Contacts of the strand formed by residues 186 - 195 (chain Y) in PDB entry 1CZ8
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 TYR 186 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154Y ASP 3.2 13.9 + - - -
155Y TYR* 2.8 48.3 + + + +
156Y PHE* 4.0 28.3 - + - -
157Y PRO* 4.5 0.7 - - + -
158Y GLU* 3.7 48.9 - - + +
178Y ALA* 4.1 4.9 - - + -
179Y VAL* 3.3 17.3 - - - -
180Y LEU* 3.4 33.5 - - + +
181Y GLN* 2.9 12.6 + - - -
185Y LEU* 1.3 72.7 - - - +
187Y SER* 1.3 60.9 + - - +
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Residues in contact with SER 187 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160X GLN* 5.9 0.2 - - - -
151Y LEU* 4.6 7.1 - - - +
152Y VAL 3.5 8.4 + - - -
153Y LYS* 3.1 34.1 + - - +
155Y TYR* 4.3 0.7 - - - -
178Y ALA* 3.4 1.5 - - - -
179Y VAL* 2.9 39.2 + - - +
181Y GLN* 3.3 22.4 - - - -
186Y TYR* 1.3 76.0 - - - +
188Y LEU* 1.3 58.7 + - - +
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Residues in contact with LEU 188 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151Y LEU* 3.7 3.3 - - - +
152Y VAL* 2.9 53.7 + - + +
155Y TYR* 3.5 22.2 - - + +
158Y GLU* 5.4 1.1 - - - +
160Y VAL* 3.7 18.8 - - + +
162Y VAL* 4.6 2.5 - - + -
175Y THR* 3.7 22.2 - - + -
176Y PHE* 3.5 21.3 - - - +
177Y PRO 4.3 2.5 - - - -
178Y ALA* 3.6 13.5 - - + +
187Y SER* 1.3 76.3 + - - +
189Y SER* 1.3 79.4 + - - +
190Y SER 4.1 0.4 - - - +
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Residues in contact with SER 189 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133X VAL* 4.0 19.8 - - - +
176X SER* 5.0 7.9 - - - -
178X THR* 5.0 2.6 + - - -
134Y LEU* 4.0 8.7 - - - +
150Y CYS 3.4 7.9 - - - -
151Y LEU* 3.6 23.4 - - - +
176Y PHE* 2.8 42.8 + - - +
188Y LEU* 1.3 78.1 - - - +
190Y SER* 1.3 62.5 + - - +
191Y VAL* 4.0 4.3 - - - -
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Residues in contact with SER 190 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149Y GLY* 3.2 4.5 - - - -
150Y CYS* 2.9 34.4 + - - -
152Y VAL* 5.6 0.7 - - - -
162Y VAL* 3.3 27.1 - - - +
164Y TRP* 3.3 23.0 + - - -
173Y VAL* 4.3 0.9 - - - +
175Y THR* 2.6 34.8 + - - +
188Y LEU* 4.1 1.0 - - - +
189Y SER* 1.3 72.8 - - - +
191Y VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 191 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118X PHE* 4.7 9.6 - - + -
133X VAL* 5.7 2.9 - - + -
135X LEU* 3.3 42.4 - - + -
137X ASN* 4.1 11.7 - - - +
134Y LEU* 5.0 10.1 - - + -
147Y ALA* 4.8 0.9 - - + -
148Y LEU 3.6 12.6 - - - +
149Y GLY* 4.6 2.5 - - - -
164Y TRP* 4.7 1.6 - - - -
172Y GLY 5.0 0.9 - - - +
173Y VAL* 3.2 4.3 - - - +
174Y HIS* 2.6 48.8 + - + +
176Y PHE* 4.4 9.0 - - + -
189Y SER* 4.0 4.4 - - - -
190Y SER* 1.3 77.9 + - - +
192Y VAL* 1.3 71.3 + - - +
193Y THR* 5.1 0.7 - - + -
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Residues in contact with VAL 192 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147Y ALA* 3.2 2.6 - - - -
148Y LEU* 2.7 64.9 + - + +
164Y TRP* 4.3 10.1 - - + -
169Y LEU* 3.4 38.1 - - + -
171Y SER 3.9 3.4 - - - +
172Y GLY 2.9 25.4 - - - +
173Y VAL* 3.4 14.8 - - + -
191Y VAL* 1.3 77.7 - - - +
193Y THR* 1.3 67.9 + - - +
194Y VAL* 4.3 4.0 - - + -
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Residues in contact with THR 193 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116X PHE* 4.3 12.1 - - + -
137X ASN* 4.4 21.3 + - - +
145Y THR* 4.7 10.7 - - - +
146Y ALA 3.1 7.6 - - - +
147Y ALA* 3.3 31.9 - - + +
169Y LEU* 5.4 1.0 - - - +
171Y SER 4.7 1.6 - - - +
172Y GLY* 3.1 26.5 + - - +
191Y VAL* 5.1 0.9 - - + -
192Y VAL* 1.3 76.1 - - - +
194Y VAL* 1.3 64.5 + - - +
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Residues in contact with VAL 194 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145Y THR* 2.8 17.8 - - - +
146Y ALA 2.9 24.0 + - - +
148Y LEU* 3.6 24.9 - - + -
169Y LEU* 4.0 21.5 - - + -
192Y VAL* 4.3 7.2 - - + -
193Y THR* 1.3 78.6 - - - +
195Y PRO* 1.3 79.5 - - + +
196Y SER* 4.3 0.2 - - - -
199Y LEU* 4.1 9.9 - - + -
204Y TYR* 3.4 40.8 - - + +
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Residues in contact with PRO 195 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144Y GLY 4.4 0.9 - - - +
145Y THR* 3.5 12.1 - - + -
194Y VAL* 1.3 93.8 - - + +
196Y SER* 1.3 60.2 + - - +
197Y SER* 3.1 11.9 - - - +
198Y SER* 2.8 53.4 + - - +
199Y LEU 4.0 1.6 + - - -
204Y TYR* 4.3 1.8 - - - +
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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