Contacts of the helix formed by residues 183 - 195 (chain A) in PDB entry 2VL7
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 GLU 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A PRO* 6.1 0.2 - - - +
39A LYS* 3.3 26.0 + - - -
58A THR* 4.5 0.9 - - - +
63A GLN* 3.6 32.3 + - + +
152A TYR* 3.0 5.5 + - - +
182A ASP* 1.3 92.0 + - + +
184A ALA* 1.3 56.3 + - - +
185A HIS* 3.1 29.6 + - + -
186A ASN* 3.0 42.0 + - - +
325A MET 2.9 8.8 + - - -
326A SER* 4.3 2.0 - - - -
327A GLY 4.8 0.7 + - - -
500A GLN* 4.1 11.6 + - - +
507A ARG* 5.9 1.0 + - - -
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Residues in contact with ALA 184 (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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152A TYR* 4.7 0.9 - - - -
181A ILE* 3.7 20.9 - - + +
182A ASP 3.8 3.6 - - - -
183A GLU* 1.3 71.0 - - - +
185A HIS* 1.3 64.9 + - - +
186A ASN 3.0 2.2 - - - -
187A LEU* 3.0 24.0 + - + +
324A LEU* 3.8 20.9 - - + -
325A MET 2.9 25.8 + - - +
326A SER* 3.9 0.6 - - - -
329A LEU* 4.3 2.2 - - + -
333A LEU* 3.7 18.7 - - + +
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Residues in contact with HIS 185 (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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59A ARG* 5.7 0.8 + - - -
183A GLU* 3.6 33.6 + - + -
184A ALA* 1.3 77.3 - - - +
186A ASN* 1.3 80.3 + - - +
187A LEU 3.1 0.2 - - - -
188A LEU* 3.2 24.4 + - - +
189A GLU* 4.7 0.7 + - - +
326A SER* 2.7 24.4 + - - +
328A THR* 3.5 24.5 - - - +
330A PRO* 3.9 20.0 - - + +
496A ILE* 4.2 22.3 - - + +
500A GLN* 3.4 28.1 + - + +
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Residues in contact with ASN 186 (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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59A ARG* 3.6 46.2 + - - +
63A GLN* 5.4 0.4 - - - +
152A TYR* 3.0 26.8 + - + +
183A GLU* 3.0 32.4 + - - +
184A ALA 3.0 0.8 - - - -
185A HIS* 1.3 90.1 + - - +
187A LEU* 1.3 65.0 + - - +
189A GLU* 3.1 19.2 + - - +
190A ALA 3.6 5.4 + - - -
193A TRP* 3.9 10.6 + - + +
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Residues in contact with LEU 187 (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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152A TYR* 5.9 1.1 - - + -
156A PHE* 3.8 20.9 - - + -
181A ILE* 4.3 15.5 - - + -
184A ALA* 3.0 18.3 + - - +
186A ASN* 1.3 77.8 - - - +
188A LEU* 1.3 60.6 + - - +
190A ALA* 3.1 18.8 + - - +
193A TRP* 3.4 32.3 - - + -
312A ILE* 3.9 38.1 - - + +
316A LEU* 5.3 0.7 - - + -
324A LEU* 3.6 31.2 - - + -
333A LEU* 4.0 14.6 - - + -
335A LEU* 5.2 0.2 - - + -
477A ARG* 4.7 4.5 + - - -
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Residues in contact with LEU 188 (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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185A HIS 3.4 14.3 - - - +
186A ASN 3.1 1.0 - - - -
187A LEU* 1.3 77.1 - - - +
189A GLU* 1.3 59.4 - - + +
190A ALA 3.4 0.7 - - - -
330A PRO* 3.9 14.4 - - + -
332A SER* 3.8 30.5 - - - +
333A LEU* 4.1 15.9 - - + +
474A ARG* 3.4 12.3 - - - +
477A ARG* 2.9 22.4 + - - +
478A LEU* 4.0 20.5 - - + +
492A ASP* 4.1 7.2 - - - +
493A LEU* 3.5 32.1 - - + -
496A ILE* 3.6 20.4 - - + -
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Residues in contact with GLU 189 (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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59A ARG* 5.4 4.9 + - - -
185A HIS 5.7 0.7 - - - +
186A ASN* 3.1 13.3 + - - +
188A LEU* 1.3 83.9 - - + +
190A ALA* 1.3 62.8 + - - +
191A ASP* 3.1 10.1 - - - -
192A LYS* 3.0 55.2 + - + +
193A TRP* 4.3 4.3 + - - +
474A ARG* 3.8 20.6 + - - +
493A LEU* 5.3 7.7 - - + +
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Residues in contact with ALA 190 (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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186A ASN 3.6 1.0 + - - -
187A LEU 3.1 19.8 + - - +
188A LEU 3.4 1.0 - - - -
189A GLU* 1.3 77.5 - - - +
191A ASP* 1.3 62.2 + - - +
192A LYS 3.1 0.7 - - - -
193A TRP* 3.0 56.8 + - + +
194A PHE* 3.3 8.7 - - + -
308A VAL* 3.6 16.8 - - + -
312A ILE* 3.9 11.9 - - + -
477A ARG* 4.6 0.4 - - - +
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Residues in contact with ASP 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 GLU 3.6 2.9 - - - -
190A ALA* 1.3 77.0 - - - +
192A LYS* 1.3 59.0 + - - +
193A TRP 3.4 0.2 + - - -
194A PHE* 3.6 9.4 + - - +
195A THR* 3.0 16.9 + - - -
304A VAL* 3.5 21.5 - - + +
305A PRO* 4.9 3.5 - - - +
308A VAL* 3.6 21.8 - - + +
470A MET* 3.8 15.6 - - - +
474A ARG* 3.0 40.4 + - - +
477A ARG* 3.0 29.6 + - - +
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Residues in contact with LYS 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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189A GLU* 3.0 42.5 + - + +
191A ASP* 1.3 77.6 - - - +
193A TRP* 1.3 68.7 + - + +
194A PHE 3.3 0.7 + - - -
195A THR* 3.4 21.7 + - - +
470A MET* 4.4 11.7 - - + +
471A VAL* 6.4 0.2 - - - +
474A ARG* 3.5 31.6 - - - +
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Residues in contact with TRP 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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152A TYR* 3.6 42.7 - + + -
153A PRO* 6.5 0.2 - - + -
156A PHE* 3.6 40.8 - + + -
157A GLN* 3.2 23.2 + - - +
186A ASN* 3.9 21.2 + - + +
187A LEU* 3.4 30.1 - - + -
189A GLU* 4.3 5.2 + - - +
190A ALA* 3.0 28.0 + - + +
192A LYS* 1.3 81.9 - - + +
194A PHE* 1.3 70.9 + + + +
195A THR 3.4 2.3 + - - +
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Residues in contact with PHE 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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156A PHE* 3.3 31.0 - + + -
157A GLN* 3.8 26.2 - - - +
158A LYS 5.6 0.2 - - - -
190A ALA* 3.3 22.0 - - + -
191A ASP* 3.6 4.4 + - - +
192A LYS 3.2 0.6 - - - -
193A TRP* 1.3 94.1 - + + +
195A THR* 1.3 58.4 + - - +
196A ARG* 4.4 1.4 - - - +
290A MET* 2.8 35.7 - - + +
305A PRO* 3.2 22.7 - - + +
308A VAL* 3.5 23.6 - - + -
311A LEU* 3.8 30.5 - - + -
312A ILE* 5.7 1.8 - - + -
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Residues in contact with THR 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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191A ASP 3.0 17.8 + - - -
192A LYS* 3.4 13.9 + - - +
193A TRP 3.4 2.6 - - - +
194A PHE* 1.3 80.4 - - - +
196A ARG* 1.3 70.6 + - - +
197A LYS* 4.3 10.3 - - + -
302A VAL* 3.1 34.3 - - + -
303A LYS 3.3 8.5 - - - +
304A VAL* 3.5 14.2 - - + +
305A PRO* 4.4 0.9 - - - -
470A MET* 3.7 10.0 - - + +
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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