Contacts of the strand formed by residues 186 - 191 (chain A) in PDB entry 1HNI
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A VAL* 4.2 11.7 - - - +
109A LEU 4.5 0.9 - - - -
110A ASP* 4.5 9.9 - - - +
111A VAL* 5.5 0.9 - - - -
181A TYR 3.9 0.9 - - - +
182A GLN* 3.5 6.4 - - - +
183A TYR* 2.5 51.5 + - + +
184A MET 3.4 0.8 + - - -
185A ASP* 1.3 79.6 - - - +
187A LEU* 1.3 60.8 - - - +
188A TYR* 3.3 34.4 + - + -
229A TRP* 5.7 2.0 - - + -
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Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A THR 3.9 0.2 - - - +
108A VAL* 3.2 4.0 - - - -
109A LEU* 2.6 56.6 + - + +
111A VAL* 3.9 17.7 - - + +
164A MET* 4.2 20.4 - - + -
168A LEU* 4.6 9.0 - - + -
180A ILE* 3.5 33.4 - - + -
181A TYR 4.0 3.4 - - - +
182A GLN* 4.9 8.7 - - + -
186A ASP* 1.3 72.2 - - - +
188A TYR* 1.3 65.3 + - - +
189A VAL* 3.9 15.9 + - + -
205A LEU* 4.9 2.5 - - + -
209A LEU* 3.9 27.8 - - + -
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Residues in contact with TYR 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A THR 3.4 5.2 - - - +
108A VAL* 3.2 30.5 - - + +
179A VAL 3.3 9.4 - - - +
181A TYR* 3.0 32.6 + + - +
183A TYR* 5.5 2.5 - - + -
186A ASP* 3.3 43.4 + - + -
187A LEU* 1.3 81.4 - - - +
189A VAL* 1.3 59.3 + - - +
227A PHE* 4.4 12.7 - - + +
228A LEU 4.7 5.4 + - - -
229A TRP* 4.1 17.0 - + + +
559A AAA 2.8 80.6 + + + +
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Residues in contact with VAL 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A VAL* 3.5 0.7 - - - -
107A THR* 2.9 41.9 + - + +
109A LEU* 3.2 31.0 - - + -
171A PHE* 6.2 0.4 - - + -
178A ILE* 3.4 29.4 - - + -
179A VAL 3.7 2.9 - - - -
180A ILE* 4.5 5.2 - - + -
187A LEU* 3.9 11.6 - - + -
188A TYR* 1.3 74.0 - - - +
190A GLY* 1.3 57.7 + - - +
198A HIS* 4.2 0.6 - - - -
201A LYS* 6.3 0.4 - - + -
202A ILE* 4.0 19.5 - - + -
205A LEU* 4.0 26.0 - - + -
559A AAA 3.2 3.3 + - - -
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Residues in contact with GLY 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LYS* 4.3 6.5 - - - -
105A SER 3.6 1.8 - - - -
106A VAL* 3.5 20.2 - - - -
178A ILE* 3.3 3.6 - - - +
179A VAL* 2.9 35.8 + - - +
189A VAL* 1.3 76.1 - - - +
191A SER* 1.3 64.0 + - - -
198A HIS* 3.6 3.4 - - - -
559A AAA 3.3 7.8 + - - -
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Residues in contact with SER 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LYS* 3.3 7.4 - - - +
104A LYS 3.1 2.9 + - - -
105A SER* 2.7 33.6 + - - +
177A ASP* 4.2 12.1 + - - -
178A ILE* 4.1 22.5 - - - +
190A GLY* 1.3 74.5 - - - -
192A ASP* 1.3 84.3 + - - +
193A LEU* 3.4 22.4 + - - +
198A HIS* 3.1 17.3 + - - -
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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