Contacts of the helix formed by residues 637 - 654 (chain A) in PDB entry 3QFR
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 ASN 637 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634A ASP* 3.2 7.1 + - - +
636A ARG* 1.3 92.7 + - - +
638A MET* 1.3 69.1 + - - +
639A ALA 3.5 1.1 - - - -
640A ARG* 3.1 30.6 + - - +
641A ASP* 3.1 26.8 + - - +
753A NAP 3.2 21.8 + - - +
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Residues in contact with MET 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A VAL* 4.7 0.2 - - - -
536A PRO* 3.7 27.6 - - + -
631A VAL* 3.9 17.7 - - + -
632A CYS 3.6 28.9 - - - +
633A GLY* 3.8 2.2 - - - -
634A ASP* 3.3 46.7 + - + +
637A ASN* 1.3 77.3 - - - +
639A ALA* 1.3 64.5 + - - +
641A ASP* 3.0 3.5 + - - +
642A VAL* 3.0 40.7 + - + +
678A VAL* 4.9 1.3 - - + -
753A NAP 3.5 36.4 + - + +
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Residues in contact with ALA 639 (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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180A THR 5.6 1.8 - - - +
631A VAL* 4.4 8.9 - - + +
634A ASP 3.2 14.6 + - - +
635A ALA* 3.9 13.5 - - - +
637A ASN 3.5 0.6 - - - -
638A MET* 1.3 85.0 - - - +
640A ARG* 1.3 56.8 + - - +
642A VAL* 3.8 2.5 + - - +
643A GLN* 3.2 30.2 + - - +
674A TYR* 4.7 1.6 + - - -
676A LEU* 4.7 8.6 - - + +
678A VAL* 4.0 24.5 - - + -
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Residues in contact with ARG 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A ALA 4.7 2.6 + - - +
636A ARG 4.4 8.6 + - - +
637A ASN* 3.1 38.8 + - - +
638A MET 3.2 1.0 - - - -
639A ALA* 1.3 77.6 - - - +
641A ASP* 1.3 83.7 + - - +
643A GLN* 3.8 6.7 - - + +
644A ASN* 2.9 48.2 + - - +
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Residues in contact with ASP 641 (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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609A GLN* 3.8 23.3 - - + +
637A ASN* 3.1 11.4 + - - +
638A MET 3.0 4.8 + - - +
640A ARG* 1.3 96.1 + - - +
642A VAL* 1.3 61.8 + - - +
643A GLN 3.1 1.8 - - - -
644A ASN* 3.2 11.2 + - - +
645A THR* 2.9 33.9 + - - -
753A NAP 3.1 27.4 + - - +
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Residues in contact with VAL 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A VAL* 3.8 16.6 - - + -
608A VAL* 3.9 3.1 - - + -
609A GLN* 3.9 24.2 - - - +
612A LEU* 3.9 10.3 - - + +
631A VAL* 4.0 20.6 - - + -
638A MET* 3.0 36.2 + - - +
639A ALA 4.1 4.3 - - - +
641A ASP* 1.3 76.3 - - - +
643A GLN* 1.3 57.7 - - - +
645A THR* 3.4 3.7 + - - -
646A PHE* 3.1 50.5 + - + -
674A TYR* 4.1 0.9 - - - +
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Residues in contact with GLN 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A GLU* 3.3 22.3 + - - +
639A ALA* 3.2 18.4 + - - +
640A ARG* 3.8 7.8 - - + +
641A ASP 3.1 0.2 - - - -
642A VAL* 1.3 79.3 - - - +
644A ASN* 1.3 64.9 + - - +
646A PHE* 3.2 3.5 + - - +
647A TYR* 2.6 63.7 + - + +
665A ILE* 4.4 3.1 - - + +
666A LYS* 3.9 7.7 - - - +
669A MET* 3.1 26.9 - - - +
674A TYR* 3.4 24.9 + - + +
676A LEU* 4.4 6.8 - - - +
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Residues in contact with ASN 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A ARG* 2.9 45.1 + - - +
641A ASP* 3.6 14.2 + - - +
643A GLN* 1.3 76.2 - - - +
645A THR* 1.3 57.9 + - - +
647A TYR* 3.1 29.5 - - - +
648A ASP* 3.0 32.5 + - - +
658A HIS* 5.1 3.3 + - + -
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Residues in contact with THR 645 (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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609A GLN* 3.2 40.0 + - - +
612A LEU* 4.1 10.8 - - + -
613A LYS* 4.0 24.9 - - + +
641A ASP 2.9 17.3 + - - -
642A VAL 3.6 6.1 - - - -
643A GLN 3.1 0.2 - - - -
644A ASN* 1.3 73.6 - - - +
646A PHE* 1.3 58.9 + - - +
647A TYR 3.1 2.0 - - - -
648A ASP* 3.4 10.5 + - + +
649A ILE* 3.0 36.3 + - + +
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Residues in contact with PHE 646 (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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532A ILE* 4.2 10.5 - - + -
534A VAL* 4.4 2.7 - - + -
612A LEU* 3.9 23.8 - - + -
619A LEU* 4.3 18.4 - - + -
623A ILE* 4.0 18.2 - - + -
629A ILE* 3.7 45.5 - - + -
642A VAL* 3.1 41.8 + - + -
643A GLN 3.2 7.1 + - - +
645A THR* 1.3 74.3 - - - +
647A TYR* 1.3 67.7 + - - +
649A ILE* 3.8 11.6 - - + +
650A VAL* 3.2 26.3 + - - +
665A ILE* 4.1 14.8 - - + +
674A TYR* 3.6 20.6 - + + -
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Residues in contact with TYR 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A GLN* 2.6 52.5 + - + -
644A ASN* 3.1 34.1 - - - +
645A THR 3.1 0.2 - - - -
646A PHE* 1.3 76.7 - - - +
648A ASP* 1.3 67.4 + - - +
650A VAL 3.2 2.8 + - - -
651A ALA* 2.9 24.7 + - - +
658A HIS* 3.8 27.4 - + + +
661A ALA* 3.5 10.9 - - + +
662A VAL* 3.7 39.5 - - + +
665A ILE* 3.7 27.8 - - + -
666A LYS* 3.2 16.6 + - - -
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Residues in contact with ASP 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A LYS* 4.1 16.7 + - + +
644A ASN* 3.0 14.3 + - - +
645A THR* 3.6 13.1 - - + +
647A TYR* 1.3 79.4 - - - +
649A ILE* 1.3 54.9 + - + +
651A ALA* 3.1 5.8 + - - +
652A GLU* 2.7 55.0 + - - +
658A HIS* 4.1 16.7 + - - -
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Residues in contact with ILE 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A LEU* 3.6 28.9 - - + +
613A LYS* 4.8 4.0 - - + -
616A ARG* 3.9 37.5 - - + +
619A LEU* 4.2 9.0 - - + -
620A TRP* 4.2 17.4 - - + +
623A ILE* 4.7 10.3 - - + -
645A THR* 3.0 28.8 + - + +
646A PHE* 3.8 23.3 - - + +
647A TYR 3.2 0.2 - - - -
648A ASP* 1.3 76.3 - - + +
650A VAL* 1.3 64.4 + - - +
652A GLU* 4.1 7.0 - - - +
653A LEU* 3.1 26.7 + - - +
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Residues in contact with VAL 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A TRP* 3.7 28.0 - - + -
623A ILE* 4.9 9.4 - - + -
646A PHE 3.2 16.5 + - - +
647A TYR 3.2 3.7 + - - +
649A ILE* 1.3 76.5 - - - +
651A ALA* 1.3 55.9 + - - +
654A GLY* 2.7 34.0 + - - -
656A MET* 3.5 32.9 - - + +
661A ALA* 3.8 10.5 - - + +
664A TYR* 3.9 18.2 - - + -
665A ILE* 3.8 20.9 - - + -
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Residues in contact with ALA 651 (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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647A TYR 2.9 18.1 + - - +
648A ASP* 3.6 7.0 - - - +
650A VAL* 1.3 80.7 - - - +
652A GLU* 1.3 63.8 + - + +
655A ALA* 3.9 1.2 + - - -
656A MET* 3.0 36.5 + - - +
658A HIS* 4.1 18.6 - - + +
661A ALA* 3.8 14.6 - - + +
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Residues in contact with GLU 652 (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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613A LYS* 3.2 26.7 + - - +
616A ARG* 3.3 40.1 + - - +
648A ASP* 2.7 36.0 + - + +
649A ILE* 4.1 7.1 - - - +
651A ALA* 1.3 76.5 - - + +
653A LEU* 1.3 63.2 + - + +
655A ALA* 4.2 4.5 + - - -
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Residues in contact with LEU 653 (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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616A ARG* 3.1 76.3 - - + +
617A GLU* 3.6 27.4 - - - +
620A TRP* 3.2 38.5 + - + -
649A ILE* 3.1 13.7 + - + +
652A GLU* 1.3 74.5 - - + +
654A GLY* 1.3 61.1 + - - +
655A ALA* 3.3 4.5 + - - +
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Residues in contact with GLY 654 (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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620A TRP* 3.5 24.6 - - - -
650A VAL 2.7 25.3 + - - -
653A LEU* 1.3 73.3 - - - +
655A ALA* 1.3 73.4 + - - +
656A MET* 3.4 15.2 - - - +
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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
------------------------------------------------------------
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