Contacts of the strand formed by residues 91 - 97 (chain E) in PDB entry 2CFX
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 91 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85E ILE* 4.3 18.4 - - + +
88E LEU* 3.9 25.7 + - + +
89E PRO 3.2 13.4 - - - +
90E ASN* 1.3 76.9 + - - +
92E GLU* 1.3 57.0 + - - +
93E PHE 3.3 22.4 - - - +
105E LEU* 4.3 11.2 - - + -
106E LYS 3.4 7.0 - - - +
107E ILE* 3.4 24.9 - - + -
118E PHE* 4.0 19.5 - - + -
139F THR* 2.7 46.5 + - + +
140F LYS* 5.4 1.9 - - - +
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Residues in contact with GLU 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E GLN* 5.3 4.0 + - - +
90E ASN 3.7 1.2 - - - -
91E ILE* 1.3 73.4 - - - +
93E PHE* 1.3 67.8 + - + +
106E LYS* 2.9 54.8 + - + +
108E ASN* 3.4 22.0 + - - +
95F TYR* 3.9 7.1 + - - -
139F THR* 3.6 7.3 + - - -
140F LYS* 6.0 0.7 - - - +
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Residues in contact with PHE 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E ILE* 4.1 11.9 - - + -
91E ILE* 3.3 10.7 - - - +
92E GLU* 1.3 89.2 - - + +
94E CYS* 1.3 63.6 + - - +
95E TYR* 3.2 47.6 - + + +
104E MET* 3.6 18.4 - - + -
105E LEU* 3.1 22.5 - - - +
106E LYS* 3.3 39.6 + - + -
68F ILE* 5.4 1.1 - - + -
93F PHE* 3.5 39.0 - + - -
95F TYR* 4.7 1.8 - + - -
136F GLU* 4.5 7.6 - - - +
137F ILE 5.4 0.7 - - - -
139F THR* 4.3 5.4 - - - -
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Residues in contact with CYS 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E PHE* 4.3 4.3 - - - -
85E ILE* 4.4 5.8 - - + -
93E PHE* 1.3 81.4 - - - +
95E TYR* 1.3 60.0 + - - +
103E TYR* 3.7 24.7 - - - -
104E MET 3.4 5.4 - - - -
105E LEU* 3.5 26.9 - - + -
136F GLU* 3.6 4.8 + - - +
137F ILE* 2.9 47.2 + - + +
139F THR* 3.8 21.4 - - + +
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Residues in contact with TYR 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E PHE* 3.2 55.6 - + + +
94E CYS* 1.3 73.7 - - - +
96E ARG* 1.3 59.6 + - - +
97E ILE* 3.5 15.5 + - + +
103E TYR* 3.0 9.6 - - - -
104E MET 2.7 36.9 + - - +
68F ILE* 3.9 15.0 - - + -
92F GLU* 3.9 7.6 + - - -
93F PHE* 5.0 0.2 - - - -
106F LYS* 2.9 43.7 + - + +
133F ILE* 4.0 24.0 - - + -
135F SER 3.7 2.2 - - - +
136F GLU* 3.5 39.6 + - + -
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Residues in contact with ARG 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C GLU* 3.4 31.6 + - - +
119C ILE* 3.4 26.9 - - - +
120C ASN* 2.5 28.3 + - - -
78E TYR* 3.4 20.4 + - - -
94E CYS 4.1 1.2 + - - -
95E TYR* 1.3 69.4 - - - +
97E ILE* 1.3 70.6 + - - +
101E ALA 4.7 0.4 + - - -
102E CYS* 3.2 39.6 + - - +
103E TYR* 3.6 29.2 + - + -
133F ILE* 3.5 5.0 - - - -
134F PHE* 2.8 37.6 + - + -
135F SER* 2.9 29.4 + - - +
136F GLU* 4.6 0.6 - - - +
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Residues in contact with ILE 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E TYR* 3.9 19.5 - - + +
96E ARG* 1.3 99.4 + - - +
98E ALA* 1.3 60.9 + - - +
99E GLY* 3.7 3.1 + - - +
101E ALA* 3.7 21.5 - - + +
102E CYS 2.8 26.6 + - - +
103E TYR* 4.0 4.0 - - - +
104E MET* 3.7 35.9 - - + +
68F ILE* 4.2 12.1 - - + -
131F HIS* 3.8 24.7 - - + +
132F VAL 3.5 9.2 - - - +
133F ILE* 4.2 10.5 - - + -
134F PHE* 3.7 7.9 - - - -
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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