Contacts of the strand formed by residues 867 - 874 (chain A) in PDB entry 3PT6
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 TYR 867 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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777A LEU* 6.0 1.0 - - - +
779A LEU* 3.6 31.6 - - + +
814A PRO 4.3 13.9 - - - -
815A LEU* 3.5 24.1 - - + +
817A LEU* 3.8 31.6 - - + -
835A VAL* 4.5 17.0 - - + -
836A LYS 3.5 19.1 + - - +
837A VAL* 3.3 14.5 - - + -
838A ILE* 2.9 24.8 + - - +
866A THR* 1.3 74.7 - - - +
868A PHE* 1.3 57.7 + - - +
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Residues in contact with PHE 868 (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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813A ASP* 3.4 25.6 - - - -
815A LEU* 2.9 32.7 + - + -
816A GLU* 3.3 45.9 - - + -
817A LEU* 2.9 25.3 + - - +
837A VAL* 4.3 3.1 - - - -
838A ILE* 3.0 19.3 - - + +
840A LYS* 3.9 48.5 - - + -
866A THR* 3.4 8.9 + - - +
867A TYR* 1.3 74.9 - - - +
869A PHE* 1.3 65.2 + - - +
870A GLN* 4.2 8.7 - - - -
1288A ARG* 5.7 1.3 - - - -
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Residues in contact with PHE 869 (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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781A ARG* 4.1 25.8 - - - -
800A PHE* 3.8 21.1 - + + -
816A GLU* 4.8 0.2 - - - -
817A LEU* 3.1 27.8 - - + +
819A LEU* 3.5 44.2 - - + -
837A VAL* 3.9 9.0 - - + -
838A ILE 2.9 14.4 + - - -
839A TYR* 3.3 46.5 - + + -
840A LYS 2.8 23.1 + - - -
868A PHE* 1.3 79.3 - - - +
870A GLN* 1.3 66.7 + - - +
871A LEU 4.4 3.6 - - - -
883A PRO* 4.8 3.8 - - + -
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Residues in contact with GLN 870 (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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816A GLU* 2.9 28.0 + - - +
817A LEU 4.3 1.4 + - - -
839A TYR* 3.8 9.0 - - - -
840A LYS* 3.4 32.8 + - + +
842A PRO* 6.0 5.1 - - + +
868A PHE* 4.2 8.6 - - + -
869A PHE* 1.3 77.6 - - - +
871A LEU* 1.3 78.3 + - + +
883A PRO* 3.2 27.3 - - - +
1291A VAL* 3.2 20.0 - - - +
1292A ARG* 4.6 5.1 + - - +
1294A GLY* 3.5 24.9 - - - -
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Residues in contact with LEU 871 (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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818A PHE* 3.4 24.4 - - + -
819A LEU* 3.2 23.3 + - - +
869A PHE* 4.4 3.5 - - - -
870A GLN* 1.3 98.2 - - + +
872A TRP* 1.3 62.3 + - - +
880A PHE* 4.0 13.0 - - + +
881A GLU* 3.2 36.6 - - - +
882A SER* 3.7 7.6 - - - +
883A PRO* 4.5 2.7 - - - -
1291A VAL* 3.5 33.0 - - + +
1294A GLY 5.0 4.7 - - - +
1295A TYR 3.6 22.2 - - - +
1296A GLN* 4.2 7.2 - - + +
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Residues in contact with TRP 872 (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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798A HIS* 3.7 22.2 - + - -
818A PHE* 4.8 0.4 - - - -
819A LEU* 3.3 35.4 - - + -
820A VAL* 3.8 1.5 - - - +
821A GLY* 3.8 33.3 - - - +
871A LEU* 1.3 75.1 - - - +
873A TYR* 1.3 72.7 + - - +
874A ASN* 4.4 6.5 - - + +
879A ARG 3.3 1.4 - - - +
880A PHE* 3.2 6.9 - - - -
881A GLU* 2.8 47.3 + - + +
882A SER 4.8 0.7 - - - +
883A PRO* 4.8 1.8 - - + -
884A PRO* 3.4 28.9 - - + -
898A LEU* 3.6 34.3 - - + -
899A SER* 4.2 6.5 - - - -
902A ARG* 4.8 10.5 - - + -
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Residues in contact with TYR 873 (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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801A CYS* 4.2 10.3 - - - -
805A ASP 4.5 4.2 + - - -
806A THR* 3.4 29.2 - - + -
807A VAL* 3.3 14.4 + - + -
818A PHE* 3.8 22.0 - - + -
819A LEU 2.8 12.6 + - - +
820A VAL* 3.8 24.5 - - + +
821A GLY 4.8 1.0 + - - -
871A LEU 4.3 0.2 - - - -
872A TRP* 1.3 78.3 + - - +
874A ASN* 1.3 68.3 + - - +
875A GLN* 3.5 32.6 + - + +
878A ALA* 4.0 4.9 - - - -
879A ARG 3.4 4.5 - - - -
880A PHE* 3.5 40.2 - + + -
1353A PHE* 3.2 29.6 - - - -
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Residues in contact with ASN 874 (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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872A TRP* 4.1 8.3 + - + +
873A TYR* 1.3 71.6 - - - +
875A GLN* 1.3 60.9 + - - +
876A GLU* 3.2 17.2 + - - +
877A TYR* 3.4 30.0 + - - -
878A ALA* 2.9 28.2 + - - -
879A ARG* 2.9 32.3 + - + +
881A GLU* 5.1 5.6 + - - +
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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