Contacts of the strand formed by residues 159 - 165 (chain A) in PDB entry 1HFC
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 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A TRP* 4.2 13.7 - - + +
114A LEU* 4.8 4.7 - - + -
115A THR 3.0 13.2 + - - +
116A TYR* 3.1 6.3 - - + +
117A ARG 3.0 24.4 + - - +
138A PHE* 3.9 37.5 - - + -
149A PHE* 4.4 6.5 - - + -
157A ALA* 3.9 1.0 - - - +
158A ASP* 1.3 81.6 - - + +
160A MET* 1.4 62.2 + - - +
161A ILE* 4.0 13.0 + - + -
193A GLY* 3.3 27.1 - - - +
194A ASP* 4.8 0.4 - - - -
195A ALA 4.9 0.7 - - - +
220A LEU* 4.1 12.3 - - + -
223A SER* 4.1 13.9 - - - +
224A LEU* 4.4 16.2 - - + -
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Residues in contact with MET 160 (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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117A ARG* 3.6 35.7 - - - +
119A GLU* 3.5 37.0 - - + +
155A GLY 4.1 3.8 - - - +
156A GLN* 4.1 23.8 - - - +
157A ALA* 3.5 42.6 - - - +
159A ILE* 1.4 72.1 - - - +
161A ILE* 1.3 63.3 + - - +
194A ASP* 2.8 31.9 + - - +
195A ALA 3.1 23.0 + - - +
196A HIS* 4.8 1.7 - - - -
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Residues in contact with ILE 161 (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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116A TYR* 4.1 18.4 - - + -
117A ARG 2.8 13.2 + - - +
118A ILE* 3.7 18.2 - - + +
119A GLU* 2.8 29.6 + - - +
120A ASN 4.2 0.3 + - - -
134A ILE* 3.8 36.6 - - + -
138A PHE* 4.1 9.4 - - + -
159A ILE* 4.1 16.4 - - + -
160A MET* 1.3 79.0 - - - +
162A SER* 1.3 65.4 + - - +
163A PHE* 4.8 6.7 - - + -
195A ALA* 3.2 15.0 - - + -
197A PHE* 3.7 26.2 - - + -
220A LEU* 4.6 4.5 - - + -
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Residues in contact with SER 162 (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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119A GLU* 4.0 20.6 + - - -
120A ASN* 3.2 14.6 - - - -
161A ILE* 1.3 77.7 - - - +
163A PHE* 1.3 66.6 + - - +
164A VAL* 3.9 16.1 - - - +
195A ALA 3.1 4.2 + - - -
196A HIS* 3.4 24.4 + - - -
197A PHE* 3.0 28.7 + - - -
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Residues in contact with PHE 163 (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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118A ILE* 4.8 0.9 - - + -
120A ASN* 2.8 53.2 + - - +
121A TYR* 3.8 0.9 - - - -
122A THR* 3.7 40.2 - - + +
130A VAL* 4.0 15.5 - - + -
134A ILE* 5.8 1.1 - - + -
161A ILE* 4.8 11.0 - - + -
162A SER* 1.3 72.3 - - - +
164A VAL* 1.3 64.6 + - - +
197A PHE* 3.3 34.3 - + + +
199A GLU* 3.7 24.2 - - + +
203A TRP* 4.2 11.2 - - - -
212A LEU* 4.0 32.3 - - + -
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Residues in contact with VAL 164 (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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120A ASN* 5.4 0.4 - - - +
162A SER* 3.9 18.6 - - - +
163A PHE* 1.3 80.9 - - - +
165A ARG* 1.3 63.0 + - - +
168A HIS* 3.5 37.2 - - + +
174A PHE* 3.4 25.0 - - + -
196A HIS* 4.0 11.9 - - + +
197A PHE 3.0 8.9 + - - +
198A ASP* 3.3 4.3 - - - -
199A GLU* 2.8 24.3 + - - +
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Residues in contact with ARG 165 (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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164A VAL* 1.3 78.7 - - - +
166A GLY* 1.3 78.2 + - - +
167A ASP 3.4 10.4 + - - +
168A HIS* 3.9 5.6 - - - +
174A PHE* 4.4 2.2 - - - -
198A ASP* 4.2 4.5 - - - +
199A GLU* 4.3 15.9 - - + -
200A ASP* 3.1 42.7 + - - +
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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