Contacts of the helix formed by residues 156 - 162 (chain B) in PDB entry 5ZCJ
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 156 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A PHE 3.9 11.0 - - - -
57A ASP* 3.0 23.0 + - - +
58A GLY* 3.7 3.1 - - - -
146B PRO* 3.8 7.4 - - - -
148B TYR* 3.6 13.9 - - - -
154B VAL 3.3 0.4 + - - -
155B GLY* 1.3 71.8 - - - -
157B PHE* 1.3 60.7 + - - -
158B PRO 3.5 0.4 - - - -
159B ASN* 3.4 2.3 + - - +
160B PHE* 2.9 28.4 + - - +
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Residues in contact with PHE 157 (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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145B VAL* 4.0 13.0 - - + -
146B PRO 3.1 23.1 + - - +
147B LEU* 3.8 21.8 - - + +
148B TYR 2.8 19.0 + - - +
149B THR* 4.2 2.7 - - - +
156B GLY* 1.3 70.8 - - - -
158B PRO* 1.3 66.6 - - + +
160B PHE* 3.2 5.1 + + - +
161B LEU* 3.0 55.0 + - + +
173B LEU* 4.5 3.4 - - + -
174B LEU* 4.4 2.5 - - + -
177B LEU* 3.7 22.7 - - + -
183B MET* 3.7 29.8 - - + -
188B LEU* 3.8 12.8 - - + -
191B ALA* 3.5 21.3 - - + -
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Residues in contact with PRO 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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149B THR* 3.4 27.1 - - + +
153B ARG 3.7 16.8 - - - +
154B VAL* 3.5 18.4 - - + +
156B GLY 3.6 0.4 - - - -
157B PHE* 1.3 90.4 - - + +
159B ASN* 1.3 62.1 + - - +
161B LEU* 3.2 9.9 + - + -
162B SER* 3.2 9.4 + - - -
191B ALA* 3.7 36.1 - - + +
194B ALA* 3.8 15.7 - - + -
195B ALA* 3.3 16.0 - - + +
198B LYS* 5.4 0.7 - - - -
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Residues in contact with ASN 159 (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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57A ASP* 3.0 30.9 + - - +
58A GLY 3.7 3.1 - - - +
59A LEU* 3.7 29.5 - - + +
164A ALA* 3.8 1.7 - - - +
152B ASP* 5.5 0.2 + - - -
154B VAL* 2.8 39.9 + - - +
155B GLY* 3.5 9.7 - - - -
156B GLY 3.7 0.4 - - - +
157B PHE 3.4 0.4 - - - -
158B PRO* 1.3 71.4 - - - +
160B PHE* 1.3 61.9 + - - +
162B SER* 2.4 25.4 + - - -
163B ASN* 3.6 6.2 + - - -
198B LYS* 3.1 26.1 - - - +
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Residues in contact with PHE 160 (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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54A MET* 3.9 19.1 - - + -
58A GLY* 3.6 3.5 + - - -
52B MET* 3.9 13.2 - - - -
60B LEU* 3.9 22.9 - - + -
143B VAL* 4.2 13.0 - - + -
144B ARG 4.6 0.9 - - - -
145B VAL* 3.6 41.3 - - + -
146B PRO* 3.7 26.7 - - + -
156B GLY 2.9 17.8 + - - +
157B PHE* 3.2 12.8 + + - +
159B ASN* 1.3 75.9 - - - +
161B LEU* 1.3 63.4 + - - +
163B ASN* 3.0 30.6 + - - +
165B PHE* 3.3 30.6 - + - -
173B LEU* 4.3 4.9 - - + -
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Residues in contact with LEU 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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157B PHE* 3.0 55.3 + - + +
158B PRO 3.2 5.8 + - - +
160B PHE* 1.3 75.9 - - + +
162B SER* 1.3 56.9 + - - +
163B ASN 3.2 3.4 + - - +
165B PHE* 3.6 8.7 - - + -
170B LYS* 3.2 46.6 + - + -
173B LEU* 4.4 13.5 - - + -
174B LEU* 4.2 14.8 - - + -
188B LEU 4.9 0.4 - - - +
191B ALA* 3.9 19.1 - - + -
192B LEU* 4.0 23.3 - - + +
195B ALA* 3.9 10.2 - - + +
199B GLN* 4.2 1.0 + - - -
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Residues in contact with SER 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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162A SER 4.6 5.0 - - - +
163A ASN 4.7 0.3 - - - -
164A ALA* 3.3 11.3 + - - +
158B PRO 3.2 8.9 + - - -
159B ASN 2.4 25.4 + - - -
161B LEU* 1.3 74.2 - - - +
163B ASN* 1.3 65.3 + - - +
195B ALA* 4.2 5.6 - - - -
198B LYS* 3.0 35.7 + - - -
199B GLN* 3.3 34.1 + - - +
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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