Contacts of the strand formed by residues 802 - 808 (chain A) in PDB entry 4D86
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 VAL 802 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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797A VAL* 3.5 5.4 - - - +
798A LEU* 2.8 44.6 + - + -
799A ALA* 3.0 25.0 + - + +
800A PRO 3.7 9.4 - - - +
801A GLY* 1.3 82.1 - - - +
803A VAL* 1.3 64.9 + - - +
945A PHE* 4.0 33.7 - - + -
952A HIS* 5.8 2.0 - - + -
954A LEU 3.7 18.6 - - - +
955A LYS* 3.4 8.7 - - + +
957A ILE* 4.6 2.9 - - + -
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Residues in contact with VAL 803 (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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795A ARG* 4.1 17.9 - - + +
796A THR 3.6 20.2 - - - +
797A VAL* 4.4 9.6 - - + +
798A LEU* 4.8 0.2 - - - -
801A GLY 4.3 0.4 - - - -
802A VAL* 1.3 81.1 - - - +
804A LEU* 1.3 69.9 + - - +
805A ILE* 3.9 26.4 - - + +
955A LYS 2.9 16.7 + - - +
956A GLU* 3.5 10.8 - - + -
957A ILE* 2.9 27.1 + - - +
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Residues in contact with LEU 804 (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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794A SER 4.0 0.9 - - - +
795A ARG* 3.4 2.8 - - - -
796A THR* 2.8 45.6 + - - +
798A LEU* 4.0 15.9 - - + +
803A VAL* 1.3 72.7 - - - +
805A ILE* 1.3 60.7 + - - +
806A VAL* 4.2 1.5 + - + +
938A VAL* 4.6 3.4 - - + -
941A ILE* 4.1 14.4 - - + -
957A ILE* 3.3 35.2 - - + +
959A LEU* 3.8 23.3 - - + -
974A VAL* 3.8 27.1 - - + -
978A PHE* 3.8 30.5 - - + -
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Residues in contact with ILE 805 (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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792A CYS* 3.9 20.0 - - - -
794A SER 3.5 3.1 - - - +
795A ARG* 3.4 34.8 - - + +
803A VAL* 3.9 21.1 - - + -
804A LEU* 1.3 78.4 - - - +
806A VAL* 1.3 64.2 + - - +
807A GLN* 3.7 23.4 + - + +
956A GLU* 4.4 8.1 - - + +
957A ILE 2.7 11.9 + - - +
958A TYR* 3.2 41.2 - - + +
959A LEU* 2.8 27.3 + - - +
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Residues in contact with VAL 806 (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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792A CYS* 3.7 2.4 - - - -
793A PHE* 2.8 26.2 + - + -
794A SER* 2.9 32.2 + - - +
804A LEU* 5.3 2.0 - - + +
805A ILE* 1.3 73.6 - - - +
807A GLN* 1.3 65.1 + - - +
959A LEU* 3.4 14.6 - - + +
967A VAL* 3.4 35.9 - - + +
970A PHE* 3.7 15.3 - - + -
971A ALA* 3.8 11.7 - - + +
974A VAL* 3.8 27.1 - - + -
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Residues in contact with GLN 807 (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 LYS 3.7 20.3 - - - +
792A CYS* 4.1 11.2 - - - +
795A ARG* 5.1 2.3 + - - -
805A ILE* 3.7 13.3 - - + +
806A VAL* 1.3 79.6 - - - +
808A GLN* 1.3 76.7 + - - +
809A GLY* 5.2 0.4 - - - -
814A LEU* 4.4 15.9 - - - +
815A PRO* 5.3 5.3 - - - +
958A TYR* 3.5 26.6 - - + -
959A LEU 3.0 6.4 + - - +
960A VAL* 3.2 38.8 - - + +
967A VAL* 3.7 8.4 - - - +
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Residues in contact with GLN 808 (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 LYS* 3.0 45.6 + - + +
793A PHE* 4.3 9.4 - - + -
807A GLN* 1.3 87.6 + - - +
809A GLY* 1.3 61.4 + - - +
961A ASP 3.4 7.6 - - - +
962A VAL* 3.0 29.0 + - - +
964A GLU* 3.5 30.9 - - - +
967A VAL* 3.7 12.4 - - + +
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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