Contacts of the helix formed by residues 687 - 701 (chain A) in PDB entry 1LQF
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 687 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685A PRO* 2.8 9.3 + - - +
686A GLU* 1.3 90.2 + - - +
688A PRO* 1.3 74.4 - - - +
689A ALA* 3.6 9.0 + - - +
690A SER* 2.9 31.4 + - - -
691A PHE* 3.1 10.0 + - - +
769A PHE* 4.1 4.7 - - - -
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Residues in contact with PRO 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A SER* 1.3 87.8 - - - +
689A ALA* 1.3 52.0 - - + +
691A PHE* 3.2 1.9 + - - +
692A LEU* 2.7 43.1 + - + +
769A PHE* 3.3 31.6 - - + -
772A LEU* 3.6 26.0 - - + -
773A ALA* 4.5 13.5 - - - -
776A GLU* 4.0 22.2 - - - +
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Residues in contact with ALA 689 (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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687A SER* 3.9 8.3 - - - +
688A PRO* 1.3 81.5 - - - +
690A SER* 1.3 56.7 + - - +
692A LEU* 4.0 5.5 - - - +
693A ASN* 3.0 30.1 + - - +
776A GLU* 4.2 12.4 + - - +
780D PHE* 4.9 3.5 - - - +
783D GLY* 4.0 23.1 - - - +
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Residues in contact with SER 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A TYR* 3.4 38.1 - - - -
653A TYR* 4.9 3.1 - - - -
676A TYR* 2.7 28.6 + - - -
686A GLU* 3.9 3.4 - - - +
687A SER* 2.9 27.4 + - - -
689A ALA* 1.3 74.4 - - - +
691A PHE* 1.3 66.4 + - - +
693A ASN* 3.5 8.0 + - - +
694A PHE* 3.1 23.0 + - - +
783D GLY* 5.7 3.8 - - - -
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Residues in contact with PHE 691 (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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676A TYR* 4.3 8.1 - + - -
679A TRP* 3.6 28.9 - + - -
685A PRO* 3.7 20.9 - - + -
687A SER 3.1 10.0 + - - +
688A PRO 3.3 6.7 - - - +
690A SER* 1.3 83.5 + - - +
692A LEU* 1.3 65.1 + - + +
694A PHE* 3.0 13.8 + + - +
695A LEU* 2.9 37.3 + - + +
724A THR* 4.6 2.2 - - + -
725A PHE* 4.0 38.8 - + - -
728A ALA* 3.9 22.9 - - + -
769A PHE* 3.9 14.6 - + + -
773A ALA* 4.0 23.1 - - + -
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Residues in contact with LEU 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A PRO* 2.7 30.9 + - + +
689A ALA* 4.0 4.9 - - - +
691A PHE* 1.3 83.7 - - + +
693A ASN* 1.3 68.8 + - - +
695A LEU* 2.9 6.5 + - + +
696A PHE* 2.7 42.3 + - + -
728A ALA* 6.4 0.2 - - + -
732A LEU* 4.2 15.3 - - + -
773A ALA* 3.4 23.8 - - + +
776A GLU* 4.1 17.0 - - + +
777A GLY* 3.5 33.7 - - - +
780A PHE* 4.5 9.0 - - + -
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Residues in contact with ASN 693 (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 TYR* 3.5 26.6 + - - -
689A ALA 3.0 19.7 + - - +
690A SER* 3.6 7.2 - - - +
692A LEU* 1.3 77.0 - - - +
694A PHE* 1.3 62.0 + - - +
696A PHE* 3.1 10.4 + - - +
697A LYS* 3.1 34.7 + - - +
736D ASP* 5.6 0.2 - - - +
780D PHE 4.1 9.1 - - - +
781D ILE* 3.3 38.9 + - - +
782D MET 5.3 0.2 - - - -
783D GLY* 4.9 3.4 + - - -
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Residues in contact with PHE 694 (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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608A VAL* 3.8 12.6 - - + -
610A LEU* 4.1 8.7 - - + -
653A TYR* 3.7 39.7 - + + -
674A PHE* 3.7 36.6 - + + -
675A HIS 4.1 1.3 - - - -
676A TYR* 3.8 42.0 - + + -
690A SER 3.1 13.5 + - - +
691A PHE* 3.0 16.5 + + - +
693A ASN* 1.3 72.4 + - - +
695A LEU* 1.3 66.4 + - - +
696A PHE 3.0 2.3 + - - -
697A LYS* 3.1 16.6 + - + +
698A VAL* 3.1 20.4 + - + +
725A PHE* 3.8 28.0 - + - -
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Residues in contact with LEU 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691A PHE* 2.9 28.8 + - + +
692A LEU* 2.9 11.2 + - + +
694A PHE* 1.3 82.1 - - - +
696A PHE* 1.3 59.9 + - + +
698A VAL* 3.3 3.6 - - + +
699A ARG* 2.7 42.1 + - + +
704A LEU* 4.6 4.0 - - + -
725A PHE* 3.7 30.7 - - + -
728A ALA 4.9 0.4 - - - -
729A ASP* 3.7 40.2 - - + +
732A LEU* 4.1 26.0 - - + -
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Residues in contact with PHE 696 (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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692A LEU* 2.7 45.5 + - + -
693A ASN* 3.3 14.6 - - - +
694A PHE 3.0 0.2 - - - -
695A LEU* 1.3 87.1 - - + +
697A LYS* 1.3 66.5 + - - +
698A VAL 3.2 0.9 - - - -
699A ARG* 4.2 12.3 - - - +
700A GLU* 2.8 33.9 + - - +
732A LEU* 5.0 3.4 - - + -
777A GLY 4.7 5.8 - - - -
780A PHE* 4.8 16.4 - + + -
781A ILE* 4.0 33.0 - - + -
696D PHE* 4.3 32.1 - + + -
700D GLU* 5.2 10.7 - - + +
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Residues in contact with LYS 697 (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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648A ASP* 5.3 0.2 + - - -
650A LYS* 4.0 5.5 - - - +
653A TYR* 2.3 47.2 + - + +
655A VAL* 5.4 2.2 - - + -
674A PHE* 4.2 15.6 - - + -
693A ASN* 3.1 26.1 + - - +
694A PHE* 3.1 10.1 + - + +
696A PHE* 1.3 77.3 - - + +
698A VAL* 1.3 68.0 + - - +
700A GLU* 3.5 22.6 - - + +
701A SER* 3.1 19.8 + - - -
736D ASP* 3.0 38.0 + - - -
781D ILE* 5.9 2.5 - - - -
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Residues in contact with VAL 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A VAL* 4.1 20.0 - - + -
674A PHE* 3.6 40.4 - - + -
694A PHE* 3.1 27.8 + - + +
695A LEU* 3.3 9.6 - - - +
697A LYS* 1.3 75.8 - - - +
699A ARG* 1.3 64.3 + - - +
701A SER* 2.5 27.2 + - - +
702A GLY 3.9 0.9 + - - -
703A SER* 4.2 7.3 + - - -
704A LEU* 3.8 24.2 - - + +
711A VAL* 5.4 1.6 - - + -
725A PHE* 4.5 6.3 - - + -
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Residues in contact with ARG 699 (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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579A ARG* 3.8 8.7 - - - +
695A LEU* 2.7 32.5 + - + +
696A PHE* 3.9 12.8 - - - +
697A LYS 3.4 0.2 - - - -
698A VAL* 1.3 73.7 - - - +
700A GLU* 1.3 62.8 + - - +
702A GLY* 3.0 15.9 + - - -
703A SER 4.5 0.2 + - - -
704A LEU* 3.5 27.7 + - + +
729A ASP* 3.0 33.4 + - - +
732A LEU* 3.4 19.1 + - - +
733A LEU* 3.0 31.9 - - - +
736A ASP* 5.9 0.2 + - - -
781A ILE* 3.5 25.7 - - - +
700D GLU* 3.1 49.8 + - + +
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Residues in contact with GLU 700 (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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696A PHE* 2.8 21.6 + - + +
697A LYS* 3.5 30.5 - - - +
699A ARG* 1.3 72.6 - - - +
701A SER* 1.3 62.8 + - - +
702A GLY 3.1 2.0 + - - -
579D ARG* 3.8 21.3 + - - -
699D ARG* 3.3 54.6 + - + +
700D GLU* 3.6 6.7 - - + +
702D GLY* 3.4 15.2 - - - -
704D LEU* 5.8 0.3 - - - +
705D SER* 4.5 6.9 + - - -
733D LEU* 5.2 2.4 - - - +
781D ILE* 5.9 1.4 - - - +
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Residues in contact with SER 701 (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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605A ARG* 3.7 10.6 + - - -
672A LEU* 3.9 10.8 - - - -
674A PHE* 3.4 20.2 - - - -
697A LYS 3.1 11.0 + - - -
698A VAL 2.5 23.1 + - - -
700A GLU* 1.3 80.0 - - - +
702A GLY* 1.3 58.8 + - - +
703A SER* 3.0 19.4 + - - -
705D SER* 3.9 7.8 + - - +
707D GLU* 3.4 15.1 - - - +
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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