Contacts of the helix formed by residues 686 - 704 (chain A) in PDB entry 1QFM
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 THR 686 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A TYR* 3.6 36.8 + - + -
91A ASN* 4.1 6.1 + - - -
94A LEU* 4.1 20.0 - - + +
95A GLN 2.7 25.9 + - - -
96A ASN* 3.1 13.8 + - - -
684A LYS 3.7 0.8 + - - -
685A PRO* 1.3 70.2 - - - +
687A ALA* 1.3 63.1 + - - +
689A VAL* 3.1 9.3 + - - +
690A ILE* 2.9 35.2 + - + +
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Residues in contact with ALA 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ASN* 3.1 23.4 + - - +
122A ASP 5.5 1.6 - - - +
685A PRO* 3.2 2.4 - - + -
686A THR* 1.3 76.8 - - - +
688A LYS* 1.3 64.3 + - + +
690A ILE* 3.4 8.6 + - - +
691A GLU* 3.1 30.0 + - + +
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Residues in contact with LYS 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ASP* 5.6 2.9 - - - -
124A THR* 4.0 12.6 - - - -
675A ASP* 2.9 29.6 + - - +
676A THR* 2.8 31.5 + - - -
677A LYS* 3.6 14.5 - - - +
678A ALA* 4.2 10.5 - - + -
684A LYS* 3.5 14.9 - - + +
685A PRO* 2.9 29.7 + - + +
687A ALA* 1.3 76.7 - - + +
689A VAL* 1.3 65.7 + - - +
691A GLU* 3.3 8.0 + - + +
692A GLU* 2.9 25.6 + - - +
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Residues in contact with VAL 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A MET* 4.9 11.9 - - + -
71A TYR* 5.4 11.7 - - + +
684A LYS* 3.9 30.7 - - + +
685A PRO 3.0 18.0 + - - +
686A THR* 3.1 11.2 + - + +
688A LYS* 1.3 75.7 - - - +
690A ILE* 1.3 63.7 + - + +
692A GLU* 3.2 9.6 + - - +
693A VAL* 3.0 33.5 + - + +
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Residues in contact with ILE 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LYS* 4.0 22.7 - - + -
67A MET* 4.1 24.9 - - + -
68A THR* 3.8 32.3 - - + +
71A TYR* 4.6 4.0 - - + -
94A LEU* 4.1 17.3 - - + -
686A THR* 2.9 37.4 + - + +
687A ALA* 3.7 7.2 - - - +
689A VAL* 1.3 77.9 - - + +
691A GLU* 1.3 61.3 + - - +
693A VAL* 3.4 7.5 - - - +
694A SER* 2.8 29.6 + - - +
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Residues in contact with GLU 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLU* 5.5 0.7 - - - +
60A ARG* 2.8 35.7 + - - +
64A LYS* 2.8 35.9 + - - -
687A ALA* 3.1 19.0 + - + +
688A LYS* 3.3 9.6 + - + +
690A ILE* 1.3 76.0 - - - +
692A GLU* 1.3 57.1 + - - +
694A SER* 3.3 1.9 + - - -
695A ASP* 2.9 37.0 + - - +
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Residues in contact with GLU 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A GLN* 3.3 24.9 + - - -
636A LEU* 4.0 24.1 - - + +
684A LYS* 2.9 33.0 + - - +
688A LYS 2.9 17.9 + - - +
689A VAL* 3.5 8.0 - - - +
691A GLU* 1.3 74.7 - - - +
693A VAL* 1.3 65.1 + - + +
695A ASP* 3.2 9.9 + - - +
696A MET* 3.0 37.4 + - - +
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Residues in contact with VAL 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A TYR* 3.8 17.4 - - + +
67A MET* 3.9 23.8 - - + -
487A SER* 3.7 26.9 - - - +
689A VAL* 3.0 22.2 + - + +
690A ILE* 3.4 12.8 - - - +
692A GLU* 1.3 79.2 - - + +
694A SER* 1.3 60.2 + - - +
696A MET* 3.3 15.9 + - - -
697A PHE* 2.9 40.2 + - + +
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Residues in contact with SER 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG* 3.8 27.8 - - - +
63A TYR* 3.7 15.8 - - - -
64A LYS* 3.3 32.3 - - - +
67A MET* 4.9 0.2 - - - +
690A ILE* 2.8 22.2 + - - +
691A GLU* 3.5 6.7 - - - -
693A VAL* 1.3 77.8 - - - +
695A ASP* 1.3 55.7 + - - +
697A PHE* 4.0 0.3 - - - +
698A ALA* 3.0 32.4 + - - +
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Residues in contact with ASP 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 3.7 33.5 - - + +
55A GLU* 5.5 0.7 - - - +
60A ARG* 2.7 36.8 + - - +
634A LEU* 4.7 5.8 - - + -
636A LEU* 5.2 6.2 - - + +
673A HIS* 3.9 22.5 + - - -
691A GLU* 2.9 20.7 + - - +
692A GLU* 3.4 10.8 - - - +
694A SER* 1.3 74.5 - - - +
696A MET* 1.3 65.7 + - + +
698A ALA* 3.4 2.1 + - - +
699A PHE* 3.0 25.5 + - - +
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Residues in contact with MET 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A PHE* 4.1 23.1 - - + -
551A ASN* 3.9 15.5 - - - +
575A ILE* 3.5 19.6 - - + +
577A GLN* 3.7 35.9 - - - +
634A LEU* 4.6 4.7 - - + +
636A LEU* 3.6 18.2 - - + -
692A GLU* 3.0 25.1 + - - +
693A VAL* 3.3 19.0 + - + +
695A ASP* 1.3 77.9 - - - +
697A PHE* 1.3 67.8 + - + +
699A PHE* 3.3 3.8 + - - +
700A ILE* 3.1 30.1 + - - +
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Residues in contact with PHE 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 4.8 1.5 - - - +
63A TYR* 3.2 51.4 - + + -
469A PHE* 3.8 26.2 - + - -
487A SER* 3.9 21.1 - - - -
488A ARG* 4.6 6.5 - - + -
491A PHE* 3.6 40.8 - + + -
495A MET* 3.7 10.7 - - - +
693A VAL* 2.9 27.9 + - + +
696A MET* 1.3 84.1 - - + +
698A ALA* 1.3 60.3 + - - +
700A ILE* 3.7 22.0 - - + -
701A ALA* 2.9 30.0 + - - +
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Residues in contact with ALA 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 3.7 16.2 - - - +
59A ILE* 4.2 15.9 - - + +
60A ARG* 3.6 33.4 - - + +
63A TYR* 5.6 0.8 - - - -
694A SER 3.0 20.6 + - - +
695A ASP* 3.8 3.6 - - - +
697A PHE* 1.3 73.6 - - - +
699A PHE* 1.3 61.5 + - - +
701A ALA* 3.7 0.3 - - - +
702A ARG* 2.8 33.8 + - - +
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Residues in contact with PHE 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PHE* 3.8 23.8 - + - -
54A LEU* 3.8 18.3 - - + +
573A CYS* 3.5 33.9 - - - -
574A VAL 4.3 0.4 - - - -
575A ILE* 4.4 4.7 - - + -
632A SER* 3.9 4.3 - - - -
633A MET 3.4 32.8 - - - -
634A LEU* 3.6 34.5 - - + -
669A PRO* 3.9 8.5 - - + -
671A LEU* 4.0 13.9 - - + -
695A ASP 3.0 18.1 + - - +
696A MET 3.4 4.5 - - - +
698A ALA* 1.3 76.6 - - - +
700A ILE* 1.3 62.3 + - - +
702A ARG* 4.0 2.6 - - - -
703A CYS* 3.0 45.7 + - - +
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Residues in contact with ILE 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A PHE* 3.8 8.3 - - + -
491A PHE* 4.2 9.4 - - + -
495A MET* 4.2 7.0 - - + -
549A THR* 3.7 39.9 - - + +
573A CYS* 4.0 10.1 - - - -
575A ILE* 3.8 17.0 - - + -
696A MET 3.1 15.1 + - - +
697A PHE* 3.7 32.5 - - + +
699A PHE* 1.3 78.4 - - - +
701A ALA* 1.3 57.3 + - - +
703A CYS 3.8 0.2 - - - -
704A LEU* 2.9 37.6 + - + +
706A ILE* 4.0 18.4 - - + -
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Residues in contact with ALA 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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59A ILE* 3.5 33.9 - - + -
495A MET* 3.7 16.4 - - + -
697A PHE 2.9 19.0 + - - +
698A ALA 3.7 1.8 - - - +
700A ILE* 1.3 77.9 - - - +
702A ARG* 1.3 59.0 + - - +
705A ASN* 2.8 25.1 + - - -
706A ILE* 2.9 23.6 + - - +
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Residues in contact with ARG 702 (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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1A MET* 3.7 44.1 + - - +
3A SER* 5.2 3.0 + - - -
53A PHE* 2.8 71.1 + - + +
56A GLN* 2.9 46.8 + - - +
57A CSX 3.7 25.0 - - - -
59A ILE* 4.8 5.1 - - + +
698A ALA 2.8 20.7 + - - +
699A PHE* 4.1 2.2 - - - +
701A ALA* 1.3 71.2 - - - +
703A CYS* 1.3 67.0 + - - +
705A ASN* 3.2 13.7 + - - +
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Residues in contact with CYS 703 (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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1A MET* 4.0 16.6 - - - +
53A PHE* 4.2 3.6 - - - -
573A CYS* 4.8 2.2 - - - -
632A SER* 3.4 38.7 + - - +
668A ASN* 5.8 0.2 - - - +
669A PRO* 3.7 18.8 - - - -
699A PHE* 3.0 35.4 + - - +
700A ILE* 4.0 3.4 - - - +
702A ARG* 1.3 76.5 - - - +
704A LEU* 1.3 70.0 + - + +
705A ASN* 3.7 0.9 + - - +
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Residues in contact with LEU 704 (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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467A PRO* 4.7 1.6 - - + -
546A LYS 3.3 18.8 - - - +
547A ARG* 3.6 36.1 - - + +
548A LEU 5.0 0.2 - - - -
549A THR* 4.1 14.6 - - - +
572A GLY* 4.2 22.4 - - - +
573A CYS* 4.3 6.5 - - + -
700A ILE* 2.9 22.4 + - + +
703A CYS* 1.3 83.4 - - + +
705A ASN* 1.3 70.5 + - - +
706A ILE* 3.3 25.8 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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