Contacts of the helix formed by residues 825 - 835 (chain B) in PDB entry 1QCO
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 825 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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776B ASN* 3.5 36.8 - - + +
777B PRO* 5.0 4.5 - - + -
793B TYR* 4.1 15.7 - - + +
794B THR* 4.0 9.9 - - - +
822B MET* 5.9 1.1 - - - +
823B TYR 5.1 1.3 - - - +
824B TRP* 1.3 77.4 - - - +
826B MET* 1.3 59.9 + - - +
827B LEU* 3.4 10.4 + - - +
828B GLN* 3.1 35.9 + - - +
829B GLN* 3.0 28.8 + - - +
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Residues in contact with MET 826 (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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704B PHE* 3.5 42.6 - - + -
725B ILE* 4.1 12.3 - - + +
728B MET* 3.7 23.8 - - - +
766B MET* 3.9 14.4 - - + -
793B TYR* 3.9 13.1 + - + +
795B PHE* 3.5 37.5 - - + -
819B PHE* 3.8 23.8 - - + -
825B THR* 1.3 74.5 - - - +
827B LEU* 1.3 56.7 + - - +
829B GLN* 3.5 14.1 - - - +
830B LEU* 2.9 31.7 + - - +
848B SER* 6.4 0.2 - - - -
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Residues in contact with LEU 827 (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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718B ILE* 4.3 12.6 - - + +
721B ALA* 3.9 10.3 - - + +
722B HIS* 3.6 35.9 - - + +
725B ILE* 3.8 6.7 - - + -
789B HIS* 4.1 15.7 - - + -
791B GLN* 3.8 27.8 - - - +
793B TYR* 3.6 45.3 - - + -
825B THR* 3.1 7.1 - - - +
826B MET* 1.3 77.6 - - - +
828B GLN* 1.3 57.3 + - - +
830B LEU* 3.4 1.6 + - - +
831B THR* 2.9 35.2 + - - -
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Residues in contact with GLN 828 (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 PRO* 4.0 2.4 - - + +
718B ILE* 4.0 9.0 - - + -
779B GLN* 3.0 38.8 + - - +
783B PRO* 4.1 2.8 - - - +
787B LEU* 2.8 44.6 + - + +
788B CYS* 5.1 0.2 - - - +
789B HIS* 5.5 1.0 - - + +
824B TRP* 3.3 23.5 - - + -
825B THR* 3.1 39.1 + - - +
827B LEU* 1.3 78.7 - - + +
829B GLN* 1.3 56.3 + - - +
832B HIS* 2.9 33.8 + - - +
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Residues in contact with GLN 829 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627B PHE* 3.5 47.3 - - + +
629B SER* 3.0 30.5 + - - +
656B PRO* 4.3 9.0 - - + -
704B PHE* 3.8 15.0 - - + -
822B MET* 5.1 0.8 - - - +
824B TRP* 4.2 5.0 + - + -
825B THR 3.0 16.6 + - - +
826B MET* 3.5 23.9 - - - +
828B GLN* 1.3 77.1 - - - +
830B LEU* 1.3 56.3 + - - +
832B HIS* 3.9 0.9 - - - +
833B HIS* 3.0 30.4 + - - +
846B LEU* 4.5 0.9 - - - -
847B ALA 4.9 0.3 - - - +
848B SER* 3.5 27.0 + - - +
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Residues in contact with LEU 830 (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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704B PHE* 3.9 23.6 - - + -
706B VAL* 4.0 15.0 - - + -
716B ILE* 4.2 10.8 - - + -
721B ALA* 3.5 36.8 - - + +
724B HIS* 3.8 19.7 - - + +
725B ILE* 4.4 6.7 - - + -
826B MET 2.9 17.2 + - - +
827B LEU 4.0 2.7 - - - +
829B GLN* 1.3 73.6 - - - +
831B THR* 1.3 64.6 + - - +
833B HIS* 3.3 3.1 + - - +
834B SER* 3.2 23.7 + - - -
840B LEU* 3.3 25.9 - - + +
846B LEU* 4.0 9.6 - - + +
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Residues in contact with THR 831 (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 ILE* 3.6 22.2 + - - +
717B PRO* 5.1 0.2 - - + -
718B ILE* 3.2 32.0 + - + +
721B ALA* 3.7 6.8 - - - +
786B TYR* 3.5 36.6 - - + +
787B LEU* 4.5 1.6 - - + -
827B LEU 2.9 19.3 + - - -
828B GLN* 3.9 3.1 - - - -
830B LEU* 1.3 76.8 - - - +
832B HIS* 1.3 62.3 + - - +
834B SER* 3.2 5.4 + - - -
835B VAL* 3.0 23.1 + - + +
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Residues in contact with HIS 832 (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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179A GLN* 5.3 4.0 - - + -
243A GLU* 5.2 3.0 + - + +
250A PHE* 4.4 13.1 - + - -
251A LEU* 3.3 36.8 - - + +
627B PHE* 4.9 1.3 - + - -
655B LEU* 3.8 31.4 - - + +
656B PRO* 3.6 40.3 + - + +
786B TYR* 2.8 36.0 + - - -
787B LEU* 4.0 4.7 - - + +
828B GLN 2.9 19.7 + - - +
829B GLN 3.9 1.6 - - - +
831B THR* 1.3 76.6 - - - +
833B HIS* 1.3 64.0 + - - +
834B SER 3.2 1.0 + - - -
835B VAL* 3.2 19.9 + - + +
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Residues in contact with HIS 833 (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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162A ARG* 3.6 26.3 + - - -
250A PHE* 4.0 20.2 - + - -
251A LEU* 3.7 14.8 - - + +
254A SER* 5.3 0.4 - - - -
625B THR* 2.7 42.2 + - + +
627B PHE* 4.1 3.3 - + + -
660B HIS* 4.9 2.5 - + - -
829B GLN 3.0 19.9 + - - +
830B LEU* 3.6 8.1 - - - +
831B THR 3.2 0.4 - - - -
832B HIS* 1.3 78.3 - - - +
834B SER* 1.3 56.9 + - - +
838B CYS* 3.5 28.8 - - - +
840B LEU* 3.9 13.8 - - + +
846B LEU* 3.8 21.7 - - + +
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Residues in contact with SER 834 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710B ASN* 3.8 13.0 - - - -
715B PRO* 3.3 11.8 - - - +
716B ILE* 3.1 32.4 + - - +
830B LEU 3.2 15.1 + - - -
831B THR 3.2 4.8 + - - -
832B HIS 3.1 0.2 - - - -
833B HIS* 1.3 75.7 - - - +
835B VAL* 1.3 58.9 + - - +
836B ASN* 3.2 3.6 - - - -
837B GLY* 2.8 21.2 + - - -
838B CYS 3.7 19.3 - - - -
840B LEU* 4.2 8.1 - - - -
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Residues in contact with VAL 835 (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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177A MET* 3.4 22.4 + - - +
178A GLY* 4.4 6.5 - - - -
190A TYR* 3.7 35.4 - - + +
251A LEU* 3.7 15.7 - - + -
715B PRO* 3.7 22.4 - - + +
786B TYR* 3.8 26.2 - - + +
831B THR* 3.0 14.5 + - + +
832B HIS* 3.2 18.3 + - + +
834B SER* 1.3 76.3 - - - +
836B ASN* 1.3 61.3 + - - +
837B GLY 3.2 1.3 + - - -
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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