Contacts of the helix formed by residues 157 - 166 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B VAL* 4.0 16.6 - - + +
15B GLY 5.5 0.4 - - - +
96B PRO 4.3 4.9 - - - +
97B ARG* 2.7 58.7 + - - +
152B THR 4.3 0.7 + - - -
153B TYR* 2.9 36.8 + - + -
156B ALA* 1.3 75.7 - - - +
158B GLU* 1.3 66.4 + - - +
159B PRO 3.2 2.0 - - - -
160B VAL* 2.8 24.6 + - + +
161B ILE* 4.0 2.3 + - - +
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Residues in contact with GLU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B TYR* 3.1 25.3 + - - +
119B ASP* 5.2 1.6 - - - +
153B TYR* 3.0 34.7 + - + +
154B TYR* 3.5 37.1 - - - +
157B THR* 1.3 73.6 - - - +
159B PRO* 1.3 68.9 - - + +
161B ILE* 3.1 30.7 + - + +
162B ALA* 3.9 2.3 + - - +
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Residues in contact with PRO 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 4.3 11.5 - - + +
154B TYR 3.9 6.1 - - - +
155B LYS 3.6 18.4 - - - +
156B ALA 3.6 14.6 - - - +
157B THR 3.3 3.8 - - - +
158B GLU* 1.3 89.8 - - + +
160B VAL* 1.3 63.6 + - - +
161B ILE 3.1 0.4 + - - -
162B ALA* 3.4 9.2 + - + +
163B PHE* 3.2 21.5 + - - +
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Residues in contact with VAL 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B VAL* 4.7 8.1 - - + -
96B PRO* 4.0 23.6 - - + +
97B ARG 4.2 1.1 - - - -
98B GLU* 3.6 43.5 - - - +
99B VAL* 3.9 5.8 - - - +
115B LEU* 4.2 11.2 - - + -
156B ALA 4.3 1.1 - - - +
157B THR* 2.8 23.3 + - + +
159B PRO* 1.3 70.6 - - - +
161B ILE* 1.3 61.0 + - - +
163B PHE* 3.3 7.5 - - - +
164B TYR* 3.0 47.6 + - + -
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Residues in contact with ILE 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B VAL* 3.7 24.5 - - + -
115B LEU* 3.9 17.9 - - + -
117B TYR* 3.6 55.0 - - + -
153B TYR* 5.0 0.4 - - - +
158B GLU* 3.1 26.2 + - + +
160B VAL* 1.3 74.4 - - - +
162B ALA* 1.3 61.8 + - - +
164B TYR* 3.3 2.1 + - - -
165B GLU* 2.9 55.6 + - + +
170B VAL* 3.9 5.5 - - + +
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Residues in contact with ALA 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B GLU 3.9 2.5 + - - +
159B PRO* 3.4 12.0 + - + +
161B ILE* 1.3 79.4 - - - +
163B PHE* 1.3 64.4 + - - +
165B GLU* 3.4 22.1 + - - +
166B LYS* 3.5 18.1 + - - +
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Residues in contact with PHE 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B VAL* 3.8 39.9 - - + -
103B GLU* 4.2 22.4 - - + -
106B GLU* 4.5 1.1 - - - -
159B PRO 3.2 13.3 + - - +
160B VAL 3.3 8.3 - - - +
161B ILE 3.2 0.2 - - - -
162B ALA* 1.3 79.2 - - - +
164B TYR* 1.3 96.7 + + - +
165B GLU 3.7 0.2 + - - -
166B LYS* 3.7 21.6 + - + +
167B ARG* 3.7 29.3 + - - +
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Residues in contact with TYR 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B PHE* 3.6 20.5 - + - -
96B PRO* 4.3 3.6 - - + -
99B VAL* 6.3 0.9 - - - -
102B GLY* 3.4 24.7 + - - -
106B GLU* 3.3 14.8 + - - -
112B PRO* 3.9 9.9 - - + -
115B LEU* 3.7 22.0 - - + -
160B VAL* 3.0 47.1 + - + +
163B PHE* 1.3 90.7 - + - +
165B GLU* 1.3 65.9 + - - +
166B LYS 3.1 2.2 - - - -
167B ARG* 3.0 54.4 + - - +
168B GLY 3.7 2.9 + - - -
169B ILE* 3.9 27.7 + - + +
170B VAL* 3.8 8.1 - - + -
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Residues in contact with GLU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B TYR* 5.4 2.3 - - - -
161B ILE* 2.9 41.7 + - - +
162B ALA* 3.4 15.0 + - - +
164B TYR* 1.3 76.9 - - - +
166B LYS* 1.3 58.3 + - - +
168B GLY* 3.0 19.9 + - - +
170B VAL* 3.6 28.6 - - + +
107C ARG* 3.4 29.2 + - - +
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Residues in contact with LYS 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B ALA 3.5 16.2 - - - +
163B PHE* 3.7 15.7 - - + +
164B TYR 3.1 0.6 - - - -
165B GLU* 1.3 76.7 - - - +
167B ARG* 1.3 59.6 + - + +
168B GLY 3.5 0.2 - - - -
103C GLU* 3.6 55.4 - - + +
106C GLU* 3.9 4.5 - - - +
107C ARG* 3.8 18.8 - - - +
163C PHE* 6.4 1.1 - - + -
167C ARG* 5.8 0.2 - - - -
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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
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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