Contacts of the strand formed by residues 115 - 120 (chain E) in PDB entry 3CQ6
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 THR 115 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113E GLY 5.2 3.1 - - - +
114E ARG* 1.3 82.5 - - - +
116E ALA* 1.3 61.0 + - - +
135E THR* 3.8 5.6 - - - +
136E GLU* 3.2 36.6 - - + +
138E ILE* 4.1 20.4 - - + +
160E LYS 5.0 1.9 + - - -
161E GLN 4.2 2.9 + - - -
162E PRO* 3.6 16.5 - - - +
163E ASP* 3.0 34.9 + - - +
164E ILE* 3.0 7.6 + - - +
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Residues in contact with ALA 116 (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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106E LEU* 4.5 4.5 - - + -
115E THR* 1.3 75.2 - - - +
117E LEU* 1.3 55.1 + - - +
130E ALA* 4.7 2.5 - - + -
135E THR* 3.8 12.5 - - + +
136E GLU 2.7 10.5 + - - +
137E PHE* 3.4 10.3 - - + -
138E ILE* 2.7 34.5 + - - +
164E ILE* 3.2 16.4 - - + -
166E PHE* 3.8 27.1 - - + -
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Residues in contact with LEU 117 (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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116E ALA* 1.3 76.4 - - - +
118E GLY* 1.3 58.1 + - - +
119E PHE* 3.3 37.5 - - + -
137E PHE* 4.3 3.4 - - - -
138E ILE* 3.4 28.5 - - + +
140E VAL* 3.7 23.3 - - + -
156E GLU* 4.4 20.0 - - + +
157E ILE* 4.6 7.2 - - + +
160E LYS* 4.9 1.8 - - + -
162E PRO* 3.8 30.1 - - + -
164E ILE 2.8 7.3 + - - +
165E VAL* 3.4 6.9 - - + -
166E PHE* 2.7 34.5 + - - +
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Residues in contact with GLY 118 (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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117E LEU* 1.3 75.0 - - - +
119E PHE* 1.3 65.7 + - - -
120E GLN* 3.7 2.1 + - - -
122E SER* 6.2 0.7 - - - -
137E PHE* 3.8 19.8 - - - -
138E ILE 3.0 9.8 + - - +
139E ALA* 3.6 3.6 - - - -
140E VAL* 3.0 25.6 + - - +
166E PHE* 3.9 15.3 - - - -
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Residues in contact with PHE 119 (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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117E LEU* 3.3 26.7 - - + -
118E GLY* 1.3 71.0 - - - -
120E GLN* 1.3 61.5 + - - +
122E SER* 3.6 14.3 - - - -
140E VAL* 3.1 27.8 - - + +
142E ARG* 2.7 46.2 + - + +
148E ILE* 3.5 27.6 - - + -
153E ALA* 4.0 19.7 - - + -
157E ILE* 4.5 5.8 - - + -
165E VAL* 3.8 11.2 - - + -
166E PHE 3.2 28.8 + - - -
167E VAL* 3.8 19.7 - - + -
186E ILE* 3.9 21.3 - - + -
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Residues in contact with GLN 120 (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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118E GLY* 4.4 1.5 - - - +
119E PHE* 1.3 73.5 + - - +
121E PRO* 1.3 65.1 - - + +
122E SER* 2.7 42.6 + - - -
123E TYR 4.8 0.7 - - - +
124E SER* 6.2 0.4 - - - +
127E PRO* 4.0 18.2 - - - +
137E PHE* 3.8 25.7 - - + -
139E ALA* 3.7 28.4 - - + +
140E VAL 3.0 8.9 + - - +
141E SER* 3.7 5.7 - - - -
142E ARG* 2.9 26.1 + - - +
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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