Contacts of the helix formed by residues 85 - 92 (chain C) in PDB entry 3P8Z
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 GLY 85 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C VAL* 3.7 4.9 - - - -
82C CYS* 2.9 16.7 + - - -
83C GLY 3.1 0.6 - - - -
84C ARG* 1.3 78.3 - - - +
86C GLY* 1.3 67.1 + - - +
87C TRP 3.3 2.9 - - - -
88C SER* 3.1 8.9 + - - -
89C TYR* 2.9 28.2 + - - -
126C LEU* 4.0 17.0 - - - -
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Residues in contact with GLY 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C VAL* 3.3 11.6 - - - +
56C SER* 3.6 10.3 - - - -
59C SER* 2.6 31.1 + - - -
85C GLY* 1.3 76.1 - - - +
87C TRP* 1.3 62.6 + - - +
89C TYR* 5.1 0.9 - - - -
90C TYR* 3.3 15.2 + - - +
263C SAH 3.1 22.0 + - - -
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Residues in contact with TRP 87 (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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58C GLY* 3.1 30.8 + - - -
61C LYS* 4.6 6.5 - - + +
62C LEU* 3.7 33.2 - - + +
65C PHE* 5.2 2.5 - + - -
79C ASP* 3.5 21.5 + - - +
85C GLY 3.3 0.2 - - - -
86C GLY* 1.3 72.7 - - - +
88C SER* 1.3 65.9 + - - +
90C TYR* 3.7 1.7 - - - +
91C CYS* 2.9 30.0 + - - -
144C LEU* 3.7 25.1 - - + -
145C CYS 3.9 19.7 - - - -
146C ASP* 3.5 26.1 + - + -
178C CYS* 3.9 22.2 - - - -
218C TYR* 3.5 34.1 - + - -
263C SAH 3.1 27.5 + - - +
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Residues in contact with SER 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ASP* 2.6 34.1 + - - +
85C GLY* 3.1 8.3 + - - -
87C TRP* 1.3 80.2 - - - +
89C TYR* 1.3 57.3 + - - +
91C CYS* 3.4 1.9 + - - +
92C ALA* 3.0 28.1 + - - +
100C VAL* 3.4 27.9 - - - +
102C GLY* 4.0 1.2 - - - -
124C VAL* 4.0 4.9 - - - +
126C LEU* 3.6 28.7 - - - +
144C LEU* 5.9 0.2 - - - -
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Residues in contact with TYR 89 (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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55C VAL* 4.1 14.1 - - + +
84C ARG 3.9 5.6 - - - -
85C GLY 2.9 26.8 + - - +
86C GLY* 4.5 2.0 - - - +
88C SER* 1.3 73.0 - - - +
90C TYR* 1.3 66.9 + - - +
92C ALA* 3.4 14.0 + - + +
93C GLY* 3.8 3.6 + - - -
114C VAL 2.6 30.9 + - - -
115C PRO* 3.4 4.7 - - - +
116C MET* 3.1 35.8 + - + -
118C THR* 3.7 24.4 + - - +
119C TYR 4.5 4.7 - - - +
121C TRP* 4.6 9.6 - - + -
124C VAL* 4.3 24.2 - - + +
126C LEU* 3.6 24.3 - - + +
257C LEU* 4.2 18.6 - - + +
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Residues in contact with TYR 90 (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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59C SER* 4.1 20.2 - - - -
62C LEU* 3.9 19.1 - - + -
63C GLN* 3.6 48.5 + - + +
66C VAL* 3.5 36.0 - - + +
67C GLU* 4.8 1.6 + - - +
86C GLY 3.3 19.4 + - - +
87C TRP* 3.7 4.0 - - - +
88C SER 3.3 0.2 - - - -
89C TYR* 1.3 78.2 - - - +
91C CYS* 1.3 65.9 + - - +
92C ALA 3.2 0.5 + - - -
93C GLY* 3.2 12.5 + - - -
94C LEU* 3.8 31.2 - - + +
255C VAL* 5.2 0.9 - - + -
257C LEU* 3.9 26.6 - - + +
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Residues in contact with CYS 91 (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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62C LEU* 3.8 12.6 - - - -
73C PRO* 3.9 23.3 - - - -
77C VAL* 4.4 5.6 - - + -
87C TRP 2.9 21.8 + - - +
88C SER* 3.8 3.6 - - - +
90C TYR* 1.3 78.4 - - - +
92C ALA* 1.3 63.9 + - - +
93C GLY 3.1 1.2 + - - -
94C LEU* 3.1 18.8 + - - +
97C VAL* 3.4 26.6 - - + +
100C VAL* 4.1 12.6 - - + -
144C LEU* 3.7 26.9 - - - -
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Residues in contact with ALA 92 (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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88C SER 3.0 10.0 + - - +
89C TYR* 3.7 9.6 - - + +
90C TYR 3.2 0.8 - - - -
91C CYS* 1.3 75.5 - - - +
93C GLY* 1.3 56.1 + - - +
94C LEU 3.4 0.2 - - - -
100C VAL* 4.1 7.8 - - - +
119C TYR 3.9 2.9 - - - +
120C GLY* 3.4 18.5 - - - +
121C TRP* 4.5 0.7 - - - +
123C ILE* 3.9 7.2 - - + +
124C VAL* 3.2 35.7 - - + -
262C ARG* 2.9 30.0 + - - -
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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