Contacts of the strand formed by residues 919 - 925 (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 MET 919 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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664A LEU* 3.9 13.7 - - + -
739A VAL* 3.6 24.1 - - + +
741A LYS 4.8 0.4 - - - -
743A GLN* 3.6 26.5 - - + +
745A VAL* 4.1 14.6 - - + -
761A VAL 5.1 1.3 - - - +
762A PHE* 3.3 6.1 - - - +
763A VAL* 2.7 41.4 + - + +
808A VAL* 4.5 12.8 - - + -
912A ALA 4.9 1.6 - - - +
916A PRO* 5.2 0.4 - - - +
918A GLY* 1.3 72.3 - - - -
920A ALA* 1.3 65.5 + - - +
921A ILE* 3.7 28.0 - - + -
950A LEU* 4.8 2.0 - - + -
954A MET* 3.6 38.4 - - + -
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Residues in contact with ALA 920 (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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742A LYS* 6.0 0.2 - - - +
743A GLN 2.9 14.0 + - - +
744A SER* 3.4 6.4 - - - +
745A VAL* 2.7 33.1 + - - +
761A VAL 3.4 5.4 - - - -
762A PHE* 3.9 16.8 - - + -
916A PRO* 4.2 16.2 - - + -
918A GLY 4.8 0.4 - - - +
919A MET* 1.3 75.4 - - - +
921A ILE* 1.3 58.6 + - - +
941A TRP* 3.7 23.1 - - + -
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Residues in contact with ILE 921 (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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661A ALA* 4.5 25.1 - - + -
664A LEU* 3.9 28.0 - - + -
745A VAL* 3.3 12.1 - - + +
747A PHE* 3.9 33.2 - - + -
759A ALA 3.4 1.3 - - - +
760A ALA* 3.1 7.8 - - - +
761A VAL* 2.8 47.1 + - + +
762A PHE* 5.1 1.7 - - - -
808A VAL* 4.7 6.5 - - + -
919A MET* 3.7 24.2 - - + -
920A ALA* 1.3 77.5 - - - +
922A LEU* 1.3 70.1 - - - +
923A SER* 4.3 3.8 - - - +
941A TRP* 5.2 0.2 - - - -
950A LEU* 5.4 0.4 - - + -
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Residues in contact with LEU 922 (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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745A VAL 2.9 10.7 + - - +
746A ILE* 3.2 11.9 - - + +
747A PHE 2.9 22.7 + - - -
758A LEU* 4.1 14.1 - - + -
759A ALA 3.5 1.1 - - - -
760A ALA* 3.7 17.5 - - + -
762A PHE* 5.3 0.7 - - + -
829A TRP* 3.6 61.5 - - + +
921A ILE* 1.3 73.4 - - - +
923A SER* 1.3 60.3 + - - +
924A GLN* 4.3 7.0 - - - +
936A VAL* 4.5 17.0 - - + -
938A PRO* 4.8 3.4 - - + -
941A TRP* 3.5 32.3 - - + -
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Residues in contact with SER 923 (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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656A GLN 4.4 0.3 + - - -
657A ALA* 2.6 37.7 + - - +
660A PRO* 3.7 18.4 - - - +
661A ALA* 5.5 2.9 - - - -
747A PHE* 3.4 21.5 + - - +
758A LEU* 3.6 4.3 - - - +
759A ALA* 2.9 35.0 + - - -
921A ILE* 4.0 5.3 - - - -
922A LEU* 1.3 73.0 - - - +
924A GLN* 1.3 59.6 + - - +
925A ILE* 5.5 1.4 - - - +
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Residues in contact with GLN 924 (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 ILE* 3.0 31.1 - - + +
747A PHE 2.8 8.3 + - - +
748A GLU* 3.5 1.0 - - - -
749A LYS* 3.0 26.5 + - - +
757A ALA 3.6 3.8 - - - -
758A LEU* 4.0 14.1 - - + -
825A PRO* 3.3 21.3 - - + +
922A LEU* 4.0 7.0 - - + +
923A SER* 1.3 77.5 + - - +
925A ILE* 1.3 66.8 + - - +
926A SER 3.9 0.4 - - - -
935A TYR* 3.1 25.5 - - + +
936A VAL* 3.0 50.7 + - - +
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Residues in contact with ILE 925 (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* 3.5 36.6 - - + +
656A GLN* 3.6 31.2 - - + +
657A ALA* 3.7 13.9 - - + +
749A LYS* 3.1 25.6 - - + +
751A GLY* 3.5 28.9 - - - +
752A ASN* 6.0 0.2 - - - +
755A ASP 4.4 3.6 - - - +
756A SER* 3.1 5.7 - - - -
757A ALA* 3.0 31.2 + - + +
825A PRO* 3.4 4.1 - - - +
923A SER* 5.5 1.6 - - - +
924A GLN* 1.3 80.7 - - - +
926A SER* 1.3 62.8 + - - +
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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