Contacts of the helix formed by residues 724 - 735 (chain B) in PDB entry 4QUN
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 724 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673B LYS* 4.0 28.0 - - + +
696B ILE* 5.1 7.4 - - - +
718B GLN* 4.5 4.8 + - - +
720B PRO* 3.6 6.9 - - - +
721B LEU* 2.9 34.2 + - + +
723B HIS* 1.3 96.9 - - + +
725B CYS* 1.3 66.1 + - - +
726B ALA 3.2 2.2 - - - -
727B GLN* 3.1 26.1 + - - +
728B PHE* 2.9 22.3 + - - +
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Residues in contact with CYS 725 (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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720B PRO* 4.1 7.6 - - - -
721B LEU 3.3 16.7 + - - -
722B PRO 3.9 7.9 - - - +
723B HIS 3.6 0.8 - - - -
724B THR* 1.3 78.0 - - - +
726B ALA* 1.3 62.2 + - - +
728B PHE* 3.3 7.8 + - - +
729B TRP* 3.1 30.3 + - - -
755B HIS* 3.6 23.6 - - - -
757B TYR* 3.6 25.8 - - + -
767B HIS* 3.5 29.8 - - + +
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Residues in contact with ALA 726 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722B PRO 5.4 0.2 + - - -
723B HIS 5.1 1.7 + - - +
724B THR 3.2 0.4 - - - +
725B CYS* 1.3 79.4 - - - +
727B GLN* 1.3 67.7 + - + +
729B TRP* 3.5 2.3 + - - +
730B GLN* 3.0 28.0 + - - +
767B HIS* 4.1 15.0 + - + +
768B GLY* 3.7 29.0 - - - +
770B PHE* 4.7 4.3 - - - -
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Residues in contact with GLN 727 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B LYS* 4.4 21.8 - - - +
689B LEU* 3.5 30.3 - - + +
693B GLU 5.7 0.7 - - - +
695B TYR 4.4 4.2 + - - +
696B ILE* 3.9 12.5 - - + +
723B HIS 3.2 19.4 + - - +
724B THR* 3.1 30.9 + - - +
726B ALA* 1.3 82.1 - - + +
728B PHE* 1.3 66.3 + - - +
730B GLN* 3.2 13.3 + - - +
731B VAL* 3.1 27.5 + - - +
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Residues in contact with PHE 728 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696B ILE* 3.8 16.5 - - + +
717B THR* 4.1 13.5 - - + -
718B GLN 5.1 0.4 - - - -
720B PRO* 3.5 28.0 - - + -
724B THR* 2.9 12.3 + - - +
725B CYS* 3.5 8.7 - - - +
727B GLN* 1.3 76.4 - - - +
729B TRP* 1.3 75.3 + + - +
731B VAL* 3.2 7.2 + - + +
732B VAL* 3.2 26.3 + - + +
740B ILE* 4.0 18.8 - - + -
757B TYR* 3.4 46.0 - + + -
839B LEU* 3.7 38.3 - - + +
841B HIS* 4.1 7.2 - + - -
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Residues in contact with TRP 729 (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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725B CYS 3.1 24.4 + - - +
726B ALA 4.0 3.6 - - - +
728B PHE* 1.3 80.8 - + - +
730B GLN* 1.3 57.2 + - - +
732B VAL* 3.3 26.6 + - + +
733B TRP* 2.9 30.7 + - - +
740B ILE* 4.2 15.9 - - + -
757B TYR* 3.0 48.1 + + + -
767B HIS* 3.9 13.2 - + + -
770B PHE* 4.0 19.3 - - + -
772B ILE* 3.7 37.1 - - + +
788B MET* 3.7 27.4 - - + -
790B VAL* 3.5 33.0 - - + +
801B VAL* 4.5 3.4 - - + -
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Residues in contact with GLN 730 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689B LEU* 3.3 38.1 - - - +
690B GLN* 3.3 33.9 + - - +
726B ALA 3.0 14.9 + - - +
727B GLN* 3.2 15.1 + - - +
729B TRP* 1.3 77.2 - - - +
731B VAL* 1.3 57.0 + - - +
733B TRP* 3.3 1.0 + - - +
734B ASP* 2.8 55.0 + - - +
770B PHE* 3.7 19.0 - - + -
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Residues in contact with VAL 731 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687B VAL* 3.9 26.2 - - + -
688B LEU 5.5 0.2 - - - +
689B LEU* 3.5 19.5 - - + -
696B ILE* 4.1 13.5 - - + -
698B ALA* 5.7 0.4 - - + -
715B ILE* 4.0 29.4 - - + -
727B GLN 3.1 14.7 + - - +
728B PHE* 3.2 8.9 + - + +
730B GLN* 1.3 73.3 - - - +
732B VAL* 1.3 65.5 + - - +
734B ASP* 3.5 6.7 + - - +
735B GLN* 3.3 28.7 + - - +
737B LEU* 4.2 6.2 - - + +
839B LEU* 4.7 8.1 - - + -
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Residues in contact with VAL 732 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728B PHE* 3.2 34.4 + - + +
729B TRP* 3.5 23.1 - - + +
731B VAL* 1.3 76.2 - - - +
733B TRP* 1.3 58.5 + - - +
736B LYS* 3.0 9.2 + - - -
737B LEU* 3.0 53.6 + - + +
740B ILE* 4.1 10.3 - - + -
790B VAL* 5.3 2.2 - - + -
799B HIS* 4.6 3.5 + - + -
801B VAL* 3.9 22.0 - - + -
839B LEU* 4.2 15.0 - - + -
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Residues in contact with TRP 733 (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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729B TRP 2.9 11.2 + - - +
730B GLN 3.7 1.6 - - - +
731B VAL 3.2 0.2 - - - -
732B VAL* 1.3 77.3 - - - +
734B ASP* 1.3 75.1 + - - +
736B LYS* 3.1 52.7 + - - +
770B PHE* 3.4 33.7 - + + -
790B VAL* 3.6 42.4 - - + -
792B ASN* 3.6 33.3 - - + +
797B GLU* 3.2 56.3 + - + -
798B GLU 4.3 1.1 - - - -
799B HIS* 3.6 16.2 - + + -
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Residues in contact with ASP 734 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688B LEU 5.1 5.2 - - - +
689B LEU* 5.1 0.7 - - - +
690B GLN* 3.9 23.4 + - - +
730B GLN* 2.8 53.8 + - - +
731B VAL* 3.5 7.3 + - - +
733B TRP* 1.3 83.9 - - - +
735B GLN* 1.3 67.6 + - + +
736B LYS* 3.4 2.5 + - - +
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Residues in contact with GLN 735 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687B VAL* 4.3 10.1 - - - +
688B LEU 5.6 1.2 + - - -
700B TYR* 3.0 34.9 + - - -
715B ILE* 3.7 22.2 - - - +
731B VAL* 3.3 19.3 + - + +
733B TRP 3.2 0.2 - - - -
734B ASP* 1.3 85.8 - - + +
736B LYS* 1.3 72.4 + - - +
737B LEU* 3.2 19.1 + - + +
836B GLU* 5.2 3.6 - - - +
837B PRO* 4.1 13.3 - - + +
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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