Contacts of the helix formed by residues 871 - 882 (chain B) in PDB entry 1QHA
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 PHE 871 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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678B VAL* 3.5 37.7 - - + -
745B ILE* 4.1 6.3 - - + -
750B LEU* 5.4 1.1 - - + -
827B SER* 4.1 9.6 - - - +
830B ALA* 3.7 13.7 - - + -
831B ALA* 3.4 37.6 - - + +
834B CYS* 3.9 21.5 - - + -
864B LEU* 4.3 14.4 - - + +
865B TYR* 4.1 21.8 - + - -
868B HIS* 3.1 32.4 + + + +
869B PRO 4.0 0.2 - - - -
870B HIS* 1.3 74.5 - - - +
872B SER* 1.3 69.8 + - - +
874B ILE* 4.9 1.3 - - - -
875B MET* 3.0 35.8 + - + +
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Residues in contact with SER 872 (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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865B TYR* 3.5 51.6 + - - -
868B HIS 4.9 6.1 + - - -
869B PRO 5.8 0.7 - - - -
870B HIS 3.4 0.7 - - - -
871B PHE* 1.3 83.2 - - - +
873B ARG* 1.3 58.1 + - - +
875B MET* 4.5 1.3 - - - -
876B HIS* 2.9 42.9 + - - -
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Residues in contact with ARG 873 (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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828B ARG* 4.4 11.1 - - - +
869B PRO 5.0 4.0 + - - +
870B HIS* 2.7 54.2 + - - +
871B PHE 3.3 0.6 - - - -
872B SER* 1.3 79.1 + - - +
874B ILE* 1.3 77.1 + - - +
876B HIS* 3.4 7.5 + - - +
877B GLN* 2.9 51.4 + - - +
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Residues in contact with ILE 874 (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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827B SER* 5.7 0.9 - - - +
828B ARG* 3.5 55.2 - - + +
831B ALA* 3.7 17.5 - - + -
832B GLN* 4.0 23.1 - - + +
870B HIS* 3.1 33.8 + - + +
871B PHE 5.0 0.7 - - - +
873B ARG* 1.3 92.8 - - - +
875B MET* 1.3 54.6 + - - +
877B GLN* 3.2 14.3 + - - +
878B THR* 2.7 35.6 + - - +
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Residues in contact with MET 875 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676B LEU* 4.1 15.7 - - + -
831B ALA* 3.5 26.4 - - + +
834B CYS* 4.1 13.7 - - + +
835B GLY* 3.7 11.7 - - - +
838B MET* 5.0 2.5 - - - -
865B TYR* 3.5 27.8 - - + -
871B PHE* 3.0 22.9 + - + +
872B SER 3.9 0.7 - - - +
874B ILE* 1.3 74.6 - - - +
876B HIS* 1.3 88.6 + - + +
878B THR* 2.9 12.1 + - - -
879B VAL* 3.1 25.6 + - - +
890B PHE* 3.5 27.6 - - + -
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Residues in contact with HIS 876 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865B TYR* 2.8 29.2 + - - -
872B SER* 2.9 43.1 + - - +
873B ARG* 4.0 6.3 + - - +
875B MET* 1.3 84.5 - - + +
877B GLN* 1.3 65.1 + - - +
878B THR 3.2 0.2 + - - -
879B VAL* 3.4 2.4 + - - +
880B LYS* 3.0 34.0 + - - +
890B PHE* 3.4 44.9 - + + -
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Residues in contact with GLN 877 (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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828B ARG* 4.9 6.5 - - - +
873B ARG* 2.9 39.7 + - - +
874B ILE* 3.4 27.5 + - - +
876B HIS* 1.3 80.3 - - - +
878B THR* 1.3 61.3 + - - +
880B LYS* 3.4 10.6 + - - +
881B GLU* 3.1 34.7 + - - +
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Residues in contact with THR 878 (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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484B LEU* 4.1 13.7 - - + -
832B GLN* 3.8 37.0 - - - +
835B GLY* 4.0 10.8 - - - -
874B ILE* 2.7 26.4 + - - +
875B MET* 2.9 7.8 + - - -
877B GLN* 1.3 69.0 - - - +
879B VAL* 1.3 65.6 + - - +
881B GLU* 3.0 21.5 + - - +
882B LEU* 3.0 48.0 + - + +
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Residues in contact with VAL 879 (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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835B GLY* 3.6 29.6 - - - +
838B MET* 4.0 21.3 - - + -
839B ALA* 4.3 5.8 - - - +
842B VAL* 4.6 8.7 - - + -
875B MET* 3.1 24.4 + - - +
876B HIS* 3.7 6.1 - - - +
878B THR* 1.3 74.6 - - - +
880B LYS* 1.3 58.3 + - - +
883B SER* 2.9 31.3 + - - +
886B CYS 5.5 0.6 - - - +
888B VAL* 3.9 36.6 - - + -
890B PHE* 4.2 4.3 - - + -
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Residues in contact with LYS 880 (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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876B HIS* 3.0 25.4 + - - +
877B GLN* 3.6 9.4 - - - +
879B VAL* 1.3 81.8 - - - +
881B GLU* 1.3 60.2 + - + +
883B SER 5.0 2.2 - - - -
884B PRO* 3.6 21.7 - - - +
886B CYS 5.6 3.6 - - - -
887B ASN* 5.4 8.0 - - - +
888B VAL 5.5 3.8 + - - -
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Residues in contact with GLU 881 (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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481B LYS* 4.0 36.6 + - + +
484B LEU* 4.6 13.9 - - - +
832B GLN* 5.4 2.9 + - - -
877B GLN* 3.1 24.7 + - - +
878B THR* 3.0 17.4 + - - +
880B LYS* 1.3 76.7 - - + +
882B LEU* 1.3 71.6 + - + +
884B PRO* 3.5 14.2 - - - +
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Residues in contact with LEU 882 (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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481B LYS* 4.3 10.1 - - + +
484B LEU* 3.9 26.5 - - + +
485B LEU* 3.4 39.6 - - + +
488B LYS* 3.0 21.7 + - + -
835B GLY 4.3 0.9 - - - +
836B ALA* 3.8 24.9 - - + +
839B ALA* 4.0 11.4 - - + -
878B THR* 3.0 39.6 + - + +
881B GLU* 1.3 86.5 - - + +
883B SER* 1.4 60.0 + - - +
884B PRO* 3.1 12.5 - - - +
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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