Contacts of the helix formed by residues 190 - 203 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A ALA 5.0 1.8 - - - +
188A SER* 2.7 21.2 + - - +
189A ASP* 1.3 71.4 - - - +
191A ALA* 1.3 62.4 + - - +
193A THR* 4.0 7.1 - - - -
194A ALA* 3.1 26.2 + - - +
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Residues in contact with ALA 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A ASP* 3.1 8.0 + - - +
190A GLN* 1.3 79.9 - - - +
192A THR* 1.3 60.8 + - - +
194A ALA* 3.6 3.4 + - - +
195A ARG* 3.1 45.9 + - - +
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Residues in contact with THR 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A VAL* 3.9 15.2 - - + +
165A GLU* 3.6 34.1 - - + +
184A ASN* 4.3 4.0 - - - +
189A ASP* 2.6 41.5 + - - -
191A ALA* 1.3 72.5 - - - +
193A THR* 1.3 66.5 + - - +
194A ALA 3.2 0.3 + - - -
195A ARG* 3.2 6.9 + - - +
196A ILE* 3.0 43.3 + - + +
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Residues in contact with THR 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A TRP* 2.9 53.2 + - + +
184A ASN* 4.3 4.1 + - - -
187A ALA 3.6 8.4 + - - -
189A ASP 2.9 16.8 + - - -
190A GLN* 4.0 9.2 - - - -
192A THR* 1.3 77.6 - - - +
194A ALA* 1.3 61.9 + - - +
196A ILE* 4.7 4.5 - - - -
197A ARG* 3.2 8.3 + - - +
214A TYR* 3.6 38.1 + - + -
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Residues in contact with ALA 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A TRP* 5.4 0.9 - - - -
190A GLN 3.1 18.4 + - - +
191A ALA* 4.0 4.3 - - - +
193A THR* 1.3 76.1 - - - +
195A ARG* 1.3 64.7 + - + +
197A ARG* 3.2 8.1 + - - +
198A ASP* 3.0 32.8 + - - +
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Residues in contact with ARG 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A PHE 5.0 3.6 - - - +
161A MET* 4.5 8.7 + - - -
162A VAL* 4.0 22.7 - - + +
191A ALA* 3.1 40.7 + - - +
192A THR* 3.2 8.1 + - - +
194A ALA* 1.3 77.7 - - - +
196A ILE* 1.3 62.8 + - - +
198A ASP* 3.3 7.5 + - - +
199A THR* 2.8 28.5 + - - +
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Residues in contact with ILE 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A TRP* 3.6 19.7 - - + -
160A PHE* 4.3 14.3 - - + -
162A VAL* 4.2 8.1 - - + -
166A ILE* 3.6 28.7 - - + -
182A ILE* 4.0 23.8 - - + +
183A TRP 5.6 0.2 - - - +
184A ASN* 3.6 22.7 - - + +
192A THR* 3.0 39.2 + - + +
193A THR* 4.0 4.9 - - - +
195A ARG* 1.3 76.0 - - - +
197A ARG* 1.3 58.0 + - - +
199A THR* 3.1 7.1 + - - -
200A LEU* 2.8 31.2 + - + +
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Residues in contact with ARG 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A TRP* 3.5 42.3 - - + +
193A THR 3.2 12.6 + - - +
194A ALA* 3.2 12.0 + - - +
196A ILE* 1.3 79.2 - - - +
198A ASP* 1.3 71.0 + - - +
200A LEU* 3.2 3.5 + - - +
201A ARG* 3.0 21.6 + - + +
210A THR 5.2 5.1 + - - -
212A MET* 4.2 38.9 + - - +
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Residues in contact with ASP 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ALA* 3.0 21.3 + - - +
195A ARG* 3.8 5.9 - - - +
197A ARG* 1.3 84.3 - - - +
199A THR* 1.3 62.5 + - - +
201A ARG* 3.4 13.7 + - - +
202A ARG* 3.3 44.4 + - - +
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Residues in contact with THR 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A GLN 4.1 6.5 - - - +
160A PHE* 3.4 50.0 + - + -
195A ARG* 2.8 22.0 + - - +
196A ILE 3.5 4.0 - - - -
198A ASP* 1.3 74.5 - - - +
200A LEU* 1.3 56.2 + - - +
202A ARG* 3.1 18.9 + - - +
203A VAL* 2.7 55.2 + - + +
46D GLU* 4.0 6.3 + - - +
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Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A TRP* 3.7 25.4 - - + +
137A ILE* 4.5 5.6 - - + -
151A LEU* 3.8 26.9 - - + -
160A PHE* 4.3 7.9 - - + -
180A ILE* 5.6 1.8 - - + -
182A ILE* 3.7 18.8 - - + -
196A ILE* 2.8 20.9 + - + +
197A ARG 3.2 6.3 + - - +
199A THR* 1.3 71.1 - - - +
201A ARG* 1.3 65.7 + - - +
203A VAL* 4.5 2.5 - - - +
204A LEU* 2.8 55.2 + - + +
206A LEU* 4.5 1.8 - - - -
212A MET* 3.4 29.4 - - + -
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Residues in contact with ARG 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A ARG* 3.0 12.0 + - + +
198A ASP* 3.4 15.4 + - - +
200A LEU* 1.3 76.2 - - - +
202A ARG* 1.3 80.7 + - - +
205A ASN* 3.1 7.8 + - - -
206A LEU* 3.0 57.6 + - + +
207A PRO 5.3 2.2 - - - +
208A PRO* 5.7 6.7 - - + +
212A MET* 5.1 4.2 - - - -
80D ALA 3.6 24.4 + - - -
81D LEU* 3.8 19.8 + - - +
82D VAL 4.4 1.0 + - - -
83D PRO* 4.0 37.2 - - - +
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Residues in contact with ARG 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ASP* 3.5 30.8 + - - +
199A THR* 3.1 17.9 + - - +
201A ARG* 1.3 102.4 - - - +
203A VAL* 1.3 63.3 + - - +
205A ASN* 3.4 20.5 + - - +
45D ARG* 4.5 15.0 + - - +
46D GLU* 2.5 47.4 + - - +
49D LEU* 4.0 9.6 - - - +
80D ALA 3.5 20.9 - - - +
81D LEU* 3.2 30.1 - - - +
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Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ASN* 3.7 28.7 + - + +
151A LEU* 4.6 1.8 - - - -
154A ALA* 3.5 33.0 - - + -
159A GLN* 5.3 0.9 - - + -
160A PHE* 5.0 4.3 - - + -
199A THR* 2.7 42.1 + - + +
200A LEU* 4.1 2.5 - - - +
202A ARG* 1.3 73.8 - - - +
204A LEU* 1.3 69.7 + - + +
205A ASN* 3.7 4.7 + - - +
45B ARG* 5.8 0.9 + - - -
46D GLU* 4.2 18.6 - - + +
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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