Contacts of the strand formed by residues 182 - 188 (chain C) in PDB entry 1Z6T
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 VAL 182 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113C VAL* 4.3 12.4 + - + +
114C LEU* 3.9 14.8 - - + -
117C GLY* 3.1 17.2 + - - -
119C VAL* 3.5 30.3 - - + -
168C VAL* 4.3 13.5 - - + -
174C LEU* 3.6 28.7 - - + -
178C PHE* 4.9 1.3 - - + -
181C GLY* 1.3 79.6 - - - +
183C HIS* 1.3 71.9 + - - +
239C LEU* 3.2 21.3 - - + +
241C ILE* 4.5 9.0 - - + -
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Residues in contact with HIS 183 (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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116C GLU* 4.5 7.3 + - - +
117C GLY* 3.6 17.0 + - - +
180C GLY 4.8 8.7 - - - -
181C GLY* 5.6 0.2 - - - -
182C VAL* 1.3 85.4 + - - +
184C TRP* 1.3 61.9 + - - +
185C VAL* 3.9 1.0 + - - +
202C LEU* 4.8 7.4 - - + -
205C ARG* 4.8 16.9 + - + +
206C LEU* 3.6 25.2 - - + +
231C MET* 5.5 1.4 - - - +
235C HIS* 3.5 35.2 - + + +
238C SER* 5.0 5.5 + - - -
239C LEU 2.9 7.5 + - - -
240C LEU* 3.6 21.5 - - + +
241C ILE* 2.9 27.2 + - - +
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Residues in contact with TRP 184 (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 GLY 2.9 10.7 + - - +
118C GLY 3.4 27.8 - - - +
119C VAL* 3.8 17.4 - - + +
120C PRO* 3.4 35.3 - - + +
161C SER* 3.4 29.8 - - - -
164C ALA* 4.3 4.3 - - + -
165C ALA* 3.9 18.8 - - + -
183C HIS* 1.3 72.7 - - - +
185C VAL* 1.3 67.6 + - - +
186C SER* 3.9 13.1 + - - +
205C ARG* 2.9 25.1 + - - -
241C ILE* 3.5 35.9 - - + -
243C ASP* 3.8 37.9 + - + +
263C THR* 6.0 0.2 - - + -
394C LYS* 4.7 6.3 - - - +
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Residues in contact with VAL 185 (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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183C HIS 4.4 5.6 - - - +
184C TRP* 1.3 80.2 - - - +
186C SER* 1.3 61.9 + - - +
187C VAL* 3.5 15.2 + - + +
198C LYS* 5.0 17.5 - - + +
202C LEU* 3.8 40.2 - - + -
205C ARG* 4.1 7.6 - - - +
240C LEU* 4.7 4.5 - - + -
241C ILE 2.7 10.8 + - - +
242C LEU* 3.5 23.6 - - + -
243C ASP* 2.7 33.4 + - - +
254C PHE* 4.6 6.3 - - + -
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Residues in contact with SER 186 (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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184C TRP* 3.9 11.4 + - - -
185C VAL* 1.3 74.1 - - - +
187C VAL* 1.3 59.1 + - - +
198C LYS* 3.1 34.2 + - - +
205C ARG* 5.2 0.8 - - - +
243C ASP* 4.2 17.6 + - - -
392C ASP* 5.2 10.6 + - - -
394C LYS* 3.7 30.7 + - - -
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Residues in contact with VAL 187 (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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185C VAL* 3.7 25.4 - - + +
186C SER* 1.3 75.2 + - - +
188C GLY* 1.3 65.7 + - - +
190C GLN* 2.8 41.7 + - + +
195C LEU* 4.3 8.3 - - + -
198C LYS* 3.7 11.4 - - + +
242C LEU* 4.3 16.8 - - + -
243C ASP 3.0 19.1 + - - +
244C ASP 3.9 6.1 - - - +
245C VAL* 4.5 6.7 - - + -
250C VAL* 4.0 24.7 - - + -
254C PHE* 4.9 6.5 - - + -
392C ASP* 3.7 6.2 - - - +
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Residues in contact with GLY 188 (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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187C VAL* 1.3 90.0 - - - +
189C LYS* 1.3 63.8 + - - -
190C GLN* 3.3 4.0 + - - +
243C ASP 3.4 3.4 + - - -
244C ASP* 2.8 35.0 + - - +
246C TRP* 3.5 7.3 + - - +
250C VAL* 5.6 1.6 - - - +
392C ASP* 3.6 20.1 + - - -
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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