Contacts of the strand formed by residues 743 - 749 (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 743 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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739A VAL* 6.4 0.2 - - + -
741A LYS* 3.5 28.9 + - + +
742A LYS* 1.3 79.4 - - - +
744A SER* 1.3 65.1 + - - +
745A VAL* 3.9 17.6 - - + +
918A GLY 3.0 9.2 + - - +
919A MET* 3.6 20.7 - - + +
920A ALA* 2.9 27.0 + - - +
944A TRP* 4.6 9.9 - - - +
950A LEU* 3.8 21.6 - - - +
953A THR* 4.9 4.4 + - - -
954A MET* 4.5 12.8 - - - +
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Residues in contact with SER 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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742A LYS* 4.2 19.4 + - - +
743A GLN* 1.3 77.4 + - - +
745A VAL* 1.3 62.6 + - - +
920A ALA* 3.4 8.1 - - - +
940A GLY 3.2 24.2 + - - +
941A TRP* 3.5 31.2 + - - -
942A LYS* 3.1 24.3 + - - +
944A TRP* 5.1 0.2 + - - -
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Residues in contact with VAL 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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743A GLN* 3.9 20.4 - - + -
744A SER* 1.3 80.1 - - - +
746A ILE* 1.3 66.8 + - - +
747A PHE* 3.8 20.2 - - + -
919A MET* 4.1 11.4 - - - -
920A ALA 2.7 12.9 + - - +
921A ILE* 3.3 9.9 - - + -
922A LEU 2.9 24.0 + - - -
941A TRP* 3.6 6.8 - - - -
942A LYS 3.7 2.2 - - - -
944A TRP* 3.4 29.2 - - + +
950A LEU* 3.7 29.4 - - + -
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Residues in contact with ILE 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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745A VAL* 1.3 78.9 - - - +
747A PHE* 1.3 98.7 + - - +
748A GLU* 3.9 9.2 - - + +
922A LEU* 3.2 16.2 - - + +
924A GLN* 3.0 31.2 - - - +
936A VAL 5.2 4.0 - - - +
938A PRO* 5.8 4.0 - - + -
941A TRP* 4.0 21.1 - - + -
942A LYS 3.1 27.2 + - - +
943A VAL* 3.4 26.2 - - + +
944A TRP 3.0 25.8 + - - -
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Residues in contact with PHE 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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660A PRO* 3.9 28.9 - - + -
664A LEU* 5.9 0.7 - - + -
745A VAL* 3.8 11.9 - - + -
746A ILE* 1.3 83.8 - - - +
748A GLU* 1.3 54.9 + - - +
921A ILE* 3.9 26.9 - - + -
922A LEU 2.9 4.6 + - - -
923A SER* 3.9 14.4 - - - +
924A GLN 2.8 32.0 + - - -
944A TRP* 3.7 33.7 - - + -
945A GLU 5.2 0.4 - - - -
946A ASN* 3.8 2.5 - - - -
947A VAL* 3.7 43.1 - - + -
950A LEU* 3.7 26.5 - - + -
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Residues in contact with GLU 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 ILE* 4.0 11.3 - - + +
747A PHE* 1.3 75.1 - - - +
749A LYS* 1.3 64.1 + - - +
924A GLN 3.5 4.7 - - - -
935A TYR* 3.3 53.4 - - + +
936A VAL 5.0 2.1 - - - +
937A HIS* 5.7 1.6 + - - -
943A VAL* 3.4 35.2 - - + +
944A TRP 5.1 1.6 + - - +
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Residues in contact with LYS 749 (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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649A GLU* 4.1 24.9 - - - +
656A GLN* 3.6 34.5 + - + +
659A MET* 4.5 12.7 - - + +
748A GLU* 1.3 76.4 - - - +
750A ALA* 1.3 76.4 + - - +
924A GLN 3.0 9.5 + - - +
925A ILE* 3.1 39.2 - - + +
926A SER 3.1 1.2 + - - -
935A TYR* 3.0 8.4 + - - -
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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