Contacts of the strand formed by residues 811 - 820 (chain A) in PDB entry 1Q2L
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 GLN 811 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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737A VAL 4.5 1.2 + - - -
738A VAL* 3.6 18.2 - - - +
739A VAL* 2.7 54.5 - - - +
763A VAL* 3.5 19.1 - - + +
764A PRO 4.1 11.1 - - - +
765A THR* 4.6 4.5 - - - -
766A GLY 5.3 0.5 + - - -
767A TYR 4.3 18.5 - - - +
768A ASP 5.6 1.1 - - - -
769A GLU 5.6 0.4 - - - +
772A SER* 4.1 4.5 - - - +
807A SER* 3.2 2.0 - - - -
808A VAL 3.0 33.5 + - - +
809A GLY 3.8 0.2 + - - -
810A ARG* 1.3 84.8 - - + +
812A TRP* 1.3 63.0 + - - +
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Residues in contact with TRP 812 (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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763A VAL* 4.0 3.9 - - - +
764A PRO* 3.7 8.8 - - - +
769A GLU* 3.7 14.8 + - - +
772A SER* 2.9 32.4 + - - +
773A SER* 3.6 30.7 + - - -
776A SER* 3.3 16.8 - - - +
805A PRO* 4.0 21.3 - - + -
806A MET* 3.6 38.8 - - - -
807A SER* 3.6 18.8 - - - -
810A ARG* 4.1 9.6 + - - +
811A GLN* 1.3 79.6 - - - +
813A GLY* 1.3 58.7 + - - +
908A PHE* 3.4 18.5 - - - -
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Residues in contact with GLY 813 (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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762A PHE 2.9 17.3 - - - -
763A VAL* 4.1 3.0 - - - +
764A PRO* 4.2 4.9 - - - -
776A SER* 3.1 19.1 + - - -
805A PRO* 3.5 1.2 - - - +
806A MET 2.8 28.9 + - - -
812A TRP* 1.3 74.1 - - - +
814A MET* 1.3 63.6 + - - +
908A PHE* 4.3 5.2 - - - -
912A ALA* 5.4 0.2 - - - -
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Residues in contact with MET 814 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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760A ALA 3.7 1.4 - - - +
761A VAL* 3.3 2.6 - - - +
762A PHE* 2.7 42.4 + - - +
776A SER* 5.0 6.1 - - - +
779A LEU* 3.8 35.2 - - + +
780A GLY* 4.3 6.5 - - - +
783A VAL* 3.9 25.1 - - + -
803A ALA* 4.7 6.5 - - + -
804A PHE 3.5 10.5 - - - +
806A MET* 4.2 5.2 - - - +
813A GLY* 1.3 78.4 - - - +
815A GLY* 1.3 59.1 + - - +
816A PHE* 3.9 28.7 - - + -
908A PHE* 5.4 2.7 - - + -
909A PHE* 3.7 33.0 - - - -
912A ALA* 5.6 1.3 - - + +
913A VAL* 4.6 8.0 - - + +
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Residues in contact with GLY 815 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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760A ALA 3.2 6.5 - - - -
761A VAL* 4.1 10.3 - - - -
803A ALA* 3.5 3.6 - - - -
804A PHE* 2.8 56.4 + - - -
806A MET* 4.3 2.5 - - - +
814A MET* 1.3 75.0 - - - +
816A PHE* 1.3 66.4 + - - -
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Residues in contact with PHE 816 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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758A LEU 3.3 2.4 - - - +
759A ALA* 3.0 5.5 - - - -
760A ALA 2.7 44.2 + - - +
761A VAL* 5.2 0.2 - - - +
762A PHE* 3.8 20.2 - + - -
783A VAL* 4.1 19.7 - - + -
787A PHE* 3.6 32.5 - + + -
802A PHE 3.4 4.3 - - - -
803A ALA* 4.2 6.7 - - + -
804A PHE* 4.2 0.8 - - - -
814A MET* 3.9 25.1 - - + -
815A GLY* 1.3 76.3 - - - -
817A LEU* 1.3 59.9 + - - +
832A TYR* 3.5 22.5 + - + -
835A PHE* 4.3 3.1 - + - -
836A PHE* 3.7 26.9 - + - -
909A PHE* 4.0 15.3 - + - -
913A VAL* 4.1 13.0 - - + -
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Residues in contact with LEU 817 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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654A PHE* 3.5 60.8 - - + +
657A ALA* 3.9 3.8 - - + -
658A ILE* 4.2 15.5 - - + +
758A LEU 3.4 7.0 - - - +
759A ALA* 3.7 24.2 - - + -
787A PHE* 3.9 1.9 - - - -
800A ALA 4.5 0.2 - - - -
801A VAL* 3.4 0.7 - - - -
802A PHE* 2.7 52.1 + - + +
804A PHE* 3.9 21.3 - - + -
816A PHE* 1.3 74.9 - - - +
818A LEU* 1.3 65.6 + - - +
832A TYR* 3.3 2.0 - - - -
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Residues in contact with LEU 818 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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654A PHE* 4.9 2.0 - - - -
757A ALA* 3.2 4.6 - - - +
758A LEU 3.0 31.1 + - - -
787A PHE* 4.8 0.7 - - + -
790A GLN* 3.5 43.7 - - + +
796A GLN* 4.1 18.6 - - + +
797A LEU* 5.1 0.2 - - - -
800A ALA 3.2 5.4 - - - -
801A VAL* 3.9 18.6 - - + -
817A LEU* 1.3 77.5 - - - +
819A GLN* 1.3 76.0 + - - +
820A SER* 4.0 6.7 - - - -
828A LEU* 4.0 22.9 - - + +
832A TYR* 3.1 22.4 - - + +
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Residues in contact with GLN 819 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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651A GLY 5.4 1.6 + - - -
652A LYS* 3.8 5.3 - - - +
653A ALA* 3.0 36.8 + - + +
654A PHE* 3.1 33.4 + - + +
755A ASP* 2.8 27.5 + - + -
756A SER 3.4 12.1 - - - +
757A ALA* 4.2 0.4 - - - +
797A LEU* 3.3 24.8 - - - -
798A GLY 4.5 0.9 + - - -
800A ALA* 3.0 27.5 + - + +
818A LEU* 1.3 73.8 - - - +
820A SER* 1.3 62.9 + - - +
821A ASN 4.3 0.4 - - - +
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Residues in contact with SER 820 (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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755A ASP* 4.2 1.1 - - - -
756A SER* 2.8 35.4 + - - -
757A ALA* 4.7 0.2 - - - +
796A GLN 3.0 22.3 + - - -
797A LEU* 4.9 0.2 - - - +
818A LEU* 4.0 11.2 - - - +
819A GLN* 1.3 73.4 - - - +
821A ASN* 1.3 58.5 + - - +
822A ASP* 2.8 12.0 + - - +
823A LYS* 2.9 39.3 + - - +
828A LEU* 4.2 11.0 - - - -
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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