Contacts of the strand formed by residues 756 - 763 (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 SER 756 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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653A ALA* 4.2 1.3 - - - -
754A THR 4.0 3.6 + - - -
755A ASP* 1.3 74.4 - - - +
757A ALA* 1.3 64.5 + - - +
819A GLN* 3.4 6.2 - - - +
820A SER 2.8 28.6 + - - -
822A ASP 5.4 0.3 + - - -
823A LYS 3.0 27.9 + - - -
824A GLN* 3.2 10.9 + - - -
825A PRO* 4.0 10.1 - - - -
828A LEU* 4.8 2.2 - - - -
925A ILE* 3.1 12.6 - - - -
926A SER 2.5 21.6 + - - -
930A ASN* 4.7 0.5 + - - -
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Residues in contact with ALA 757 (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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653A ALA* 3.4 37.5 - - + +
654A PHE* 3.8 4.3 - - - +
657A ALA* 3.9 9.6 - - + -
756A SER* 1.3 78.5 - - - +
758A LEU* 1.3 61.9 - - - +
818A LEU 3.2 13.0 - - - +
819A GLN* 4.2 1.3 - - - -
825A PRO* 3.9 4.2 - - - +
828A LEU* 4.3 4.3 - - - -
924A GLN* 3.6 3.1 - - - -
925A ILE* 3.0 33.0 + - + +
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Residues in contact with LEU 758 (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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657A ALA* 4.4 0.4 - - - -
757A ALA* 1.3 75.5 - - - +
759A ALA* 1.3 67.6 + - - +
816A PHE 3.3 0.3 - - - +
817A LEU* 3.4 3.0 - - - -
818A LEU 3.0 19.0 + - - -
825A PRO* 4.2 6.7 - - + +
828A LEU* 4.0 15.7 - - + +
829A TRP* 3.5 44.2 - - + +
832A TYR* 2.8 52.0 + - + +
922A LEU* 4.1 19.1 - - + -
923A SER 3.6 11.7 - - - +
924A GLN* 4.0 21.8 - - + -
936A VAL* 5.4 0.4 - - + -
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Residues in contact with ALA 759 (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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657A ALA* 3.8 24.9 - - + +
658A ILE* 4.0 15.7 - - + +
661A ALA* 5.9 0.7 - - + -
758A LEU* 1.3 76.3 - - - +
760A ALA* 1.3 60.6 + - - +
761A VAL* 4.0 4.7 - - + +
816A PHE 3.0 6.5 - - - +
817A LEU* 3.7 19.5 - - + -
921A ILE* 3.4 3.6 - - - +
922A LEU* 3.5 1.9 - - - -
923A SER* 2.9 34.6 + - - +
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Residues in contact with ALA 760 (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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759A ALA* 1.3 74.6 - - - +
761A VAL* 1.3 60.6 + - - +
762A PHE* 3.5 28.4 - - + -
815A GLY* 3.2 2.1 - - - -
816A PHE* 2.7 37.2 + - + +
829A TRP* 4.1 0.2 - - + -
832A TYR* 3.8 24.2 - - + -
921A ILE 3.1 4.9 - - - -
922A LEU* 3.7 20.9 - - + -
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Residues in contact with VAL 761 (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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658A ILE* 4.2 8.7 - - + -
661A ALA* 3.8 22.7 - - + -
759A ALA* 4.9 3.4 - - + -
760A ALA* 1.3 78.8 - - - +
762A PHE* 1.3 68.1 + - - +
763A VAL* 4.5 15.0 - - + -
806A MET* 3.9 37.2 - - + -
808A VAL* 4.6 9.0 - - + -
814A MET 3.3 7.6 - - - +
815A GLY* 4.2 5.8 - - - -
816A PHE 5.2 0.2 - - - +
919A MET* 3.7 1.5 - - + +
920A ALA* 3.4 3.5 - - - -
921A ILE* 2.8 50.5 + - + +
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Residues in contact with PHE 762 (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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760A ALA* 3.5 37.0 - - + -
761A VAL* 1.3 79.3 - - - +
763A VAL* 1.3 62.3 + - - +
764A PRO* 4.1 2.4 - - - +
813A GLY* 2.9 5.0 - - - -
814A MET 2.7 45.6 + - - +
816A PHE* 3.8 13.7 - + - -
829A TRP* 3.9 23.1 - + - -
836A PHE* 3.8 13.9 - + - -
912A ALA* 3.1 32.7 - - - +
913A VAL* 3.9 29.4 - - + -
916A PRO* 4.0 5.8 - - + -
919A MET 3.3 4.3 - - - +
920A ALA* 3.9 22.7 - - + -
921A ILE 5.3 1.1 - - - -
922A LEU* 5.3 0.7 - - + -
941A TRP* 5.1 4.5 - + - -
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Residues in contact with VAL 763 (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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739A VAL* 3.8 11.9 - - + +
761A VAL* 4.5 5.6 - - + -
762A PHE* 1.3 79.4 - - - +
764A PRO* 1.3 67.9 - - - +
806A MET 4.1 4.7 - - - +
807A SER 4.5 0.2 - - - -
808A VAL* 3.5 31.2 - - + +
811A GLN* 3.5 44.9 - - + +
812A TRP 4.0 3.1 - - - +
813A GLY* 4.1 8.1 - - - +
912A ALA* 4.9 1.8 + - - -
918A GLY* 3.4 0.6 - - - -
919A MET* 2.7 48.7 + - + +
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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