Contacts of the helix formed by residues 157 - 168 (chain E) in PDB entry 2NVX
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 157 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71E LYS* 3.7 27.6 - - - +
72E PHE* 3.7 16.4 - - - -
156E LEU* 1.3 76.9 - - - +
158E SER* 1.3 57.9 + - - +
159E ASP* 3.8 8.8 + - - +
160E GLU* 2.7 55.1 + - - +
161E LYS* 2.9 12.5 + - - +
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Residues in contact with SER 158 (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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72E PHE* 4.9 2.2 - - - -
156E LEU 4.1 0.2 + - - -
157E SER* 1.3 72.8 - - - +
159E ASP* 1.3 68.7 + - - +
161E LYS* 3.5 14.2 - - - +
162E ARG* 3.4 20.4 + - - +
194E GLU* 6.1 1.1 - - - -
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Residues in contact with ASP 159 (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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157E SER* 3.1 8.6 - - - +
158E SER* 1.3 85.2 + - - +
160E GLU* 1.3 62.8 + - + +
161E LYS 3.3 0.2 - - - -
162E ARG* 3.8 6.2 + - - +
163E GLU* 3.4 19.6 + - - +
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Residues in contact with GLU 160 (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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1006A ILE* 6.1 0.9 - - - +
71E LYS* 4.0 29.4 + - - +
156E LEU* 3.9 22.9 - - + +
157E SER* 2.7 36.3 + - - +
159E ASP* 1.3 78.7 - - + +
161E LYS* 1.3 59.6 + - - +
163E GLU* 3.4 13.1 - - + +
164E LEU* 2.9 26.9 + - - +
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Residues in contact with LYS 161 (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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156E LEU* 4.0 9.3 - - + +
157E SER 2.9 10.2 + - - +
158E SER* 3.5 16.6 - - - +
160E GLU* 1.3 75.9 - - - +
162E ARG* 1.3 52.3 + - - +
164E LEU* 2.6 27.9 + - + +
165E LEU* 2.7 39.5 + - + +
172E GLU* 4.0 23.1 + - - +
193E GLY* 3.2 38.1 + - - +
195E VAL* 3.7 17.0 - - + -
213E ILE* 3.7 17.1 - - - +
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Residues in contact with ARG 162 (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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158E SER 3.4 11.2 + - - +
159E ASP* 4.1 6.7 - - - +
160E GLU 3.5 0.2 - - - -
161E LYS* 1.3 79.0 - - - +
163E GLU* 1.3 55.8 + - - +
165E LEU* 4.2 8.7 - - + -
166E LYS* 3.0 70.8 + - + +
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Residues in contact with GLU 163 (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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1004A ASN* 5.4 0.5 - - - +
1005A GLU* 4.9 14.7 + - - +
1006A ILE* 3.7 36.4 + - + +
159E ASP 3.4 14.4 + - - +
160E GLU* 3.4 17.2 + - + +
161E LYS 3.0 0.2 - - - -
162E ARG* 1.3 76.5 - - - +
164E LEU* 1.3 61.4 + - - +
166E LYS* 5.2 0.9 - - - -
167E ARG* 3.2 48.5 + - - +
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Residues in contact with LEU 164 (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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866A PHE* 5.6 0.7 - - + -
1006A ILE* 4.4 14.6 - - + -
156E LEU* 5.1 5.2 - - + -
160E GLU 2.9 12.4 + - - +
161E LYS* 2.6 16.0 + - + +
163E GLU* 1.3 73.7 - - - +
165E LEU* 1.3 60.9 + - + +
167E ARG* 5.1 0.4 - - - -
168E TYR* 3.1 49.3 + - + +
170E LEU* 5.1 2.9 - - + +
175E LEU* 4.2 21.8 - - + -
195E VAL* 5.1 4.9 - - + -
211E TYR* 3.5 63.3 - - + +
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Residues in contact with LEU 165 (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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161E LYS* 2.7 42.9 + - + +
162E ARG* 3.9 10.1 - - + +
164E LEU* 1.3 80.0 - - + +
166E LYS* 1.3 59.2 + - - +
169E ARG* 3.6 0.9 - - - -
170E LEU* 3.0 46.7 + - + +
171E LYS 3.9 7.6 - - - +
172E GLU* 3.7 36.1 - - + +
175E LEU* 4.1 27.4 - - + -
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Residues in contact with LYS 166 (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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162E ARG* 3.0 48.1 + - + +
163E GLU* 4.7 0.9 - - - +
165E LEU* 1.3 76.4 - - - +
167E ARG* 1.3 92.0 + - + +
168E TYR 3.3 2.0 - - - -
169E ARG* 3.0 26.0 + - - +
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Residues in contact with ARG 167 (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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1004A ASN* 3.3 54.0 + - - +
1006A ILE* 4.9 8.3 - - + -
1007A ILE* 4.5 12.3 - - + +
163E GLU* 3.2 41.8 + - - +
164E LEU* 4.6 0.9 - - - +
166E LYS* 1.3 104.6 - - + +
168E TYR* 1.3 61.7 + - + +
169E ARG* 3.4 5.0 - - - +
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Residues in contact with TYR 168 (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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853A ASP* 4.5 25.6 - - + +
855A THR* 5.4 3.1 - - - -
857A ARG* 4.8 1.7 + - - -
863A VAL* 6.4 0.9 - - + -
866A PHE* 4.0 49.8 + + - +
867A ILE* 5.5 0.9 - - - +
1000A LEU* 4.9 9.3 - - + +
1006A ILE* 4.8 14.5 + - + +
1007A ILE* 4.5 21.2 - - + +
1010A ALA* 4.4 18.0 - - - +
164E LEU* 3.1 41.3 + - + +
167E ARG* 1.3 78.1 - - + +
169E ARG* 1.3 78.0 + - - +
170E LEU* 3.5 26.2 - - + +
209E ALA* 6.1 0.3 - - - +
211E TYR* 5.0 6.8 - + - -
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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