Contacts of the helix formed by residues 84 - 89 (chain F) in PDB entry 2WJZ
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 CYS 84 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50F GLY 3.1 13.0 - - - +
51F VAL* 4.7 2.2 - - + -
83F VAL* 1.3 75.7 - - + +
85F LEU* 1.3 71.7 + - - +
87F MET* 2.8 21.3 + - - +
88F GLN* 3.5 2.9 + - - +
140F VAL 5.9 0.9 - - - +
175F PHE 2.8 17.2 + - - -
176F GLN* 3.9 24.9 + - - +
177F PHE 3.6 14.1 - - - -
178F HIS* 3.0 49.8 - - + +
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Residues in contact with LEU 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F PRO* 6.2 2.2 - - + -
49F PRO 5.0 0.2 - - - +
50F GLY* 3.1 24.6 + - - +
51F VAL* 4.1 6.5 - - - +
52F GLY 4.4 13.5 - - - +
53F HIS 6.1 1.8 - - - +
54F PHE* 6.2 1.1 - - - +
84F CYS* 1.3 78.4 - - - +
86F GLY* 1.3 64.0 + - - +
88F GLN* 2.9 27.9 + - - +
89F LEU* 3.0 27.6 + - + +
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Residues in contact with GLY 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F ILE* 3.2 33.5 - - - +
49F PRO 3.8 9.9 + - - -
82F GLY* 3.7 8.8 - - - -
83F VAL 3.0 4.8 + - - -
84F CYS 3.0 1.6 - - - -
85F LEU* 1.3 79.9 - - - +
87F MET* 1.3 60.4 + - - +
89F LEU* 3.4 17.2 + - - +
90F LEU* 3.6 12.8 - - - +
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Residues in contact with MET 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F GLY 3.7 19.0 - - - +
84F CYS 2.8 18.9 + - - +
86F GLY* 1.3 68.4 - - - -
88F GLN* 1.3 65.8 + - - +
90F LEU* 3.1 29.4 + - + +
91F PHE* 3.5 9.7 - - + -
145F ALA* 3.8 23.6 - - + -
164F PRO 3.4 25.8 - - - +
165F SER 4.3 0.7 - - - +
166F ALA 4.6 0.9 - - - +
167F VAL* 3.9 20.9 - - + -
174F GLY* 3.5 30.5 - - - +
175F PHE 4.0 4.3 - - - +
176F GLN* 3.6 30.1 - - - +
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Residues in contact with GLN 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F GLY 5.4 1.2 - - - +
54F PHE* 3.1 26.7 - - + +
84F CYS 3.5 2.9 + - - +
85F LEU* 2.9 19.4 + - - +
87F MET* 1.3 78.0 - - + +
89F LEU* 1.3 61.6 + - - +
91F PHE* 3.2 21.3 + - - +
94F SER* 4.9 0.2 + - - -
96F GLU* 4.1 14.7 - - - +
110F VAL* 3.7 32.2 - - + +
141F HIS* 4.8 2.8 + - - +
143F TYR* 2.8 41.5 + - - +
144F ARG 5.4 2.0 - - - -
145F ALA* 5.5 2.0 - - + +
176F GLN* 3.7 23.4 + - - +
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Residues in contact with LEU 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F ILE* 4.7 11.0 - - + -
49F PRO 5.1 3.1 - - - +
54F PHE* 3.6 38.1 - - + +
56F GLU 5.4 0.9 - - - +
57F GLY* 4.5 22.4 - - - +
58F MET* 3.8 20.0 - - + +
85F LEU* 3.0 24.4 + - + +
86F GLY* 3.6 18.2 - - - +
87F MET 3.1 0.4 - - - -
88F GLN* 1.3 74.2 - - + +
90F LEU* 1.3 56.1 + - - +
91F PHE 3.0 5.8 + - - -
103F LEU* 2.8 49.1 + - + +
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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