Contacts of the strand formed by residues 114 - 121 (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 SER 114 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A PRO* 3.5 5.9 - - - +
104A ARG* 2.8 40.0 + - - +
112A GLN 4.0 2.0 + - - -
113A LYS* 1.3 76.7 - - - +
115A VAL* 1.3 62.0 + - - +
168A SER 2.9 19.8 + - - -
169A ASN* 3.4 25.3 - - - +
171A MET 3.3 14.6 - - - -
172A ALA* 4.7 1.1 - - - -
173A TRP* 3.7 5.4 - - - +
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Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A PHE* 4.3 7.0 - - + -
101A VAL* 4.5 2.9 - - + -
102A MET 4.1 0.9 - - - -
114A SER* 1.3 72.0 - - - +
116A GLY* 1.3 69.7 + - - +
117A PHE* 4.7 2.7 - - + +
140A ILE* 4.4 7.0 - - + -
168A SER 3.3 2.7 - - - +
170A PHE* 3.0 30.2 + - + +
171A MET* 2.8 26.4 + - + +
172A ALA 4.4 0.4 - - - +
173A TRP* 3.6 26.9 - - + +
176A VAL* 3.6 29.6 - - + -
191A PHE* 4.0 28.7 - - + -
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Residues in contact with GLY 116 (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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101A VAL* 3.3 11.1 - - - +
102A MET* 2.7 42.7 + - - -
104A ARG* 3.9 7.4 - - - +
114A SER 3.7 1.4 + - - -
115A VAL* 1.3 71.6 - - - +
117A PHE* 1.3 59.9 + - - +
118A PHE* 4.0 13.7 - - - -
167A PHE 3.4 8.1 - - - -
168A SER 3.6 8.4 + - - -
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Residues in contact with PHE 117 (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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99A ILE* 3.5 29.8 - - + -
100A MET 3.6 2.2 - - - -
101A VAL* 4.9 0.7 - - - +
115A VAL* 3.7 1.3 + - + -
116A GLY* 1.3 73.5 - - - -
118A PHE* 1.3 68.1 + - - +
138A LEU* 3.6 19.8 - - + +
139A LYS 3.5 27.6 - - - -
140A ILE* 4.3 0.2 - - + -
166A GLY* 3.4 2.9 - - - -
167A PHE* 2.9 30.1 + - - +
170A PHE* 3.8 42.2 - + + -
191A PHE* 3.8 34.5 - + + -
192A GLU 3.7 18.4 - - - -
193A VAL* 3.8 14.4 - - + -
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Residues in contact with PHE 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ILE* 3.5 5.0 - - - -
100A MET* 2.8 57.1 + - + +
102A MET* 3.9 30.5 - - + -
104A ARG* 4.4 7.9 - - - -
116A GLY* 4.0 5.2 - - - -
117A PHE* 1.3 94.7 - - - +
119A LEU* 1.3 59.6 - - - +
138A LEU* 4.4 1.3 - - - -
164A ASP* 4.7 10.1 - - + -
165A TRP* 3.6 13.0 - - - +
166A GLY* 3.4 25.6 - - - -
167A PHE 3.7 10.1 - - - -
168A SER* 3.5 30.3 - - - -
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Residues in contact with LEU 119 (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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71A PHE* 4.2 12.8 - - + -
97A TRP* 3.8 31.4 - - + -
98A LYS 3.4 13.9 - - - +
99A ILE* 4.9 0.2 - - - +
118A PHE* 1.3 72.2 - - - +
120A GLN* 1.3 59.8 - - - +
134A ALA* 5.7 0.2 - - + -
136A ALA* 4.0 25.4 - - + -
138A LEU* 4.4 8.7 - - + +
154A ILE* 4.3 8.5 - - + -
158A PHE* 3.4 25.2 - - + -
164A ASP* 3.0 4.9 - - - -
165A TRP 2.8 39.1 + - - +
193A VAL* 3.9 22.4 - - + -
195A VAL* 4.1 7.2 - - + -
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Residues in contact with GLN 120 (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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86A LEU* 3.8 22.8 - - + +
96A PRO 3.7 0.9 + - - +
97A TRP* 3.2 7.2 - - - +
98A LYS* 2.6 82.9 + - + +
100A MET* 4.0 17.0 - - + +
118A PHE 4.0 0.2 + - - -
119A LEU* 1.3 73.9 - - - +
121A CYS* 1.3 65.2 + - - +
122A ASN 5.6 0.4 - - - +
123A ALA* 3.5 34.1 - - + +
124A GLU* 5.7 1.4 - - - +
163A ASN* 3.4 11.1 + - - +
164A ASP* 3.8 8.3 - - + -
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Residues in contact with CYS 121 (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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95A LEU* 3.8 17.7 - - - -
96A PRO 3.6 2.0 - - - -
97A TRP* 3.5 47.3 - - + -
119A LEU 4.2 0.4 + - - -
120A GLN* 1.3 74.9 - - - +
122A ASN* 1.3 72.3 + - - +
123A ALA 3.0 3.8 + - - -
130A TRP* 3.3 34.9 - - - -
158A PHE* 3.8 15.5 - - + -
163A ASN* 2.6 19.5 + - - +
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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