Contacts of the strand formed by residues 186 - 191 (chain C) in PDB entry 5HP1
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 ASP 186 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108C VAL* 5.8 5.2 - - + +
109C LEU 4.1 3.6 - - - +
110C ASP* 2.5 10.3 - - - +
181C TYR 3.5 2.4 - - - +
183C TYR* 2.9 37.6 + - + +
185C ASP* 1.3 89.3 - - - +
187C LEU* 1.3 63.6 + - - +
229C TRP* 5.4 11.6 + - + +
230C MET* 5.4 5.3 + - - +
603C MG 2.1 32.5 - - - -
33E G 2.8 36.0 + - - +
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Residues in contact with LEU 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C VAL* 3.6 6.9 - - - +
109C LEU* 3.1 49.3 + - + +
111C VAL* 5.4 1.6 - - + +
164C MET* 3.7 26.0 - - + -
168C LEU* 3.7 26.5 - - + -
180C ILE* 4.2 10.1 - - + -
181C TYR 3.5 1.8 - - - +
182C GLN* 3.5 26.5 - - + -
184C MET 5.0 0.4 - - - +
185C ASP 4.1 7.9 - - - +
186C ASP* 1.3 82.2 - - - +
188C TYR* 1.3 60.7 + - - +
189C VAL* 4.5 2.5 - - + -
205C LEU* 4.2 19.5 - - + -
209C LEU* 4.3 8.5 - - + -
229C TRP* 4.8 2.2 - - - -
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Residues in contact with TYR 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C LEU* 4.2 24.8 - - + +
101C LYS 4.3 9.2 + - - -
103C LYS* 4.3 14.0 + - + +
106C VAL* 3.6 44.8 - - + +
107C THR 3.6 4.9 - - - -
108C VAL* 4.4 4.7 - - + +
179C VAL* 4.3 9.9 - - + -
180C ILE* 3.1 7.3 - - - +
181C TYR* 2.9 57.1 + + + +
187C LEU* 1.3 71.6 - - - +
189C VAL* 1.3 63.3 + - - +
190C GLY* 4.3 12.3 - - - -
229C TRP* 3.3 30.0 - + + +
234C LEU* 4.0 23.3 - - + -
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Residues in contact with VAL 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C VAL* 3.4 1.6 - - - -
107C THR* 2.7 42.7 + - - +
109C LEU* 4.5 14.4 - - + -
171C PHE* 6.1 0.9 - - + -
178C ILE* 3.5 30.5 - - + -
179C VAL 3.2 2.5 - - - +
180C ILE* 4.2 12.8 - - + -
187C LEU* 4.5 1.3 - - + -
188C TYR* 1.3 82.9 - - - +
190C GLY* 1.3 60.7 + - - +
198C HIS* 3.8 5.3 - - + -
202C ILE* 3.7 26.7 - - + -
205C LEU* 3.9 26.5 - - + -
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Residues in contact with GLY 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LYS* 4.2 14.8 - - - -
105C SER 3.4 8.7 - - - -
106C VAL* 4.4 2.5 - - - -
178C ILE* 3.5 2.6 - - - +
179C VAL* 2.9 38.6 + - - +
188C TYR* 4.3 11.2 - - - -
189C VAL* 1.3 76.7 - - - +
191C SER* 1.3 62.9 + - - -
198C HIS* 4.6 1.3 - - - -
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Residues in contact with SER 191 (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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103C LYS* 3.8 9.4 - - - +
105C SER* 2.9 31.6 + - - +
177C ASP 3.6 19.3 - - - -
178C ILE* 4.3 9.9 - - - -
190C GLY* 1.3 74.8 - - - -
192C ASP* 1.3 65.0 + - - +
193C LEU* 3.4 24.4 + - - +
198C HIS* 2.8 29.8 + - - +
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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