Contacts of the strand formed by residues 741 - 748 (chain A) in PDB entry 6N8Q
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 THR 741 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630A PRO* 4.7 11.4 - - + +
710A THR 5.2 0.9 + - - -
735A ALA 3.6 1.2 - - - +
736A GLY* 3.3 3.8 - - - -
737A THR* 3.0 40.9 + - - +
739A GLY* 4.2 5.0 + - - -
740A GLY* 1.3 75.3 - - - +
742A ILE* 1.3 64.1 - - - +
743A TYR* 3.5 39.3 + - + +
767A GLU* 3.9 16.2 - - + +
768A ILE 3.3 9.6 - - - +
769A GLN* 3.1 20.1 + - + +
776A VAL* 4.2 0.2 - - - +
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Residues in contact with ILE 742 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734A TRP* 3.6 34.5 - - + -
735A ALA 3.2 7.4 - - - +
740A GLY 3.7 16.8 - - - +
741A THR* 1.3 74.7 - - - +
743A TYR* 1.3 64.5 + - - +
744A ALA 4.0 0.3 + - - -
766A LYS 4.0 0.2 - - - +
767A GLU* 3.4 3.1 + - - -
768A ILE* 2.7 60.2 + - + +
770A LEU* 3.7 26.7 - - + -
776A VAL* 4.1 10.1 - - + -
779A ILE* 4.1 15.0 - - + -
813A VAL* 3.9 25.8 - - + -
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Residues in contact with TYR 743 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A PHE* 4.0 18.4 - + + -
625A LYS* 3.6 29.7 + - - -
626A CYS 5.5 0.2 + - - -
627A THR* 3.8 21.9 - - + +
629A HIS 4.7 2.9 + - - -
630A PRO* 4.4 13.7 - - - +
733A LEU 3.8 1.0 - - - +
734A TRP* 3.3 5.2 - - - +
735A ALA* 2.8 42.3 + - + +
737A THR* 3.6 26.5 - - + +
741A THR* 3.5 18.5 - - + +
742A ILE* 1.3 74.7 - - - +
744A ALA* 1.3 58.8 + - - +
745A PHE* 3.8 20.2 - - + -
764A GLN* 3.7 11.9 - - - -
766A LYS 3.6 3.6 - - - +
767A GLU* 3.5 33.1 + - + -
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Residues in contact with ALA 744 (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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723A LEU* 4.1 9.6 - - + -
733A LEU 3.5 4.0 - - - -
734A TRP* 3.5 40.8 - - + -
742A ILE 4.0 0.2 + - - -
743A TYR* 1.3 73.4 - - - +
745A PHE* 1.3 61.5 + - - +
764A GLN* 3.6 4.0 - - - -
765A ALA* 2.8 22.8 + - - -
766A LYS* 3.0 31.4 + - + +
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Residues in contact with PHE 745 (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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611A PHE* 3.6 25.4 - + - -
623A PHE* 3.6 41.5 - + + -
625A LYS* 3.5 26.0 - - + -
723A LEU* 3.9 3.8 - - - +
732A SER* 3.1 7.8 - - - -
733A LEU* 2.9 42.0 + - + +
735A ALA* 6.0 0.2 - - + -
743A TYR* 3.8 14.8 - - + -
744A ALA* 1.3 80.8 - - - +
746A SER* 1.3 64.7 + - - +
747A LEU* 3.7 8.5 + - + +
762A ALA* 4.6 1.1 - - + -
763A GLU* 3.4 10.8 - - - +
764A GLN* 3.5 38.6 - - + -
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Residues in contact with SER 746 (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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723A LEU* 3.7 16.8 - - - +
724A LYS* 5.2 9.9 - - - +
730A CYS* 2.9 26.5 - - - +
731A PRO 3.8 3.8 - - - -
745A PHE* 1.3 72.9 - - - +
747A LEU* 1.3 60.6 + - - +
748A ARG 4.2 0.2 - - - -
761A ARG 3.9 0.2 - - - +
762A ALA* 3.2 7.6 - - - -
763A GLU* 2.9 37.3 + - - -
765A ALA* 4.1 8.4 - - - +
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Residues in contact with LEU 747 (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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600A TRP* 4.3 3.8 - - + -
602A LEU* 3.8 28.3 - - + -
613A LEU* 3.6 17.5 - - + -
718A PHE* 3.9 14.6 - - + -
730A CYS* 4.4 3.6 - - - +
731A PRO* 2.8 46.5 + - + +
732A SER* 3.8 23.1 - - - +
733A LEU* 3.9 3.4 - - + +
745A PHE* 3.8 17.3 - - + +
746A SER* 1.3 86.2 + - - +
748A ARG* 1.3 60.5 + - - +
749A VAL* 3.7 1.8 - - + +
760A VAL* 5.2 3.8 - - + -
761A ARG 3.6 2.7 - - - +
762A ALA* 3.6 21.3 - - + -
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Residues in contact with ARG 748 (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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746A SER 4.2 0.6 - - - -
747A LEU* 1.3 70.0 - - - +
749A VAL* 1.3 58.8 + - - +
750A PRO* 4.0 2.0 - - - +
759A PRO 4.5 1.0 - - - +
760A VAL* 3.3 7.3 - - - +
761A ARG* 2.8 47.4 + - + +
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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