Contacts of the strand formed by residues 81 - 86 (chain C) in PDB entry 6DWM
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 81 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C ARG* 3.5 2.8 - - - -
78C ILE 3.1 34.2 + - - -
79C GLY 3.5 0.2 - - - -
80C SER* 1.3 82.1 + - - +
82C PRO* 1.3 78.3 - - + +
83C VAL* 3.8 2.8 + - + +
236C PHE* 3.7 34.5 + - + +
406C CYS* 5.2 5.6 - - + -
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Residues in contact with PRO 82 (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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75C GLN* 3.8 16.8 - - - +
76C ILE 3.5 7.4 - - - +
77C ARG* 4.4 11.0 - - + -
80C SER 3.6 8.7 - - - +
81C THR* 1.3 96.1 - - + +
83C VAL* 1.3 65.7 + - - +
405C ARG* 3.8 46.6 + - - +
406C CYS* 4.2 5.5 + - - +
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Residues in contact with VAL 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C GLN* 3.6 3.5 - - - +
76C ILE* 3.0 46.5 + - + +
78C ILE* 4.3 12.8 - - + -
81C THR 4.0 8.5 - - - +
82C PRO* 1.3 81.4 - - - +
84C VAL* 1.3 69.2 + - - +
85C VAL* 4.1 4.2 + - + -
236C PHE* 4.2 24.7 - - + -
405C ARG* 4.5 0.2 - - - +
406C CYS* 3.6 18.8 - - + +
408C PHE* 3.7 40.6 - - + -
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Residues in contact with VAL 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C PRO* 4.8 12.8 - - + -
73C VAL* 4.2 13.2 - - + -
74C LEU 3.5 13.0 - - - +
75C GLN* 4.8 7.2 - - + -
83C VAL* 1.3 76.8 - - - +
85C VAL* 1.3 59.8 + - - +
86C LEU* 3.9 23.8 - - + -
401C ILE* 4.4 19.3 - - + -
405C ARG* 3.7 28.3 - - + +
406C CYS 3.1 9.1 + - - +
407C VAL* 3.3 11.3 - - + +
408C PHE* 2.8 31.5 + - - +
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Residues in contact with VAL 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C LEU* 3.8 44.9 - - + +
72C ASP 3.3 10.9 - - - +
73C VAL* 3.9 1.0 - - - -
74C LEU* 3.1 47.9 + - + +
76C ILE* 4.1 17.5 - - + -
83C VAL* 4.6 0.4 - - + -
84C VAL* 1.3 76.1 - - - +
86C LEU* 1.3 69.6 + - - +
87C SER* 4.4 9.7 + - - +
408C PHE* 3.4 20.4 - - + +
410C ASN* 4.5 8.3 - - + -
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Residues in contact with LEU 86 (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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72C ASP 3.4 2.0 - - - +
73C VAL* 4.2 12.8 - - + -
84C VAL* 3.9 21.3 - - + -
85C VAL* 1.3 71.9 - - - +
87C SER* 1.3 64.1 + - - +
91C THR* 5.1 2.2 - - + -
92C ILE* 3.7 21.8 - - + +
95C ALA* 3.9 26.2 - - + -
96C LEU* 5.4 3.4 - - + -
103C PHE* 4.8 5.8 - - + -
396C LEU* 3.8 22.9 - - + -
401C ILE* 5.5 1.3 - - + -
407C VAL* 3.7 27.6 - - + -
408C PHE 2.9 10.1 + - - +
409C VAL* 4.5 12.1 - - + -
410C ASN* 3.1 27.2 + - - +
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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
------------------------------------------------------------
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