Contacts of the strand formed by residues 183 - 187 (chain C) in PDB entry 3ELP
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 ILE 183 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C ILE* 5.7 0.2 - - + -
100C LEU* 4.6 13.0 - - + -
101C LEU* 4.5 17.3 - - + -
152C LYS 3.0 13.7 + - - +
153C LEU* 3.4 19.0 - - + +
154C VAL* 2.8 27.7 + - - +
181C ASP* 5.4 5.8 - - - +
182C ILE* 1.3 79.6 - - - +
184C LEU* 1.3 62.9 + - - +
185C VAL* 3.8 3.8 - - + -
204C ASP* 3.2 17.0 - - + +
205C ILE* 3.7 27.6 - - + -
232C LEU* 4.4 20.9 - - + -
235C ARG* 5.2 7.9 - - - +
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Residues in contact with LEU 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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154C VAL* 3.4 35.4 - - + +
156C ILE* 4.0 15.5 - - + -
169C ILE* 3.9 12.6 - - + +
172C CYS* 4.0 9.0 - - + -
173C ALA* 3.7 34.5 - - - +
176C VAL* 4.5 12.3 - - + -
177C HIS* 4.6 4.3 - - + -
183C ILE* 1.3 74.7 - - - +
185C VAL* 1.3 63.1 + - - +
186C VAL* 4.6 1.6 - - + -
202C GLY 4.8 0.2 - - - -
203C ALA* 3.7 22.5 - - + +
204C ASP* 2.9 43.5 + - - +
205C ILE 3.2 4.9 + - - -
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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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97C ILE* 3.9 19.1 - - + -
153C LEU* 3.3 26.7 - - + -
154C VAL 2.8 10.5 + - - +
155C TRP* 3.5 35.9 - - + -
156C ILE* 2.9 26.7 + - - +
183C ILE* 3.8 5.6 - - + -
184C LEU* 1.3 76.8 - - - +
186C VAL* 1.3 73.1 + - - +
205C ILE* 3.3 31.6 - - + +
207C MET* 4.5 2.9 - - + -
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Residues in contact with VAL 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C ILE* 3.3 16.8 - - + +
158C THR* 4.4 5.6 - - + -
169C ILE* 3.8 35.9 - - + -
184C LEU* 4.6 5.6 - - + -
185C VAL* 1.3 81.9 - - - +
187C ASP* 1.3 68.3 + - - +
188C ASN* 3.2 6.6 + - - +
196C GLN* 5.0 1.1 - - - +
198C PRO* 3.6 28.0 - - + -
203C ALA* 3.7 20.4 - - + -
205C ILE 2.7 9.9 + - - +
206C SER* 3.5 3.3 - - - -
207C MET 2.9 25.3 + - - -
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Residues in contact with ASP 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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155C TRP* 4.0 17.1 + - + +
156C ILE 2.9 7.3 + - - -
157C GLU* 3.9 37.7 - - + +
158C THR 4.1 9.0 + - - +
185C VAL* 4.2 2.0 - - - +
186C VAL* 1.3 74.3 - - - +
188C ASN* 1.3 57.1 + - - +
189C THR* 2.5 37.8 + - - -
190C PHE* 4.6 6.8 + - - -
207C MET* 3.4 29.5 - - - +
209C SER* 5.2 0.7 - - - -
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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