Contacts of the helix formed by residues 157 - 166 (chain C) in PDB entry 1Z83
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 157 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C VAL* 4.1 17.7 - - + +
15C GLY 5.6 0.2 - - - +
96C PRO 4.1 4.9 - - - +
97C ARG* 2.8 61.7 + - - +
152C THR 4.0 1.2 + - - -
153C TYR* 3.0 33.1 + - + -
156C ALA* 1.3 75.2 - - - +
158C GLU* 1.3 68.4 + - - +
159C PRO* 3.2 2.0 - - - -
160C VAL* 2.8 23.7 + - + +
161C ILE* 3.9 3.1 + - - +
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Residues in contact with GLU 158 (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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117C TYR* 4.2 16.3 + - - +
153C TYR* 3.0 28.4 + - + +
154C TYR* 3.5 45.3 - - - +
157C THR* 1.3 74.3 - - - +
159C PRO* 1.4 61.6 - - + +
161C ILE* 2.9 37.3 + - + +
162C ALA* 3.8 2.6 + - - +
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Residues in contact with PRO 159 (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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99C VAL* 4.1 13.7 - - + +
154C TYR 4.0 4.7 - - - +
155C LYS 3.6 18.8 - - - +
156C ALA 3.6 13.7 - - - +
157C THR 3.4 3.8 - - - -
158C GLU* 1.4 93.4 - - + +
160C VAL* 1.3 59.5 + - - +
161C ILE 3.2 0.2 - - - -
162C ALA* 3.5 10.1 + - + +
163C PHE* 3.2 22.0 + - - +
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Residues in contact with VAL 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C VAL* 4.9 7.9 - - + -
96C PRO* 4.0 22.2 - - + +
97C ARG 4.2 1.1 - - - -
98C GLU* 3.5 44.2 - - - +
99C VAL* 3.7 6.3 - - - +
115C LEU* 4.4 9.6 - - + +
156C ALA 4.2 1.6 - - - +
157C THR* 2.8 21.7 + - + +
159C PRO* 1.3 69.7 - - - +
161C ILE* 1.3 64.5 + - - +
163C PHE* 3.3 7.2 + - - +
164C TYR* 3.1 46.9 + - + -
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Residues in contact with ILE 161 (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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14C VAL* 3.7 32.8 - - + -
115C LEU* 4.0 13.5 - - + -
117C TYR* 3.9 53.2 - - + -
153C TYR* 5.1 1.1 - - - +
157C THR 4.6 0.2 - - - +
158C GLU* 2.9 25.7 + - + +
160C VAL* 1.3 77.7 - - - +
162C ALA* 1.3 57.7 + - - +
164C TYR 3.1 2.8 + - - -
165C GLU* 2.9 50.7 + - + +
170C VAL* 4.1 7.7 - - + +
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Residues in contact with ALA 162 (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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158C GLU 3.8 2.1 + - - +
159C PRO* 3.5 13.2 + - + +
160C VAL 3.4 0.4 - - - -
161C ILE* 1.3 80.4 - - - +
163C PHE* 1.3 63.4 + - - +
164C TYR 3.4 0.3 + - - -
165C GLU* 3.6 19.6 + - - +
166C LYS* 3.7 23.1 + - - +
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Residues in contact with PHE 163 (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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166B LYS* 6.4 0.9 - - + -
99C VAL* 3.3 42.4 - - + -
103C GLU* 3.9 24.0 - - + -
106C GLU* 4.6 1.6 - - - -
159C PRO 3.2 12.7 + - - +
160C VAL* 3.3 12.1 - - - +
162C ALA* 1.3 82.5 - - - +
164C TYR* 1.3 97.7 + + - +
166C LYS* 3.8 24.8 - - + +
167C ARG* 4.2 18.8 + - - +
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Residues in contact with TYR 164 (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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12C PHE* 3.6 20.1 - + - -
96C PRO* 4.5 3.4 - - + -
99C VAL* 6.3 0.7 - - - -
102C GLY* 3.4 23.9 + - - -
106C GLU* 2.8 29.0 + - - -
112C PRO* 3.7 11.9 - - + -
115C LEU* 3.8 23.8 - - + -
160C VAL* 3.1 41.3 + - + +
161C ILE 4.2 1.1 - - - +
163C PHE* 1.3 92.7 - + - +
165C GLU* 1.3 65.0 + - - +
166C LYS 3.2 2.2 - - - -
167C ARG* 3.0 44.7 + - - +
168C GLY 3.8 0.9 + - - -
169C ILE* 3.7 30.4 + - + +
170C VAL* 3.9 3.8 - - + -
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Residues in contact with GLU 165 (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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50A GLY 4.7 0.7 - - - +
51A SER* 3.4 17.8 - - - -
52A ALA* 3.2 45.2 + - - +
53A ARG 4.7 0.7 + - - -
117C TYR* 5.8 1.6 - - - -
161C ILE* 2.9 33.5 + - + +
162C ALA* 3.6 12.8 + - - +
164C TYR* 1.3 75.5 - - - +
166C LYS* 1.3 64.2 - - - +
168C GLY* 2.9 16.2 + - - +
170C VAL* 3.6 28.6 - - + +
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Residues in contact with LYS 166 (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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103B GLU* 4.0 29.4 + - + +
106B GLU* 4.3 3.9 - - - +
107B ARG* 4.2 21.8 + - - +
167B ARG* 6.3 0.2 - - - +
162C ALA* 3.7 19.0 + - - +
163C PHE* 3.8 21.8 - - + +
165C GLU* 1.3 78.2 - - - +
167C ARG* 1.3 61.9 + - + +
168C GLY 3.3 1.1 + - - -
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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