Contacts of the helix formed by residues 114 - 126 (chain C) in PDB entry 3Q91
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113C LEU* 1.3 75.7 - - - +
115C LEU* 1.3 60.1 + - - +
116C GLU* 3.8 19.3 + - - +
117C GLU* 2.7 49.1 + - - +
118C VAL* 3.1 9.5 + - - +
133C PRO* 5.4 1.0 - - - +
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Residues in contact with LEU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ASP* 5.5 8.1 - - + +
42C SER 5.5 0.7 - - - +
43C VAL* 3.7 17.8 - - + +
108C VAL* 3.9 26.9 - - + -
113C LEU 4.7 1.3 - - - +
114C SER* 1.3 72.1 - - - +
116C GLU* 1.3 65.7 + - - +
118C VAL* 3.1 9.7 + - - +
119C ALA* 3.0 21.8 + - - +
138C ARG* 6.0 0.7 - - - -
154C THR* 3.3 36.1 - - + +
156C PHE* 3.9 12.1 - - + -
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Residues in contact with GLU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C SER* 3.0 18.1 - - - +
115C LEU* 1.3 82.5 + - - +
117C GLU* 1.3 61.1 + - - +
119C ALA 3.3 1.6 + - - -
120C CYS* 3.1 28.3 + - - -
133C PRO* 3.8 34.3 - - + +
136C LEU* 3.4 21.3 - - + +
138C ARG* 5.8 0.2 - - - -
156C PHE* 3.2 29.4 - - + -
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Residues in contact with GLU 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C GLY 5.9 0.2 - - - -
113C LEU* 4.1 29.4 - - + +
114C SER* 2.7 44.0 + - - +
116C GLU* 1.3 72.6 - - - +
118C VAL* 1.3 60.9 + - - +
120C CYS* 3.2 10.6 + - - +
121C LYS* 3.0 21.8 + - - +
133C PRO* 4.4 18.7 - - + +
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Residues in contact with VAL 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C VAL* 3.5 21.1 - - + -
106C GLY 4.1 2.7 - - - +
107C LEU 3.4 24.9 - - - +
108C VAL* 4.1 22.0 - - + -
109C ASP 5.6 0.9 - - - +
110C GLN* 5.6 2.2 - - + +
113C LEU* 4.3 24.2 - - + +
114C SER 3.1 9.8 + - - +
115C LEU 3.1 7.7 + - - +
117C GLU* 1.3 75.7 - - - +
119C ALA* 1.3 62.0 + - - +
121C LYS* 3.3 11.5 + - - +
122C GLU* 3.2 32.5 + - + +
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Residues in contact with ALA 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C VAL* 3.9 11.1 - - + +
44C THR 5.4 0.7 - - - +
45C VAL* 4.0 22.6 - - + +
115C LEU 3.0 12.0 + - - +
116C GLU 3.5 8.5 - - - +
118C VAL* 1.3 77.9 - - - +
120C CYS* 1.3 50.9 + - - +
122C GLU* 3.8 2.3 - - - +
123C ALA* 2.7 35.8 + - - +
131C LEU* 5.0 0.7 - - - -
136C LEU* 3.5 19.3 - - + -
156C PHE* 4.1 14.8 - - + -
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Residues in contact with CYS 120 (chain C).
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 3.1 15.1 + - - -
117C GLU* 3.2 8.7 + - - +
119C ALA* 1.3 73.7 - - - +
121C LYS* 1.3 66.8 + - - +
123C ALA* 3.2 9.1 - - - +
124C TRP* 2.9 24.3 + - - +
129C TYR 4.5 0.9 - - - +
131C LEU* 3.9 24.8 + - + +
132C ALA 3.9 2.2 - - - -
133C PRO* 3.5 39.9 - - + -
136C LEU* 4.1 5.2 - - - -
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Residues in contact with LYS 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C LEU 5.7 1.8 - - - -
109C ASP* 6.2 0.2 - - - -
110C GLN* 6.5 1.1 - - - -
113C LEU* 5.3 13.5 - - + -
117C GLU 3.0 13.3 + - - +
118C VAL* 3.3 17.7 + - - +
120C CYS* 1.3 74.1 - - - +
122C GLU* 1.3 78.2 + - - +
124C TRP* 3.0 8.7 + - - +
125C GLU* 2.7 71.2 + - + +
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Residues in contact with GLU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C VAL* 5.5 0.7 - - + -
104C CYS* 3.4 13.3 - - - -
105C ALA 3.3 34.4 - - - +
106C GLY* 3.9 12.9 - - - +
107C LEU 4.8 2.8 + - - +
118C VAL* 3.2 20.5 + - + +
119C ALA* 4.1 2.5 - - - +
121C LYS* 1.3 99.8 + - - +
123C ALA* 1.3 63.0 + - - +
124C TRP 3.0 1.8 - - - -
125C GLU* 4.2 10.8 - - - +
126C GLU* 2.7 48.7 + - - +
177C GLU* 5.6 1.9 - - - +
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Residues in contact with ALA 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C VAL* 4.5 4.9 - - + -
47C LEU* 4.9 4.5 - - + -
104C CYS* 3.5 11.7 - - - -
119C ALA 2.7 24.7 + - - +
120C CYS* 3.2 7.6 - - - +
122C GLU* 1.3 72.5 - - - +
124C TRP* 1.3 57.1 + - - +
127C CYS* 3.3 11.4 - - - +
128C GLY 3.2 7.8 + - - -
129C TYR* 3.0 21.6 + - - +
131C LEU* 3.2 35.4 - - + -
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Residues in contact with TRP 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C CYS 2.9 12.2 + - - +
121C LYS* 3.3 9.4 - - - +
123C ALA* 1.3 75.7 - - - +
125C GLU* 1.3 75.0 + - + +
128C GLY* 2.9 27.3 + - - -
129C TYR 3.2 27.4 - - - +
130C HIS* 3.9 21.3 - - + -
131C LEU 6.0 0.2 - - - +
164C GLN 5.4 0.4 - - - -
166C SER* 3.8 33.9 - - - -
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Residues in contact with GLU 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C LYS* 2.7 61.0 + - + +
122C GLU* 4.2 11.5 - - - +
124C TRP* 1.3 88.2 - - + +
126C GLU* 1.3 62.2 + - + +
128C GLY 4.7 0.5 + - - -
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Residues in contact with GLU 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C VAL* 4.5 5.3 - - + +
60C GLN* 4.5 13.4 + - - -
103C LEU 4.7 0.2 - - - +
104C CYS* 3.3 12.9 - - - -
105C ALA 2.8 46.9 + - - +
122C GLU* 2.7 32.9 + - - +
125C GLU* 1.3 76.3 - - + +
127C CYS* 1.3 63.9 + - - +
128C GLY 3.6 0.2 - - - -
177C GLU* 5.0 7.5 - - - +
179C ILE* 3.6 44.6 - - + +
181C VAL* 3.7 10.7 - - - +
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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