Contacts of the helix formed by residues 136 - 152 (chain E) in PDB entry 2C2V
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 ASN 136 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E GLN* 2.4 25.9 + - - +
133E TRP 3.9 0.2 - - - -
135E THR* 1.3 79.2 + - - +
137E GLU* 1.4 56.8 + - - +
138E ALA* 3.2 12.2 - - - +
139E GLN* 3.3 41.4 + - + +
140E ALA* 2.7 34.0 + - - +
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Residues in contact with GLU 137 (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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133E TRP* 3.3 28.8 + - - +
134E LYS 4.9 0.4 - - - -
135E THR 3.8 1.2 - - - -
136E ASN* 1.4 77.1 - - - +
138E ALA* 1.3 69.0 + - + +
140E ALA* 3.5 3.0 - - - +
141E ILE* 3.1 41.7 + - + +
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Residues in contact with ALA 138 (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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136E ASN* 3.2 11.2 - - - +
137E GLU* 1.3 82.6 - - + +
139E GLN* 1.3 63.5 + - - +
141E ILE* 3.0 17.8 + - - +
142E GLU* 3.3 16.0 + - - +
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Residues in contact with GLN 139 (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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145B ARG* 6.1 0.6 - - - +
149B ARG* 3.2 49.7 + - - +
132E GLN* 4.7 11.2 + - - +
136E ASN* 3.1 31.1 + - + +
138E ALA* 1.3 79.6 - - - +
140E ALA* 1.3 63.2 + - - +
142E GLU* 4.6 8.7 - - + -
143E THR* 3.1 22.1 + - - -
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Residues in contact with ALA 140 (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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80E TYR* 3.7 14.4 - - - +
132E GLN* 4.3 3.8 + - + +
133E TRP* 3.9 41.8 - - + +
136E ASN* 2.7 18.4 + - - +
137E GLU 3.5 4.0 - - - +
139E GLN* 1.3 80.1 - - - +
141E ILE* 1.3 66.1 + - - +
143E THR* 3.3 6.4 + - - +
144E ALA* 2.9 20.8 + - - +
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Residues in contact with ILE 141 (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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50E PRO* 3.8 26.5 - - + -
133E TRP* 4.5 12.6 - - + +
137E GLU* 3.1 44.1 + - + +
138E ALA* 3.0 9.1 + - - +
140E ALA* 1.3 78.5 - - - +
142E GLU* 1.3 55.3 + - - +
144E ALA* 2.7 28.1 + - - +
145E ARG* 2.8 42.0 + - - +
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Residues in contact with GLU 142 (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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142B GLU* 2.8 47.4 - - + +
145B ARG* 2.6 36.2 + - + +
149B ARG* 4.3 13.9 + - - +
138E ALA 3.3 12.9 + - - +
139E GLN* 4.2 7.6 - - - +
141E ILE* 1.3 77.3 - - - +
143E THR* 1.3 66.4 + - - +
145E ARG* 3.9 20.2 + - - +
146E ALA* 2.9 21.0 + - - +
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Residues in contact with THR 143 (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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146B ALA* 4.4 4.2 - - + +
149B ARG* 2.8 32.5 + - - +
80E TYR* 3.3 35.7 + - + -
139E GLN 3.1 15.3 + - - -
140E ALA* 3.6 4.9 - - - -
141E ILE 3.1 0.2 - - - -
142E GLU* 1.3 79.9 - - - +
144E ALA* 1.4 58.0 + - - +
146E ALA* 3.0 7.3 + - - +
147E TRP* 2.9 49.2 + - + +
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Residues in contact with ALA 144 (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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50E PRO* 3.8 21.1 - - + -
51E PHE* 4.6 6.6 - - + -
80E TYR* 3.7 31.8 - - + +
133E TRP* 4.1 6.5 - - + -
140E ALA 2.9 11.3 + - - +
141E ILE 2.7 16.2 + - - +
143E THR* 1.4 70.9 - - - +
145E ARG* 1.3 60.6 + - - -
147E TRP* 3.2 2.4 + - - +
148E THR* 3.0 25.3 + - - -
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Residues in contact with ARG 145 (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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142B GLU* 3.0 39.0 + - - -
50E PRO* 3.2 27.9 - - + +
141E ILE* 2.8 40.4 + - - +
142E GLU* 3.4 13.9 + - - +
144E ALA* 1.3 73.7 - - - +
146E ALA* 1.3 64.3 + - - +
148E THR* 3.3 3.5 + - - -
149E ARG* 3.0 41.0 + - - +
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Residues in contact with ALA 146 (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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142B GLU* 4.4 2.5 - - - +
143B THR* 4.4 13.7 - - + +
146B ALA* 3.7 25.8 - - + -
147B TRP* 5.4 4.9 + - + -
142E GLU 2.9 14.1 + - - +
143E THR 3.4 7.9 - - - +
145E ARG* 1.3 75.6 - - - +
147E TRP* 1.4 59.2 + - + +
149E ARG* 3.5 21.9 + - - +
150E LEU* 2.9 27.6 + - - +
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Residues in contact with TRP 147 (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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146B ALA* 6.0 1.7 - - + +
150B LEU* 4.3 28.7 - - + +
78E LYS* 3.0 55.2 - - + +
79E ILE* 3.6 20.0 - - - -
80E TYR* 3.2 47.1 - + + +
86E LYS* 5.8 6.3 - - + -
129E VAL* 6.4 0.2 - - + -
143E THR* 2.9 37.6 + - + +
144E ALA 3.2 3.5 + - - +
146E ALA* 1.4 75.3 - - + +
148E THR* 1.4 59.5 + - - +
150E LEU* 4.1 3.1 - - + +
151E TYR* 2.6 57.2 + + + +
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Residues in contact with THR 148 (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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50E PRO 3.6 13.7 + - - -
51E PHE* 3.7 27.5 - - - +
53E GLY 4.7 3.1 - - - +
54E GLY* 4.0 21.3 - - - +
56E PHE* 3.8 17.2 - - + -
144E ALA 3.0 14.0 + - - -
145E ARG* 3.6 8.1 - - - -
147E TRP* 1.4 82.6 - - - +
149E ARG* 1.4 63.8 + - - +
152E ALA* 3.1 23.8 + - + +
153E MET* 3.8 9.5 - - + +
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Residues in contact with ARG 149 (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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80B TYR* 6.0 0.7 - - - -
132B GLN* 5.0 5.4 - - - +
139B GLN* 3.7 35.4 + - - +
142B GLU* 2.9 32.7 + - - -
143B THR* 2.8 31.6 + - - -
145E ARG* 3.0 26.8 + - - +
146E ALA* 3.8 15.5 - - - +
148E THR* 1.4 77.8 - - - +
150E LEU* 1.3 64.9 + - - +
152E ALA 4.4 0.2 + - - -
153E MET* 3.8 40.3 + - + +
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Residues in contact with LEU 150 (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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78B LYS* 5.5 3.6 - - - -
147B TRP* 4.4 31.4 - - + +
150B LEU* 4.1 14.1 - - + -
151B TYR* 4.1 7.2 - - - +
68C GLU* 5.4 8.1 - - - +
146E ALA 2.9 18.8 + - - +
147E TRP* 3.1 4.9 + - + +
149E ARG* 1.3 79.9 - - - +
151E TYR* 1.3 108.5 + - + +
153E MET 5.5 1.4 + - - +
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Residues in contact with TYR 151 (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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150B LEU* 3.4 22.4 - - + +
151B TYR* 4.2 3.9 + - - -
77E THR* 3.3 14.1 - - - +
78E LYS* 3.5 53.5 - - + +
147E TRP* 2.6 56.9 + + + +
150E LEU* 1.3 111.9 - - + +
152E ALA* 1.4 57.1 + - - +
153E MET 3.9 2.5 - - - -
155E ASN* 4.1 9.1 + - - +
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Residues in contact with ALA 152 (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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54E GLY* 3.5 2.8 - - - -
55E THR* 2.8 52.2 + - - +
56E PHE* 3.6 32.5 - - + -
77E THR* 4.1 1.8 - - + -
78E LYS 5.6 0.2 - - - +
147E TRP 5.2 0.2 - - - +
148E THR* 3.1 13.3 + - + +
151E TYR* 1.4 75.6 - - - +
153E MET* 1.3 61.7 + - - +
155E ASN* 2.9 15.7 - - - -
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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