Contacts of the helix formed by residues 886 - 891 (chain C) in PDB entry 7CN9
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 TRP 886 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1047B TYR* 3.1 40.2 - + + +
1107B ARG* 4.5 17.5 - - + -
1108B ASN* 4.5 4.7 - - - -
884C SER 3.4 2.2 + - - -
885C GLY* 1.3 74.6 - - - -
887C THR* 1.3 68.5 + - + +
888C PHE* 5.1 0.2 - - - -
889C GLY* 2.9 18.1 + - - +
890C ALA* 3.9 3.1 + - - +
896C ILE* 4.9 3.1 - - + +
901C GLN* 4.8 14.4 + - + -
904C TYR* 3.2 66.9 - + + -
905C ARG* 4.9 6.7 - - + +
1034C LEU 3.4 24.8 - - - +
1035C GLY* 4.3 10.9 - - - -
1036C GLN* 4.9 10.9 + - - +
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Residues in contact with THR 887 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713B ALA 4.9 2.2 - - - +
715B PRO* 6.0 0.9 - - + -
1047B TYR* 5.5 6.5 - - + +
1069B PRO* 5.4 5.2 - - + +
1108B ASN* 6.0 2.2 - - - +
884C SER* 2.5 20.7 + - - +
885C GLY 2.9 1.4 + - - -
886C TRP* 1.3 79.3 - - + +
888C PHE* 1.3 56.0 + - - +
890C ALA* 2.9 24.1 + - - +
891C GLY 3.1 8.3 + - - -
892C ALA 2.9 15.1 + - - +
894C LEU* 2.3 60.1 + - + +
896C ILE* 5.5 2.7 - - + -
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Residues in contact with PHE 888 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784C GLN 4.8 8.3 - - - +
785C VAL* 4.8 18.6 - - + +
786C LYS* 4.8 4.7 + - - +
789C TYR* 5.2 6.1 - + + +
877C LEU* 4.5 9.2 - - + -
880C GLY* 3.1 39.0 - - - -
881C THR* 3.2 23.6 - - + -
884C SER* 4.2 7.0 - - - -
885C GLY 2.9 28.7 + - - -
887C THR* 1.3 76.4 + - - +
889C GLY* 1.3 83.9 + - - +
890C ALA 2.9 2.7 + - - -
891C GLY* 3.1 23.1 + - - +
893C ALA* 4.0 16.6 - - + +
1033C VAL 5.2 0.4 - - - -
1034C LEU* 3.6 37.7 - - + -
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Residues in contact with GLY 889 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040B VAL* 5.6 7.6 - - - +
1045B LYS* 4.1 3.1 - - - +
1046B GLY* 4.0 15.1 + - - -
784C GLN 5.7 1.1 - - - -
786C LYS* 5.2 3.3 + - - -
886C TRP 2.9 12.2 + - - -
888C PHE* 1.3 83.6 - - - +
890C ALA* 1.3 57.8 + - - +
1034C LEU* 3.4 28.5 - - - -
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Residues in contact with ALA 890 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045B LYS 3.8 15.6 - - - +
1046B GLY* 3.6 18.6 - - - -
1047B TYR* 4.5 11.2 - - + +
1068B VAL* 3.9 19.7 - - + +
1069B PRO* 4.0 26.2 - - + -
786C LYS* 4.4 7.3 + - - -
886C TRP 3.9 1.7 + - - +
887C THR 2.9 10.5 + - - +
889C GLY* 1.3 79.2 - - - +
891C GLY* 1.3 55.7 + - - +
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Residues in contact with GLY 891 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068B VAL* 5.7 1.3 - - - -
786C LYS* 4.0 23.3 - - - +
787C GLN* 5.3 1.0 - - - +
789C TYR* 4.2 6.8 + - - -
887C THR 3.1 2.0 + - - -
888C PHE* 3.1 19.9 + - - +
890C ALA* 1.3 80.9 - - - +
892C ALA* 1.3 66.6 + - - -
893C ALA 3.0 4.0 + - - -
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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