Contacts of the strand formed by residues 789 - 796 (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 SER 789 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678A PRO* 3.8 4.9 - - - -
788A ASN* 1.3 75.5 - - - +
790A GLY* 1.3 57.4 + - - +
850A ILE 3.9 0.3 - - - +
851A GLN* 3.3 5.7 - - - +
852A SER 2.8 33.0 + - - -
854A LYS 2.9 23.4 + - - -
856A PRO* 3.6 15.7 - - - +
859A LEU* 4.2 5.9 - - - +
958A VAL 3.1 17.9 - - - -
960A ALA 3.8 3.1 - - - -
963A MET* 3.7 19.0 - - - +
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Residues in contact with GLY 790 (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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678A PRO* 3.5 18.6 - - - +
679A HIS 4.1 10.5 - - - -
682A ALA* 4.4 3.4 - - - -
789A SER* 1.3 75.0 - - - +
791A ILE* 1.3 63.3 + - - +
850A ILE 3.5 7.2 - - - -
851A GLN* 4.4 0.2 - - - -
856A PRO* 4.5 3.5 - - - +
859A LEU* 5.4 0.7 - - - -
957A HIS* 3.8 1.0 - - - -
958A VAL* 2.7 35.7 + - - +
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Residues in contact with ILE 791 (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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679A HIS* 5.0 0.8 - - - +
682A ALA* 4.1 6.0 - - - +
790A GLY* 1.3 75.5 - - - +
792A GLU* 1.3 65.1 + - - +
793A ILE* 4.2 20.2 - - + -
848A PHE* 3.7 1.3 - - + +
849A ILE* 3.4 8.2 - - - +
850A ILE* 2.9 47.5 + - + +
856A PRO* 3.4 28.7 - - + +
859A LEU* 3.7 23.8 - - + -
860A GLU* 3.7 16.2 - - + +
956A VAL 3.3 12.6 - - - +
957A HIS* 3.5 25.1 - - + +
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Residues in contact with GLU 792 (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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682A ALA* 3.9 15.8 - - + +
683A MET* 3.3 26.8 - - - +
686A LEU* 3.3 35.9 - - + +
791A ILE* 1.3 74.0 - - - +
793A ILE* 1.3 70.9 + - - +
794A TYR 4.1 0.4 + - - -
838A ARG* 4.0 5.4 + - - -
847A ARG* 3.1 35.7 + - + +
848A PHE 3.2 11.7 - - - +
849A ILE* 3.9 15.7 - - + -
954A VAL 4.0 0.3 - - - +
955A SER* 3.3 4.7 - - - -
956A VAL* 2.9 34.3 + - + +
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Residues in contact with ILE 793 (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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791A ILE* 4.2 16.4 - - + -
792A GLU* 1.3 76.6 - - - +
794A TYR* 1.3 62.4 + - - +
795A TYR* 3.5 39.9 - - + +
846A LEU 3.8 0.2 - - - +
847A ARG* 3.0 9.7 - - - +
848A PHE* 2.9 38.4 + - + +
850A ILE* 6.2 0.2 - - + -
860A GLU* 3.6 26.5 - - - +
863A VAL* 3.9 34.8 - - + -
953A LYS* 3.8 12.1 - - - -
954A VAL 3.5 3.6 - - - +
955A SER* 3.6 14.1 - - - +
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Residues in contact with TYR 794 (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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686A LEU* 4.0 24.0 - - + -
690A MET* 4.5 11.2 - - + -
768A GLU* 2.9 30.6 + - - -
792A GLU 4.1 0.2 - - - -
793A ILE* 1.3 73.8 - - - +
795A TYR* 1.3 63.9 + - - +
796A GLN* 3.7 17.6 + - + +
838A ARG* 3.7 35.8 + - + -
840A ALA 5.6 0.7 + - - -
843A ILE 4.4 0.3 + - - -
844A GLN* 3.2 25.3 + - - -
845A GLY* 3.5 23.8 - - - -
846A LEU 3.5 8.3 - - - -
847A ARG* 4.5 2.2 - - + +
952A HIS 3.4 1.9 - - - +
953A LYS* 3.3 5.0 - - - +
954A VAL* 2.7 59.4 + - + +
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Residues in contact with TYR 795 (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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793A ILE* 3.5 22.1 - - + +
794A TYR* 1.3 70.4 - - - +
796A GLN* 1.3 64.7 + - - +
797A THR* 3.3 3.9 + - - +
845A GLY* 3.0 4.3 - - - -
846A LEU* 2.7 48.8 + - + +
848A PHE* 3.8 26.7 - + - -
863A VAL* 4.2 6.1 - - - +
864A GLU* 2.8 25.2 + - - +
867A LEU* 3.7 16.2 - - + +
943A MET 5.2 2.0 - - - +
944A LEU* 3.8 26.5 - - + -
951A ARG* 3.4 37.9 - - + -
952A HIS 3.4 3.4 - - - +
953A LYS* 3.5 28.7 + - + -
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Residues in contact with GLN 796 (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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690A MET* 5.1 0.6 - - - -
768A GLU* 3.0 22.8 + - - +
769A VAL 3.0 21.8 + - - -
771A LEU* 3.0 48.9 + - + +
794A TYR* 3.7 15.6 + - + +
795A TYR* 1.3 72.7 - - - +
797A THR* 1.3 62.7 + - - +
843A ILE* 3.8 6.4 - - + +
844A GLN 3.6 13.0 - - - +
943A MET* 4.1 4.9 - - - +
952A HIS* 2.9 46.6 + - + +
1005A PHE* 3.3 22.5 - - + -
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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