Contacts of the strand formed by residues 164 - 172 (chain A) in PDB entry 2F1X
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 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A MET* 3.1 24.7 - - + +
118A PHE* 4.7 12.6 - - + +
119A LEU 3.0 13.7 - - - +
120A GLN* 3.8 11.9 - - + -
156A HIS* 4.2 3.1 - - - -
158A PHE* 3.9 3.1 - - - -
162A GLU* 3.2 5.9 - - - +
163A ASN* 1.3 91.5 + - - +
165A TRP* 1.3 76.2 + - - +
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Residues in contact with TRP 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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118A PHE* 3.8 6.5 - - - -
119A LEU* 2.8 36.1 + - - +
138A LEU* 4.3 0.2 - - - +
154A ILE* 3.7 33.5 - - + +
155A SER 4.0 11.2 + - - +
156A HIS* 3.3 58.3 - + + +
158A PHE* 3.8 9.2 - - + -
162A GLU* 4.2 10.5 - - + -
164A ASP* 1.3 85.4 - - - +
166A GLY* 1.3 65.4 + - - +
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Residues in contact with GLY 166 (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 PHE 3.4 12.1 - - - -
118A PHE* 3.4 13.0 - - - -
138A LEU* 4.0 11.2 - - - -
154A ILE* 4.5 5.3 - - - +
165A TRP* 1.3 85.8 + - - +
167A PHE* 1.3 75.6 + - - -
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Residues in contact with PHE 167 (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 PHE 2.9 30.6 + - - -
118A PHE* 3.7 4.8 - - - -
138A LEU* 4.4 7.4 - - + -
152A ARG* 3.4 57.0 - - + -
153A ARG 3.7 11.7 - - - -
154A ILE* 3.4 32.8 - - + -
166A GLY* 1.3 81.5 - - - -
168A SER* 1.3 64.7 + - - +
169A ASN 3.3 2.6 + - - +
170A PHE* 3.3 40.4 + + + +
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Residues in contact with SER 168 (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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104A ARG* 3.2 46.8 - - - +
114A SER* 2.9 16.3 + - - -
115A VAL 3.3 6.6 - - - +
116A GLY* 4.1 3.4 - - - -
118A PHE* 3.5 17.1 - - - -
167A PHE* 1.3 72.6 - - - +
169A ASN* 1.3 61.9 + - - +
170A PHE 3.4 0.2 - - - -
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Residues in contact with ASN 169 (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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114A SER* 3.4 24.6 - - - +
152A ARG* 3.2 12.2 + - - -
167A PHE* 3.1 2.4 - - - +
168A SER* 1.3 83.0 + - - +
170A PHE* 1.3 66.1 + - - +
171A MET* 3.3 8.3 - - - +
172A ALA* 4.8 1.6 + - - +
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Residues in contact with PHE 170 (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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115A VAL* 3.0 18.0 + - + +
117A PHE* 3.8 28.0 - + + -
138A LEU* 3.4 32.1 - - + -
140A ILE* 3.4 38.8 - - + -
150A PHE* 3.4 48.9 - + - -
151A SER* 4.4 0.2 - - - -
152A ARG* 3.1 33.9 + - + +
167A PHE* 3.3 36.4 + + + +
169A ASN* 1.3 79.7 - - - +
171A MET* 1.3 62.8 + - + +
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Residues in contact with MET 171 (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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114A SER* 3.3 8.0 - - - -
115A VAL* 2.8 29.5 + - + -
140A ILE* 3.3 31.0 - - + -
150A PHE* 3.1 58.1 - - + -
169A ASN* 4.2 6.1 - - - -
170A PHE* 1.3 87.3 - - + +
172A ALA* 1.3 69.5 + - - +
175A GLU* 4.4 8.7 - - - +
176A VAL* 3.5 37.2 - - - -
183A PHE* 4.5 9.0 - - + -
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Residues in contact with ALA 172 (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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113A LYS 4.0 7.6 - - - +
114A SER* 4.3 1.6 - - - +
115A VAL* 4.5 0.9 - - - -
169A ASN* 5.1 1.1 - - - -
171A MET* 1.3 78.3 - - - +
173A TRP* 1.3 67.1 + - - +
174A SER* 4.1 14.8 - - - +
175A GLU* 3.1 18.3 + - + +
176A VAL* 3.1 22.2 + - - +
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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