Contacts of the helix formed by residues 156 - 170 (chain C) in PDB entry 2NVU
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 156 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152C VAL* 2.5 31.7 + - + +
153C LEU 4.5 0.2 - - - -
155C ASN* 1.3 76.6 - - + +
157C ARG* 1.3 60.8 + - - +
158C ARG* 3.1 9.0 + - - +
159C LEU* 2.6 54.6 + - + +
160C PHE* 3.4 12.6 + - - +
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Residues in contact with ARG 157 (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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70C PHE* 3.6 21.9 - - + -
138C GLU* 2.7 40.6 + - - -
153C LEU* 3.8 33.0 + - - +
154C GLN 4.8 2.2 + - - +
155C ASN 3.9 2.8 + - - -
156C ASN* 1.3 71.5 + - - +
158C ARG* 1.3 64.8 + - - +
160C PHE* 3.7 4.8 - - - +
161C GLU* 3.4 19.6 + - - +
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Residues in contact with ARG 158 (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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156C ASN* 3.1 5.2 + - - +
157C ARG* 1.3 78.5 - - - +
159C LEU* 1.3 67.0 + - - +
160C PHE 3.2 0.2 - - - -
161C GLU* 3.2 33.9 + - - +
162C GLN* 2.9 44.0 + - + +
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Residues in contact with LEU 159 (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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152C VAL* 4.1 13.2 - - + -
156C ASN* 2.6 38.5 + - + +
158C ARG* 1.3 73.0 - - - +
160C PHE* 1.3 53.7 + - - +
162C GLN* 2.9 29.4 + - - +
163C ASN* 2.8 55.5 + - - +
166C ARG* 6.2 0.2 - - - +
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Residues in contact with PHE 160 (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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70C PHE* 3.3 50.3 - + + -
71C TYR* 3.6 20.4 - - - -
100C TYR* 4.0 20.6 - + - -
102C PRO* 3.8 22.4 - - + -
139C PRO* 4.2 6.5 - - + -
149C ALA 3.6 25.1 - - - -
152C VAL* 3.5 12.7 - - + +
153C LEU* 3.7 23.8 - - + -
156C ASN 3.4 17.1 + - - +
157C ARG 3.7 4.9 - - - +
158C ARG 3.2 0.2 - - - -
159C LEU* 1.3 78.1 - - - +
161C GLU* 1.3 60.9 + - - +
163C ASN* 3.2 5.6 + - - +
164C VAL* 2.9 33.1 + - + +
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Residues in contact with GLU 161 (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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70C PHE* 3.9 34.2 + - + +
157C ARG 3.4 10.8 + - - +
158C ARG* 3.2 40.4 + - - +
160C PHE* 1.3 78.2 - - - +
162C GLN* 1.3 65.3 + - - +
164C VAL* 3.3 5.8 + - - +
165C GLN* 3.2 27.7 + - + +
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Residues in contact with GLN 162 (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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158C ARG* 2.9 29.9 + - - +
159C LEU* 3.1 30.2 - - - +
161C GLU* 1.3 72.2 - - - +
163C ASN* 1.3 68.4 + - - +
164C VAL 2.8 3.1 + - - -
165C GLN* 2.9 17.9 + - - +
166C ARG* 3.0 35.1 + - + +
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Residues in contact with ASN 163 (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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100C TYR* 3.9 20.3 + - + -
152C VAL* 3.9 14.3 - - - +
159C LEU* 2.8 50.4 + - - +
160C PHE* 3.5 5.6 - - - +
162C GLN* 1.3 73.0 - - - +
164C VAL* 1.3 57.9 + - - +
166C ARG* 4.1 19.3 + - - +
167C SER* 2.8 24.4 + - - -
173C ILE* 3.2 35.5 - - + +
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Residues in contact with VAL 164 (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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70C PHE* 3.0 33.9 - - + +
71C TYR* 3.8 23.8 - - + +
100C TYR* 4.2 9.6 - - + +
160C PHE* 2.9 55.4 + - + +
161C GLU 3.4 8.3 - - - +
162C GLN 2.8 1.4 + - - -
163C ASN* 1.3 75.4 - - - +
165C GLN* 1.3 64.2 + - - +
167C SER* 2.6 20.9 + - - +
168C MET* 3.0 21.8 + - + +
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Residues in contact with GLN 165 (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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69C GLY 5.3 0.8 + - - -
70C PHE* 3.3 24.8 + - - +
72C LYS* 4.0 11.5 + - - +
73C SER* 5.8 1.2 - - - -
161C GLU* 3.2 17.4 + - + +
162C GLN* 2.9 9.5 + - - +
164C VAL* 1.3 79.4 - - - +
166C ARG* 1.3 61.2 + - - +
168C MET* 3.3 19.4 + - - +
169C ARG* 2.9 72.5 + - - +
182C LEU* 5.3 2.4 - - - +
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Residues in contact with ARG 166 (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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162C GLN* 3.0 37.0 + - + +
163C ASN* 4.1 21.2 + - - +
165C GLN* 1.3 76.9 - - - +
167C SER* 1.3 60.1 + - - +
169C ARG* 3.7 10.1 + - - +
170C GLY 3.4 24.6 + - - +
171C GLY* 3.8 5.3 + - - -
172C TYR 3.0 35.0 + - - +
173C ILE* 4.6 7.2 - - - +
174C GLY 5.4 1.0 - - - +
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Residues in contact with SER 167 (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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100C TYR* 3.7 17.6 + - - +
163C ASN 2.8 16.3 + - - -
164C VAL* 2.6 26.3 + - - +
166C ARG* 1.3 76.4 - - - +
168C MET* 1.3 63.6 + - - +
170C GLY 3.4 7.3 + - - +
171C GLY 4.8 4.9 - - - -
173C ILE* 4.2 9.0 - - - -
178C PHE* 3.6 41.7 - - - +
179C GLU 3.6 8.1 - - - +
181C CYS* 5.1 0.8 - - - -
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Residues in contact with MET 168 (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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70C PHE 3.1 27.4 - - - +
71C TYR* 3.4 32.1 - - + +
72C LYS 4.0 2.2 - - - +
74C GLY* 4.1 17.7 - - - -
76C PHE* 4.2 9.9 - - + -
99C VAL* 5.8 2.0 - - + -
164C VAL* 3.0 23.7 + - + +
165C GLN* 3.4 26.9 - - - +
167C SER* 1.3 77.7 - - - +
169C ARG* 1.3 63.2 + - + +
180C ARG* 3.2 5.2 - - - +
181C CYS* 3.0 43.8 + - - -
182C LEU* 3.7 18.0 + - + +
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Residues in contact with ARG 169 (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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165C GLN* 2.9 63.8 + - - +
166C ARG* 3.9 8.8 - - + +
167C SER 3.3 0.2 - - - -
168C MET* 1.3 75.7 - - - +
170C GLY* 1.3 61.4 + - - +
180C ARG* 3.4 23.0 + - - +
182C LEU* 4.7 22.9 - - + +
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Residues in contact with GLY 170 (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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166C ARG* 3.4 9.6 + - - +
167C SER 3.4 3.2 + - - -
168C MET 3.1 4.6 - - - -
169C ARG* 1.3 85.4 - - - +
171C GLY* 1.3 58.2 + - - -
177C TYR* 3.4 18.6 - - - -
178C PHE 3.6 10.8 - - - -
180C ARG* 4.0 9.2 - - - -
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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