Contacts of the helix formed by residues 178 - 193 (chain A) in PDB entry 1V9P
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 PRO 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A TYR* 3.8 25.1 - - + +
177A MET* 1.3 88.2 - - + +
179A ILE* 1.3 57.1 + - - +
180A GLU* 4.4 5.6 - - + +
181A ALA* 2.9 15.2 + - + +
182A PHE 2.7 31.5 + - - -
220A GLY 4.6 9.0 - - - +
222A ARG* 4.2 22.4 - - + -
282A PRO* 3.2 21.8 - - + +
283A PHE* 4.5 3.4 - - - -
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Residues in contact with ILE 179 (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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177A MET 3.8 0.8 + - - -
178A PRO* 1.3 72.1 - - - +
180A GLU* 1.3 65.3 + - - +
182A PHE* 3.9 10.8 - - + -
183A LEU* 2.7 49.5 + - + +
200A PRO* 5.1 3.4 - - + -
279A HIS* 6.1 5.2 - - - -
281A LEU 4.5 9.2 - - - +
282A PRO 3.5 5.2 + - - +
283A PHE* 4.0 7.6 - - - +
284A GLU* 3.7 30.7 - - + +
382A GLY* 3.4 24.9 - - - +
384A VAL* 3.7 20.9 - - + -
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Residues in contact with GLU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A PRO* 3.0 6.6 + - + +
179A ILE* 1.3 77.7 - - - +
181A ALA* 1.3 53.6 + - - +
183A LEU* 3.4 8.6 - - + +
184A ARG* 2.7 35.5 + - - +
282A PRO 5.1 0.4 + - - -
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Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A MET* 3.5 19.3 - - + -
178A PRO* 2.9 15.6 + - + +
180A GLU* 1.3 75.6 - - - +
182A PHE* 1.3 69.4 + - - +
184A ARG* 2.6 28.9 + - - +
185A LEU* 2.7 13.8 + - - +
220A GLY* 3.9 25.8 - - - +
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Residues in contact with PHE 182 (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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177A MET* 3.4 17.5 - - + +
178A PRO 2.7 19.6 + - - +
179A ILE* 3.6 9.6 - - + +
181A ALA* 1.3 70.8 - - - +
183A LEU* 1.3 75.3 + - + +
185A LEU* 3.4 3.3 + - - +
186A ASN* 2.9 40.7 + - - +
197A PHE* 3.7 24.7 - + + -
198A LYS 4.2 1.8 - - - -
199A ASN* 3.3 36.3 - - - -
200A PRO* 3.7 20.6 - - + -
203A ALA* 3.6 21.8 - - + -
381A ALA* 4.1 26.7 - - + -
382A GLY* 4.3 5.2 - - - -
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Residues in contact with LEU 183 (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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179A ILE* 2.7 46.1 + - + +
180A GLU* 3.4 6.7 - - - +
182A PHE* 1.3 86.0 - - + +
184A ARG* 1.3 65.8 + - - +
186A ASN* 3.4 8.1 + - + +
187A GLU* 3.0 36.5 + - - +
384A VAL* 4.6 15.7 - - + -
385A ILE* 3.3 36.3 - - + -
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Residues in contact with ARG 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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180A GLU 2.7 13.5 + - - +
181A ALA* 2.6 24.8 + - - +
183A LEU* 1.3 68.5 - - - +
185A LEU* 1.3 77.2 + - - +
187A GLU* 2.9 24.3 + - + +
188A GLU* 2.8 46.2 + - + +
218A LYS* 3.2 40.5 + - - +
219A ARG* 4.5 7.4 - - - +
220A GLY* 4.4 11.1 - - - +
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Residues in contact with LEU 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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177A MET* 3.7 20.6 - - + -
181A ALA 2.7 17.2 + - - +
182A PHE 3.6 4.7 - - - +
184A ARG* 1.3 82.2 - - - +
186A ASN* 1.3 57.8 + - - +
188A GLU* 3.6 11.1 + - + +
189A LEU* 3.0 43.2 + - + +
192A ARG* 5.6 1.3 - - - +
197A PHE* 3.6 27.6 - - + -
203A ALA* 4.2 1.8 - - + +
207A SER* 3.6 20.6 - - - +
219A ARG* 3.9 30.3 - - - +
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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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182A PHE* 2.9 30.5 + - + +
183A LEU* 3.6 12.8 - - + +
184A ARG 3.0 0.2 - - - -
185A LEU* 1.3 77.5 - - - +
187A GLU* 1.3 60.9 + - - +
189A LEU* 3.6 4.4 + - - +
190A GLU* 3.1 32.8 + - - +
196A VAL* 3.0 29.0 - - - +
197A PHE* 2.9 44.6 + - - +
360A HIS* 4.0 10.1 - - - -
381A ALA* 5.7 1.0 - - - +
387A GLU* 4.8 3.6 + - - -
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Residues in contact with GLU 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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183A LEU* 3.0 26.3 + - - +
184A ARG* 2.9 15.8 + - + +
186A ASN* 1.3 73.6 - - - +
188A GLU* 1.3 65.4 + - + +
189A LEU 3.1 2.6 + - - -
190A GLU* 3.2 23.5 + - - +
191A GLU* 3.3 18.8 + - + +
334A ARG* 5.7 7.7 + - - +
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Residues in contact with GLU 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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184A ARG* 2.8 58.4 + - + +
185A LEU* 4.0 8.0 - - + +
187A GLU* 1.3 77.1 - - + +
189A LEU* 1.3 60.8 + - + +
191A GLU* 3.7 6.3 + - - +
192A ARG* 3.2 35.9 + - + +
218A LYS* 5.5 7.9 + - - +
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Residues in contact with LEU 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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185A LEU* 3.0 49.0 + - + +
186A ASN* 3.8 11.2 - - - +
187A GLU 3.1 0.4 - - - -
188A GLU* 1.3 77.6 - - + +
190A GLU* 1.3 65.6 + - - +
192A ARG* 3.1 35.2 + - - +
193A GLY 3.0 17.2 + - - -
194A GLU* 3.0 31.3 + - + -
195A LYS 4.5 10.1 - - - +
196A VAL* 4.1 9.4 - - + -
197A PHE* 4.2 18.8 - - + -
219A ARG* 5.8 1.3 - - - +
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Residues in contact with GLU 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* 3.1 18.7 + - - +
187A GLU* 3.2 16.9 + - - +
189A LEU* 1.3 75.7 - - - +
191A GLU* 1.3 64.7 + - - +
193A GLY* 3.0 14.4 + - - -
196A VAL* 3.3 14.8 - - + +
337A ARG* 3.5 31.3 + - - +
339A THR* 5.4 1.0 - - - +
358A THR* 4.4 5.6 + - - +
360A HIS* 3.0 47.6 + - + +
361A ASN* 3.6 14.7 + - - +
422A VAL* 4.0 1.2 - - - +
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Residues in contact with GLU 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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187A GLU 3.3 12.7 + - - +
188A GLU* 4.0 9.0 - - - +
189A LEU 3.2 0.2 - - - -
190A GLU* 1.3 80.7 - - - +
192A ARG* 1.3 64.1 + - + +
193A GLY 3.1 0.9 + - - -
334A ARG* 4.6 20.8 + - - +
335A THR* 3.1 32.1 + - - +
337A ARG* 2.5 51.6 + - - +
339A THR* 5.2 0.2 + - - -
422A VAL* 4.0 10.2 - - - +
424A ARG* 4.2 8.5 + - - +
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Residues in contact with ARG 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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185A LEU* 5.6 1.6 - - - +
188A GLU* 3.2 21.7 + - + +
189A LEU* 3.1 34.2 + - - +
191A GLU* 1.3 78.2 - - + +
193A GLY* 1.3 58.9 + - - +
194A GLU* 3.3 37.3 + - + +
218A LYS* 5.8 4.0 - - - +
219A ARG* 4.8 12.3 - - - +
421A LYS* 4.2 16.1 + - - +
422A VAL* 4.5 1.7 - - - +
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Residues in contact with GLY 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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189A LEU 3.0 0.4 + - - -
190A GLU 3.0 7.7 + - - -
191A GLU 3.0 4.2 - - - -
192A ARG* 1.3 79.8 - - - +
194A GLU* 1.3 58.9 + - - +
361A ASN* 3.5 4.2 - - - -
363A SER* 2.6 28.9 + - - -
421A LYS* 3.6 17.3 - - - +
422A VAL* 3.2 27.3 - - - +
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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