Contacts of the helix formed by residues 657 - 671 (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 GLU 657 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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651B ALA* 4.5 0.7 - - - -
656B MET* 1.3 78.6 - - - +
658B HIS* 1.3 69.3 + - - +
659B ALA* 4.4 7.4 - - + +
660B GLN* 2.9 37.9 + - + +
661B ALA* 3.2 8.7 + - - +
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Residues in contact with HIS 658 (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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644B ASN* 5.3 3.5 + - - -
647B TYR* 3.6 40.2 - + + +
648B ASP* 4.2 15.7 + - - -
651B ALA* 4.3 14.1 - - + +
656B MET 3.9 1.2 + - - -
657B GLU* 1.3 73.3 + - - +
659B ALA* 1.3 66.5 + - - +
661B ALA* 3.1 13.7 + - - +
662B VAL* 3.2 25.6 + - + +
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Residues in contact with ALA 659 (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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657B GLU* 3.2 5.2 - - + +
658B HIS* 1.3 82.1 - - + +
660B GLN* 1.3 62.0 + - + +
662B VAL* 3.3 11.9 + - - +
663B ASP* 3.1 28.3 + - - +
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Residues in contact with GLN 660 (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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656B MET* 3.6 22.9 - - - +
657B GLU* 2.9 47.1 + - + +
659B ALA* 1.3 76.5 - - + +
661B ALA* 1.3 62.0 + - - +
663B ASP* 3.1 17.5 + - + +
664B TYR* 2.8 26.7 + - - +
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Residues in contact with ALA 661 (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* 3.4 31.4 - - + +
650B VAL* 3.8 9.9 - - + -
651B ALA* 3.8 21.8 - - + +
656B MET* 3.6 9.8 - - - -
657B GLU 3.2 2.2 + - - -
658B HIS 3.1 10.2 + - - +
660B GLN* 1.3 74.7 - - - +
662B VAL* 1.3 68.4 + - - +
664B TYR* 3.1 2.3 + - - +
665B ILE* 2.8 29.0 + - - +
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Residues in contact with VAL 662 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647B TYR* 3.9 48.2 - - + +
658B HIS* 3.2 26.4 + - + +
659B ALA* 3.4 10.8 - - - +
660B GLN 3.2 0.2 - - - -
661B ALA* 1.3 78.1 - - - +
663B ASP* 1.3 59.1 + - - +
665B ILE* 3.3 0.9 + - - +
666B LYS* 2.9 50.6 + - + +
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Residues in contact with ASP 663 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659B ALA* 3.1 17.6 + - - +
660B GLN* 3.2 20.8 - - + +
662B VAL* 1.3 79.3 - - - +
664B TYR* 1.3 54.2 + - - +
666B LYS* 3.8 3.8 - - - +
667B LYS* 2.8 39.3 + - + +
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Residues in contact with TYR 664 (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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620B TRP* 4.0 26.3 - + - -
623B ILE* 3.9 36.3 + - + +
624B GLU* 4.3 8.0 - - - +
650B VAL* 3.9 12.1 - - + -
656B MET* 3.9 18.4 - - + -
660B GLN 2.8 14.2 + - - +
661B ALA* 3.3 13.7 - - - +
663B ASP* 1.3 75.2 - - - +
665B ILE* 1.3 67.9 + - + +
667B LYS* 3.2 7.9 + - - +
668B LEU* 3.0 39.9 + - + +
673B ARG* 5.0 2.9 + - - -
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Residues in contact with ILE 665 (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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623B ILE* 5.8 0.4 - - + -
629B ILE* 5.3 2.5 - - + -
643B GLN* 4.3 2.9 - - + -
646B PHE* 4.2 15.5 - - + -
647B TYR* 3.6 34.5 - - + +
650B VAL* 3.8 26.7 - - + -
661B ALA 2.8 21.7 + - - +
662B VAL 3.7 2.9 - - - +
664B TYR* 1.3 69.7 - - + +
666B LYS* 1.3 63.7 + - - +
668B LEU* 2.8 43.1 + - + +
669B MET* 3.2 27.2 + - + +
674B TYR* 3.9 21.3 - - + +
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Residues in contact with LYS 666 (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* 2.6 44.1 + - - +
643B GLN* 3.9 7.3 - - - +
647B TYR* 4.2 4.1 + - - +
662B VAL* 2.9 43.2 + - + +
663B ASP* 4.1 3.8 - - - +
665B ILE* 1.3 74.0 - - + +
667B LYS* 1.3 60.9 + - - +
669B MET* 3.1 33.8 - - + +
670B THR* 3.3 13.8 + - - +
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Residues in contact with LYS 667 (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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663B ASP* 2.8 23.1 + - + +
664B TYR* 3.4 8.3 - - - +
665B ILE 3.0 0.2 - - - -
666B LYS* 1.3 74.8 - - - +
668B LEU* 1.3 63.0 + - - +
670B THR* 2.8 35.1 + - - +
671B LYS* 3.1 31.8 - - - +
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Residues in contact with LEU 668 (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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623B ILE* 4.3 11.2 - - + -
627B ALA 5.5 0.2 - - - +
629B ILE* 4.5 9.2 - - + -
664B TYR* 3.0 41.5 + - + +
665B ILE* 2.8 24.0 + - + +
667B LYS* 1.3 77.2 - - - +
669B MET* 1.3 61.0 + - - +
671B LYS* 3.2 12.0 + - + +
673B ARG* 2.9 75.8 + - + +
674B TYR* 3.9 22.7 - - + +
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Residues in contact with MET 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B GLU* 5.2 5.4 - - - +
182B GLU* 3.5 33.2 - - + +
183B HIS* 5.9 4.7 - - - +
643B GLN* 3.5 26.7 - - - +
665B ILE* 3.5 32.5 - - + +
666B LYS* 3.1 22.0 - - + +
667B LYS 3.2 0.2 - - - -
668B LEU* 1.3 74.5 - - - +
670B THR* 1.3 64.9 + - + +
671B LYS 3.1 1.6 - - - -
672B GLY* 3.1 13.2 + - - -
674B TYR* 3.5 38.3 - - + +
676B LEU* 4.6 6.5 - - + -
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Residues in contact with THR 670 (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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183B HIS* 6.4 1.6 - - + -
666B LYS 3.3 13.7 + - - +
667B LYS* 2.8 35.6 + - - +
669B MET* 1.3 76.5 - - + +
671B LYS* 1.3 62.0 + - - +
672B GLY 3.3 1.4 + - - -
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Residues in contact with LYS 671 (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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628B HIS* 5.5 0.2 + - - -
667B LYS* 3.1 32.1 - - - +
668B LEU* 3.5 11.9 - - + +
669B MET 3.1 0.8 - - - -
670B THR* 1.3 81.8 - - - +
672B GLY* 1.3 60.8 + - - +
673B ARG* 3.4 36.2 + - - +
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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
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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