Contacts of the helix formed by residues 637 - 653 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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634B ASP* 3.4 11.9 + - - +
635B ALA 3.4 0.6 - - - -
636B ARG* 1.3 104.9 + - - +
638B MET* 1.3 63.0 + - - +
639B ALA 3.5 1.1 - - - -
640B ARG* 3.6 13.0 + - - +
641B ASP* 2.9 38.5 + - - +
753B NAP 3.5 19.5 + - + +
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Residues in contact with MET 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534B VAL* 4.9 1.8 - - - -
536B PRO* 4.0 25.4 - - + -
608B VAL* 4.6 0.2 - - + -
631B VAL* 3.9 11.4 - - + -
632B CYS 3.2 26.5 - - - +
633B GLY* 3.7 1.8 - - - -
634B ASP* 3.1 46.9 + - + +
637B ASN* 1.3 74.9 - - - +
639B ALA* 1.3 72.0 + - + +
641B ASP* 3.1 2.4 + - - +
642B VAL* 2.8 42.1 + - + +
678B VAL* 4.7 0.4 - - + -
753B NAP 3.6 39.7 + - + +
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Residues in contact with ALA 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B THR 5.7 2.0 - - - +
631B VAL* 4.1 11.2 - - + +
634B ASP 3.0 18.5 + - - +
635B ALA* 3.9 10.8 - - - +
637B ASN 3.5 0.4 - - - -
638B MET* 1.3 85.2 - - - +
640B ARG* 1.3 65.6 + - - +
642B VAL* 3.1 2.3 + - - +
643B GLN* 2.9 26.9 + - - +
674B TYR* 5.3 0.2 + - - -
676B LEU* 4.6 10.5 - - + -
678B VAL* 3.9 21.5 - - + -
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Residues in contact with ARG 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B THR 6.0 2.2 - - - +
635B ALA 4.3 4.2 + - - +
636B ARG 3.8 22.4 - - - +
637B ASN* 3.6 14.7 + - - +
638B MET 3.3 0.4 - - - -
639B ALA* 1.3 78.3 - - - +
641B ASP* 1.3 71.5 + - - +
643B GLN* 3.4 9.2 + - - +
644B ASN* 2.7 50.1 + - - +
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Residues in contact with ASP 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B TYR* 5.6 0.5 - - - -
609B GLN* 3.8 23.0 - - + +
637B ASN* 2.9 26.9 + - - +
638B MET 3.6 3.4 - - - +
640B ARG* 1.3 89.2 + - - +
642B VAL* 1.3 68.5 + - - +
644B ASN* 3.3 9.8 + - - +
645B THR* 3.2 21.7 + - - -
753B NAP 3.1 24.5 + - - +
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Residues in contact with VAL 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B VAL* 4.1 15.0 - - + -
608B VAL* 4.2 11.0 - - + -
609B GLN* 4.3 12.8 - - + +
612B LEU* 4.1 11.4 - - + -
631B VAL* 3.9 24.2 - - + -
638B MET* 2.8 44.7 + - + +
639B ALA* 3.3 8.5 - - - +
641B ASP* 1.3 70.3 - - - +
643B GLN* 1.3 56.1 + - - +
645B THR* 2.6 27.9 + - - -
646B PHE* 3.0 28.8 + - + +
674B TYR* 4.2 0.2 - - - +
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Residues in contact with GLN 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B GLU* 3.3 26.9 + - - +
639B ALA* 2.9 15.9 + - - +
640B ARG* 3.6 8.5 - - - +
642B VAL* 1.3 78.8 - - - +
644B ASN* 1.3 63.3 + - - +
646B PHE* 3.3 4.4 + - - +
647B TYR* 2.6 62.2 + - + +
665B ILE* 4.3 3.1 - - + -
666B LYS* 3.9 1.6 - - - +
669B MET* 3.5 20.8 - - - +
674B TYR* 3.5 24.9 + - + +
676B LEU* 4.8 13.9 - - - +
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Residues in contact with ASN 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640B ARG* 2.7 48.5 + - - +
641B ASP* 3.5 12.6 + - - +
642B VAL 3.0 0.2 - - - -
643B GLN* 1.3 74.3 - - - +
645B THR* 1.3 64.7 + - - +
647B TYR* 3.4 26.7 - - - +
648B ASP* 3.2 27.6 + - - +
658B HIS* 5.3 3.5 + - - -
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Residues in contact with THR 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609B GLN* 3.2 45.5 + - - +
612B LEU* 4.2 11.2 - - + -
613B LYS* 4.0 24.5 - - + +
641B ASP 3.2 6.8 + - - -
642B VAL* 2.6 18.7 + - - -
644B ASN* 1.3 70.1 - - - +
646B PHE* 1.3 57.0 + - - +
648B ASP* 3.1 10.3 + - - +
649B ILE* 2.8 38.1 + - + +
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Residues in contact with PHE 646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532B ILE* 4.8 7.9 - - + -
534B VAL* 4.8 2.2 - - + -
612B LEU* 4.2 26.0 - - + -
619B LEU* 4.7 7.6 - - + -
623B ILE* 4.2 14.8 - - + -
629B ILE* 3.3 46.0 - - + -
631B VAL* 4.8 1.3 - - + -
642B VAL* 3.0 29.6 + - + -
643B GLN* 3.6 8.3 - - - +
645B THR* 1.3 75.1 - - - +
647B TYR* 1.3 65.3 + - - +
649B ILE* 3.1 24.8 + - + +
650B VAL* 2.8 30.3 + - + +
665B ILE* 4.2 15.0 - - + -
674B TYR* 3.4 26.7 - + + +
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Residues in contact with TYR 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643B GLN* 2.6 54.5 + - + -
644B ASN* 3.4 32.8 - - - +
646B PHE* 1.3 77.0 - - - +
648B ASP* 1.3 58.8 + - - +
650B VAL 3.1 0.3 + - - -
651B ALA* 2.8 28.3 + - - +
658B HIS* 3.6 28.9 - + + -
661B ALA* 3.4 15.3 - - + +
662B VAL* 3.9 35.7 - - + +
665B ILE* 3.6 36.6 - - + -
666B LYS* 4.2 6.1 + - - +
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Residues in contact with ASP 648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B LYS* 3.9 24.3 + - + +
644B ASN* 3.2 17.3 + - - +
645B THR* 3.1 11.1 + - - +
647B TYR* 1.3 79.3 - - - +
649B ILE* 1.3 63.6 + - - +
651B ALA* 3.8 6.3 - - - +
652B GLU* 3.0 28.7 + - - +
658B HIS* 4.2 16.1 + - - -
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Residues in contact with ILE 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612B LEU* 3.5 30.5 - - + +
613B LYS* 4.8 5.4 - - + +
616B ARG* 4.2 31.9 - - + +
619B LEU* 4.1 13.5 - - + -
620B TRP* 4.6 16.6 - - + +
623B ILE* 5.3 2.7 - - + -
645B THR* 2.8 28.1 + - + +
646B PHE* 3.5 31.4 - - + +
648B ASP* 1.3 74.1 - - - +
650B VAL* 1.3 67.8 + - + +
652B GLU* 5.4 1.1 - - - -
653B LEU* 3.2 31.6 + - + +
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Residues in contact with VAL 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620B TRP* 4.1 25.6 - - + -
623B ILE* 5.2 7.4 - - + -
646B PHE* 2.8 24.1 + - + +
647B TYR 3.6 3.4 - - - +
649B ILE* 1.3 74.7 - - + +
651B ALA* 1.3 62.9 + - - +
654B GLY* 3.1 21.1 + - - -
656B MET* 3.6 31.5 - - + +
661B ALA* 3.8 10.1 - - + -
664B TYR* 3.9 19.5 - - + -
665B ILE* 3.8 22.7 - - + -
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Residues in contact with ALA 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647B TYR 2.8 20.1 + - - +
648B ASP* 3.8 7.6 - - - +
650B VAL* 1.3 74.2 - - - +
652B GLU* 1.3 60.3 + - - +
655B ALA* 3.5 2.3 + - - -
656B MET* 3.0 47.8 + - - +
658B HIS* 4.3 17.3 - - + +
661B ALA* 3.8 9.6 - - + +
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Residues in contact with GLU 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613B LYS* 3.7 14.3 + - - -
616B ARG* 3.1 36.2 + - - -
648B ASP 3.0 14.8 + - - +
651B ALA* 1.3 74.6 - - - +
653B LEU* 1.3 69.8 + - + +
654B GLY 3.1 8.0 + - - -
655B ALA* 3.4 11.1 + - - +
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Residues in contact with LEU 653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616B ARG* 3.6 47.1 - - + +
617B GLU* 4.5 15.0 - - + +
620B TRP* 2.7 58.0 + - + -
649B ILE* 3.2 19.5 + - + +
650B VAL 4.2 0.4 - - - -
652B GLU* 1.3 91.0 - - + +
654B GLY* 1.3 52.5 + - - +
655B ALA 3.4 1.8 - - - -
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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
------------------------------------------------------------
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