Contacts of the helix formed by residues 711 - 726 (chain B) in PDB entry 5QSY
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 ASP 711 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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666B VAL* 5.7 2.2 - - - +
670B ASN* 5.4 0.9 - - - +
708B THR 4.7 0.9 - - - -
709B LYS 4.4 0.2 + - - -
710B TRP* 1.3 69.3 - - - +
712B LEU* 1.3 63.3 + - - +
713B PHE* 3.4 2.6 + - - +
714B GLY* 3.4 23.6 + - - -
715B ASN* 3.9 11.6 + - - +
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Residues in contact with LEU 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666B VAL* 4.1 24.0 - - + -
669B PHE* 3.9 29.8 - - + -
670B ASN* 5.2 2.0 - - - +
698B LEU* 4.2 25.4 - - + -
702B HIS* 3.8 30.7 - - + +
707B LEU* 4.3 10.3 - - + +
710B TRP* 3.1 17.3 + - + +
711B ASP* 1.3 76.8 - - - +
713B PHE* 1.3 67.2 + - - +
715B ASN* 3.3 3.3 + - - +
716B CYS* 3.0 27.6 + - - -
740B CYS* 4.1 19.7 - - - -
744B SER* 5.6 2.0 - - - +
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Residues in contact with PHE 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711B ASP* 3.4 2.4 - - - +
712B LEU* 1.3 75.7 - - - +
714B GLY* 1.3 58.7 + - - +
716B CYS* 3.1 6.5 + - - +
717B TYR* 2.7 65.0 + + + +
741B SER* 3.7 43.5 - - - +
744B SER* 4.2 20.2 + - - +
745B ILE* 4.0 10.8 - - + -
748B GLN* 5.2 3.6 - - - +
768B THR* 3.5 46.2 - - + -
771B SER* 5.2 1.6 - - - -
772B PHE* 4.1 15.3 - + + -
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Residues in contact with GLY 714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711B ASP* 3.4 20.0 + - - -
712B LEU 3.3 1.0 - - - -
713B PHE* 1.3 81.7 - - - +
715B ASN* 1.3 61.1 + - - +
717B TYR* 3.1 7.9 + - - +
718B ARG* 3.1 27.8 + - - +
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Residues in contact with ASN 715 (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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669B PHE* 3.6 21.5 - - + -
670B ASN* 2.5 40.4 + - - +
673B VAL* 3.4 19.5 - - - +
711B ASP 3.9 9.8 + - - +
712B LEU 3.3 3.6 + - - +
713B PHE 3.2 0.4 - - - -
714B GLY* 1.3 73.4 - - - +
716B CYS* 1.3 65.6 + - - +
718B ARG* 3.1 35.2 + - - +
719B LEU* 3.2 28.6 + - - +
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Residues in contact with CYS 716 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669B PHE* 4.4 7.6 - - - -
695B LEU* 3.9 17.7 - - - -
712B LEU 3.0 21.3 + - - +
713B PHE* 3.7 3.6 - - - +
715B ASN* 1.3 78.1 - - - +
717B TYR* 1.3 61.1 + - - +
719B LEU* 3.6 5.2 + - - +
720B LEU* 3.2 28.8 + - - +
737B ALA* 3.9 12.9 - - + +
740B CYS* 3.7 36.1 - - - -
741B SER* 3.3 23.3 - - - +
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Residues in contact with TYR 717 (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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713B PHE* 2.7 42.3 + + + +
714B GLY* 3.3 11.7 - - - +
716B CYS* 1.3 71.0 - - - +
718B ARG* 1.3 64.8 + - + +
720B LEU* 3.3 6.5 + - + +
721B LYS* 2.7 68.0 + - + +
741B SER* 4.8 1.1 + - - -
771B SER* 3.7 31.9 + - - -
772B PHE* 5.6 2.0 - + - -
774B ALA* 6.0 0.2 - - - +
775B VAL* 3.6 25.6 - - + -
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Residues in contact with ARG 718 (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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673B VAL* 4.5 5.0 + - + +
674B GLU* 3.2 35.8 + - - -
677B LEU* 3.7 32.0 - - + +
714B GLY 3.1 18.4 + - - +
715B ASN* 3.1 33.9 + - - +
717B TYR* 1.3 82.0 - - + +
719B LEU* 1.3 51.6 - - + +
721B LYS* 3.7 4.2 - - - +
722B THR* 2.7 43.9 + - - +
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Residues in contact with LEU 719 (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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669B PHE* 4.2 20.2 - - + -
673B VAL* 4.0 20.9 - - + -
676B LEU* 3.8 28.3 - - + -
677B LEU* 4.7 5.4 - - + -
691B VAL* 4.1 20.9 - - + -
695B LEU* 4.2 9.0 - - + -
715B ASN 3.2 18.4 + - - +
716B CYS* 3.8 8.3 - - - +
717B TYR 3.3 0.2 - - - -
718B ARG* 1.3 78.4 - - - +
720B LEU* 1.3 58.3 + - - +
722B THR* 4.5 1.1 - - - -
723B GLY* 2.9 22.9 + - - -
729B MET* 3.3 28.4 - - + +
733B ILE* 4.2 11.0 - - + -
734B VAL* 5.4 1.0 - - - +
737B ALA* 4.6 7.0 - - + -
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Residues in contact with LEU 720 (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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716B CYS 3.2 19.5 + - - +
717B TYR* 3.9 6.7 - - + +
718B ARG 3.2 0.2 - - - -
719B LEU* 1.3 77.9 - - - +
721B LYS* 1.3 61.1 + - - +
723B GLY* 3.3 2.3 + - - -
724B ILE* 2.9 35.0 + - - +
734B VAL* 3.5 46.0 - - + +
737B ALA* 3.9 11.0 - - + +
738B LEU* 3.9 29.2 - - + +
741B SER* 4.1 7.9 - - - +
772B PHE* 4.2 4.5 - - + -
775B VAL* 3.6 31.0 - - + -
779B CYS* 4.7 4.2 - - - -
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Residues in contact with LYS 721 (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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717B TYR* 2.7 67.5 + - + +
718B ARG* 3.9 4.0 - - - +
720B LEU* 1.3 74.1 - - - +
722B THR* 1.3 58.8 + - - +
724B ILE* 3.4 11.9 + - + +
725B GLU* 3.1 31.3 + - + +
771B SER 5.6 0.2 + - - -
774B ALA* 6.1 2.0 - - - +
775B VAL* 4.6 6.8 - - + +
778B GLN* 4.5 20.5 + - - +
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Residues in contact with THR 722 (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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677B LEU* 3.6 37.2 - - + +
718B ARG* 2.7 29.3 + - - +
719B LEU 4.0 3.8 - - - -
721B LYS* 1.3 70.5 - - - +
723B GLY* 1.3 65.0 + - - +
725B GLU* 4.4 8.4 + - - +
726B HIS* 3.5 36.2 + - + +
728B ALA* 5.1 3.0 + - + +
729B MET* 4.2 6.7 - - + -
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Residues in contact with GLY 723 (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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719B LEU 2.9 19.1 + - - -
720B LEU* 3.7 2.9 - - - -
721B LYS 3.3 0.4 - - - -
722B THR* 1.3 76.5 - - - +
724B ILE* 1.3 56.5 + - - +
727B GLY* 2.9 31.1 + - - -
729B MET* 3.7 24.4 - - - +
734B VAL* 5.2 4.7 - - - -
782B ASN* 5.1 9.5 + - - -
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Residues in contact with ILE 724 (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 LEU 2.9 21.7 + - - +
721B LYS* 3.7 13.9 - - + +
722B THR 3.3 0.2 - - - -
723B GLY* 1.3 76.1 - - - +
725B GLU* 1.3 69.9 + - + +
726B HIS 3.2 2.6 + - - -
727B GLY* 4.1 2.4 + - - -
775B VAL* 4.1 26.7 - - + +
778B GLN* 3.4 60.6 - - + +
779B CYS* 4.6 11.9 - - - -
782B ASN* 6.1 3.1 - - - +
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Residues in contact with GLU 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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721B LYS* 3.1 17.7 + - + +
722B THR* 4.3 7.2 + - - +
724B ILE* 1.3 82.0 - - + +
726B HIS* 1.3 93.8 + - - +
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Residues in contact with HIS 726 (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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722B THR* 3.5 22.9 + - + +
724B ILE 3.2 2.4 - - - -
725B GLU* 1.3 119.9 + - + +
727B GLY* 1.3 60.2 + - - +
728B ALA* 3.5 14.4 - - + +
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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