Contacts of the helix formed by residues 190 - 204 (chain C) in PDB entry 5NVL
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 GLN 190 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188C SER 3.1 15.4 + - - +
189C ASP* 1.3 72.3 + - - +
191C ALA* 1.3 64.3 + - - +
193C THR* 3.3 9.5 + - - +
194C ALA* 2.9 30.1 + - + +
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Residues in contact with ALA 191 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189C ASP* 3.2 10.2 + - - +
190C GLN* 1.3 77.5 - - - +
192C THR* 1.3 62.9 + - - +
194C ALA* 4.2 3.1 - - - +
195C ARG* 3.1 37.4 + - - +
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Residues in contact with THR 192 (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 VAL* 4.0 15.0 + - + +
165C GLU* 3.5 38.7 - - + +
184C ASN* 4.3 3.8 - - - +
189C ASP* 2.4 39.7 + - - -
191C ALA* 1.3 76.8 - - - +
193C THR* 1.3 60.2 + - - +
195C ARG* 3.1 7.7 + - - +
196C ILE* 2.9 42.3 + - + +
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Residues in contact with THR 193 (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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135C TRP* 2.8 37.2 + - - +
184C ASN* 3.6 15.5 - - - +
186C THR 4.0 0.4 - - - +
187C ALA 3.9 11.5 + - - +
189C ASP 2.9 16.2 + - - +
190C GLN* 3.3 15.4 + - - +
192C THR* 1.3 75.7 - - - +
194C ALA* 1.3 62.9 + - - +
196C ILE* 3.6 5.1 + - - +
197C ARG* 3.1 9.5 + - - +
214C TYR* 3.4 37.0 - - + +
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Residues in contact with ALA 194 (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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135C TRP* 5.3 1.3 - - - -
190C GLN* 2.9 19.3 + - + +
191C ALA* 4.2 3.4 - - - +
193C THR* 1.3 75.7 + - - +
195C ARG* 1.3 61.0 + - + +
197C ARG* 3.4 25.7 + - - +
198C ASP* 3.0 29.3 + - - +
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Residues in contact with ARG 195 (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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50B ALA* 5.8 6.9 + - - +
160C PHE 5.0 3.4 - - - +
161C MET* 4.5 15.2 + - - +
162C VAL* 4.1 22.2 - - + -
191C ALA* 3.1 25.4 + - - +
192C THR* 3.1 5.7 + - - +
194C ALA* 1.3 75.8 - - + +
196C ILE* 1.3 60.8 + - - +
198C ASP* 3.2 6.4 + - - +
199C THR* 2.8 35.8 + - - +
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Residues in contact with ILE 196 (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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135C TRP* 3.7 18.2 - - + -
160C PHE* 3.9 19.6 - - + -
162C VAL* 4.3 9.6 - - + -
166C ILE* 3.5 30.5 - - + -
182C ILE* 3.8 25.4 - - + +
183C TRP 5.5 1.1 - - - -
184C ASN* 3.5 31.2 - - + +
192C THR* 2.9 28.5 + - + +
193C THR* 3.9 5.2 - - - +
195C ARG* 1.3 74.4 - - - +
197C ARG* 1.3 58.1 + - - +
199C THR* 3.7 0.7 - - - -
200C LEU* 2.7 34.2 + - + +
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Residues in contact with ARG 197 (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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135C TRP* 3.5 48.6 - - + +
193C THR 3.1 9.4 + - - +
194C ALA* 3.6 25.7 + - - +
195C ARG 3.2 0.2 - - - -
196C ILE* 1.3 77.3 - - - +
198C ASP* 1.3 81.4 + - - +
200C LEU* 3.3 5.4 + - - +
201C ARG* 2.9 26.7 + - - +
212C MET* 4.2 18.2 - - + +
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Residues in contact with ASP 198 (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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81B LEU* 4.3 6.6 - - - +
194C ALA 3.0 17.6 + - - +
195C ARG* 3.6 7.0 - - - +
197C ARG* 1.3 93.0 + - - +
199C THR* 1.3 63.0 + - - +
201C ARG* 3.3 26.9 + - - +
202C ARG* 2.5 49.0 + - - +
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Residues in contact with THR 199 (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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46B GLU* 3.5 14.7 + - - +
159C GLN 3.8 16.8 + - - +
160C PHE* 3.4 44.5 + - + -
161C MET* 5.7 0.7 - - - +
195C ARG* 2.8 23.0 + - - +
198C ASP* 1.3 69.8 - - - +
200C LEU* 1.3 67.3 + - - +
202C ARG* 3.1 15.9 + - - +
203C VAL* 2.8 42.3 + - + +
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Residues in contact with LEU 200 (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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135C TRP* 4.0 29.2 - - + +
137C ILE* 3.8 19.7 - - + -
151C LEU* 3.7 31.4 - - + -
160C PHE* 4.1 6.9 - - + -
180C ILE* 5.5 1.1 - - + -
181C SER* 6.3 0.9 - - - -
182C ILE* 4.1 12.3 - - + -
196C ILE* 2.7 22.9 + - + +
197C ARG* 3.7 3.8 - - - +
199C THR* 1.3 72.7 - - - +
201C ARG* 1.3 64.2 + - - +
203C VAL* 4.3 4.7 - - + -
204C LEU* 3.1 59.4 + - + +
212C MET* 4.0 11.8 - - + +
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Residues in contact with ARG 201 (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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80B ALA 3.5 20.4 + - - -
81B LEU* 3.4 27.2 + - - +
82B VAL 4.2 1.2 + - - -
83B PRO* 4.0 30.4 - - - +
84B PHE 5.3 0.4 - - - +
197C ARG* 2.9 15.6 + - - +
198C ASP* 3.4 26.3 + - - +
199C THR 3.1 0.4 - - - -
200C LEU* 1.3 77.8 - - - +
202C ARG* 1.3 81.0 + - - +
204C LEU* 3.8 1.2 + - - +
205C ASN* 3.5 14.4 + - - -
206C LEU* 4.1 17.7 + - + +
208C PRO* 5.9 7.0 - - + +
212C MET* 3.9 18.5 - - + +
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Residues in contact with ARG 202 (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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45B ARG* 4.1 21.7 + - - +
46B GLU* 2.5 46.8 + - - +
49B LEU* 3.9 13.9 - - - +
80B ALA 3.6 17.7 - - - +
81B LEU* 3.3 20.7 - - - +
198C ASP* 2.5 43.8 + - - +
199C THR* 3.1 18.8 + - - +
201C ARG* 1.3 101.1 - - - +
203C VAL* 1.3 65.9 + - - +
205C ASN* 3.4 22.1 + - - +
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Residues in contact with VAL 203 (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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46B GLU* 4.5 15.3 - - + +
150C ASN* 3.6 41.3 + - + +
151C LEU* 4.3 6.3 - - + -
154C ALA* 3.6 21.5 - - + -
159C GLN* 5.6 0.4 - - + -
160C PHE* 5.0 1.1 - - + -
199C THR* 2.8 38.6 + - + +
200C LEU* 3.2 5.6 + - - +
202C ARG* 1.3 78.1 - - - +
204C LEU* 1.3 66.1 + - + +
205C ASN* 3.7 8.5 + - - +
45D ARG* 5.8 1.0 + - - -
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Residues in contact with LEU 204 (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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137C ILE* 3.3 33.9 - - + -
139C LEU* 6.3 0.4 - - + -
147C CYS* 3.4 41.5 - - + +
150C ASN* 4.1 14.0 + - + +
151C LEU* 3.9 20.0 - - + +
180C ILE* 4.9 5.6 - - + -
200C LEU* 3.1 29.7 + - + +
201C ARG 4.6 0.4 - - - +
203C VAL* 1.3 82.4 - - + +
205C ASN* 1.3 72.5 + - - +
206C LEU* 3.3 29.7 + - + +
212C MET* 5.0 0.4 - - + -
92D PHE* 5.7 3.1 - - - -
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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