Contacts of the helix formed by residues 939 - 946 (chain B) in PDB entry 3P23
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 HIS 939 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797B PRO 3.3 25.4 + - - -
798B GLU* 4.0 13.1 - - + +
803B VAL* 4.2 21.8 - - + +
807B GLU* 5.1 4.4 + - - -
868B ALA 5.5 7.0 - - - -
869B VAL* 3.9 25.9 + - + +
937B PHE 3.1 1.2 - - - -
938B PRO* 1.3 91.1 - - + +
940B LEU* 1.3 58.5 + - - +
941B LEU 3.5 0.9 - - - -
942B ALA* 4.2 1.8 - - + +
943B HIS* 2.8 37.3 + - + +
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Residues in contact with LEU 940 (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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800B HIS* 6.0 0.2 - - - +
842B PHE* 4.0 20.2 - - + -
869B VAL* 3.8 13.3 - - + +
897B VAL* 4.3 13.9 - - + -
900B LEU* 4.2 21.8 - - + -
901B LEU* 3.7 16.4 - - + -
904B MET* 4.1 20.6 - - + -
933B PHE* 4.6 9.9 - - + +
934B THR* 5.9 1.3 - - - -
937B PHE* 3.0 30.4 + - + +
938B PRO 3.3 0.4 - - - -
939B HIS* 1.3 78.8 - - - +
941B LEU* 1.3 58.4 + - - +
943B HIS* 3.6 1.0 - - - +
944B THR* 2.8 49.4 + - - +
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Residues in contact with LEU 941 (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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800B HIS* 3.1 41.8 + - + +
804B ILE* 3.7 15.5 - - + -
830B PRO* 4.3 11.9 - - + +
833B TRP* 4.1 11.0 - - + -
838B GLN* 3.7 28.7 - - + +
841B PHE* 3.9 29.2 - - + -
842B PHE* 3.8 21.2 - - + -
939B HIS 3.5 0.2 - - - -
940B LEU* 1.3 77.4 - - - +
942B ALA* 1.3 56.7 + - - +
944B THR* 3.1 1.6 + - - -
945B TYR* 2.8 36.1 + - + +
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Residues in contact with ALA 942 (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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803B VAL* 3.6 23.1 - - + +
804B ILE* 3.8 17.1 - - + +
807B GLU* 3.5 32.1 - - + +
938B PRO 5.1 1.4 + - - +
939B HIS* 3.7 5.5 + - + +
940B LEU 3.4 0.2 - - - -
941B LEU* 1.3 80.5 - - - +
943B HIS* 1.3 65.5 + - - +
945B TYR* 3.2 4.6 + - - +
946B ARG* 3.1 25.2 + - - +
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Residues in contact with HIS 943 (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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807B GLU* 5.0 0.8 + - - -
861B GLN 4.4 3.8 - - - -
862B LEU* 2.9 34.4 + - + -
865B GLY* 3.3 41.0 - - - -
866B GLY 4.2 3.4 + - - -
869B VAL* 3.8 20.3 - - + +
897B VAL* 4.3 17.3 - - + -
939B HIS* 2.8 25.2 + - + +
940B LEU 3.6 2.9 - - - +
942B ALA* 1.3 72.7 - - - +
944B THR* 1.3 57.6 + - - +
946B ARG* 2.4 43.7 - - - +
947B ALA* 3.7 4.9 - - + +
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Residues in contact with THR 944 (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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841B PHE* 3.5 24.5 - - + -
842B PHE* 4.6 6.1 - - + -
845B VAL* 4.1 24.2 - - + -
862B LEU* 5.7 5.8 - - + +
897B VAL* 4.5 1.4 - - - +
901B LEU* 4.2 12.8 - - + +
940B LEU* 2.8 36.8 + - - +
941B LEU* 3.6 4.7 - - - -
943B HIS* 1.3 80.2 - - - +
945B TYR* 1.3 57.1 + - - +
946B ARG 2.5 18.8 - - - +
947B ALA* 4.2 1.7 - - - +
948B MET* 3.0 24.3 + - + +
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Residues in contact with TYR 945 (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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825B HIS 5.2 1.2 + - - -
828B LYS* 3.3 9.9 + - - +
829B HIS* 4.1 15.8 - + - -
830B PRO* 3.5 31.4 - - + -
833B TRP* 3.6 25.1 - + - -
841B PHE* 3.9 10.7 - + + -
941B LEU* 2.8 20.7 + - + +
942B ALA* 3.7 5.8 - - - +
944B THR* 1.3 73.7 - - - +
946B ARG* 1.3 65.5 + - + +
948B MET 3.3 3.1 + - - -
949B GLU* 3.5 11.3 + - - +
960B TYR 2.5 30.6 + - - -
961B TYR* 2.5 65.1 + + - -
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Residues in contact with ARG 946 (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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807B GLU* 3.0 45.7 + - - +
810B GLU* 5.3 4.6 + - - -
811B LYS* 5.8 5.5 - - - +
942B ALA 3.1 8.7 + - - +
943B HIS* 2.4 48.6 - - - +
944B THR 2.5 16.1 - - - +
945B TYR* 1.3 82.2 - - + +
947B ALA* 1.3 59.6 + - + +
949B GLU* 4.3 15.5 + - - +
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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