - - +
782A ARG 4.9 0.2 - - - +
957A HIS* 3.3 24.8 - - + +
959A LEU* 3.0 39.1 - - - +
965A SER 3.7 23.4 - - - +
991A VAL* 5.4 10.4 - - + +
992A ILE 5.0 2.0 + - - -
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Residues in contact with GLN 781 (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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685A TYR* 3.6 39.3 + - + +
779A TYR* 3.2 37.5 + - + -
780A GLN* 1.3 87.5 + - - +
782A ARG* 1.3 64.6 + - - +
957A HIS 2.8 8.4 + - - +
958A VAL* 3.1 6.5 - - + -
959A LEU* 2.7 33.7 + - - +
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Residues in contact with ARG 782 (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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681A HIS* 4.8 4.7 + - - -
685A TYR* 4.8 2.6 + - - -
780A GLN* 4.9 0.2 - - - +
781A GLN* 1.3 90.0 + - - +
783A ASN* 1.3 73.3 + - - +
784A GLU* 3.8 11.5 + - + +
958A VAL* 4.4 2.7 - - - +
959A LEU* 3.8 23.2 - - + +
960A ALA 2.6 32.4 + - - +
961A ARG 3.0 18.6 + - - -
962A GLU* 3.6 0.6 - - - +
963A MET* 3.0 39.1 + - - +
964A ASP* 4.1 3.4 - - - +
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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