Contacts of the helix formed by residues 176 - 191 (chain A) in PDB entry 5V2C
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 ILE 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A ILE* 3.7 31.6 + - + +
78A ILE* 3.5 34.1 - - + +
80A GLY 3.7 5.5 + - - -
175A GLY* 1.3 72.4 - - - +
177A SER* 1.3 63.7 + - - +
179A THR* 3.3 15.7 + - - -
180A PHE* 3.3 39.2 + - + -
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Residues in contact with SER 177 (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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78A ILE* 2.8 37.8 + - - +
79A THR* 3.7 18.7 - - - +
80A GLY 4.9 0.6 + - - -
176A ILE* 1.3 71.3 - - - +
178A GLY* 1.3 66.1 + - - +
180A PHE* 3.1 17.0 + - - +
181A ASN* 3.0 21.7 + - - +
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Residues in contact with GLY 178 (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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79A THR 5.2 2.8 + - - -
81A ALA* 5.2 4.8 - - - +
173A PRO* 3.3 37.7 - - - +
175A GLY* 3.5 6.7 + - - -
176A ILE 3.2 0.8 - - - -
177A SER* 1.3 79.0 - - - +
179A THR* 1.3 60.8 + - - +
181A ASN* 3.3 7.9 + - - +
182A PHE 3.0 18.4 + - - -
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Residues in contact with THR 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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172A MET* 3.5 39.7 - - + +
173A PRO 4.0 0.9 + - - -
175A GLY 2.8 21.6 + - - -
176A ILE* 3.4 11.7 - - - -
177A SER 3.2 0.2 - - - -
178A GLY* 1.3 76.3 - - - +
180A PHE* 1.3 70.3 + - + +
182A PHE* 3.2 5.2 + - - +
183A MET* 3.0 38.4 + - + +
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Residues in contact with PHE 180 (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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78A ILE* 5.3 4.5 - - + -
176A ILE* 3.5 39.3 - - + -
177A SER* 3.1 17.3 + - - +
179A THR* 1.3 83.4 - - + +
181A ASN* 1.3 56.9 + - - +
183A MET* 3.1 20.8 + - - +
184A ILE* 2.9 46.3 + - + +
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Residues in contact with ASN 181 (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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60A ILE* 6.1 1.0 - - - +
173A PRO* 5.2 5.9 - - + +
177A SER 3.0 12.3 + - - +
178A GLY* 3.3 12.8 + - - +
180A PHE* 1.3 74.8 - - - +
182A PHE* 1.3 66.4 + - - +
184A ILE* 3.3 7.5 + - - +
185A VAL* 3.0 44.2 + - - +
332A HIS* 6.2 0.2 - - - +
333A GLU* 5.6 1.6 - - - +
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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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157A VAL* 3.9 37.0 - - + -
161A TYR* 4.0 13.0 - + + -
170A ASP 3.4 24.2 - - - -
171A GLY 4.1 2.0 - - - -
172A MET* 3.6 39.5 - - + -
173A PRO* 3.9 5.8 - - + +
178A GLY 3.0 12.7 + - - +
179A THR 3.4 9.4 - - - +
181A ASN* 1.3 79.4 + - - +
183A MET* 1.3 63.1 + - + +
185A VAL* 3.9 3.5 - - - +
186A PHE* 2.9 59.6 + + + +
290A ILE* 4.9 5.6 - - + -
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Residues in contact with MET 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 THR* 3.0 35.1 + - + +
180A PHE* 3.1 21.7 + - - +
182A PHE* 1.3 83.1 - - + +
184A ILE* 1.3 62.1 + - + +
186A PHE* 3.3 6.9 + - - +
187A GLN* 3.0 27.9 + - - +
192A ILE* 5.0 2.3 - - - +
198A HIS* 6.0 3.8 - - - +
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Residues in contact with ILE 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 PHE* 2.9 34.0 + - + +
181A ASN* 3.3 5.8 + - - +
183A MET* 1.3 76.8 - - + +
185A VAL* 1.3 69.4 + - + +
187A GLN* 3.2 5.3 + - - +
188A ALA* 3.1 19.6 + - - +
328A MET* 3.4 37.1 - - + +
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Residues in contact with VAL 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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170A ASP* 5.9 2.9 - - - +
181A ASN* 3.0 33.8 + - - +
182A PHE* 4.2 4.0 - - - +
184A ILE* 1.3 80.0 - - + +
186A PHE* 1.3 63.8 + - - +
188A ALA* 3.4 5.9 + - - +
189A GLU* 3.0 52.4 + - - +
328A MET* 5.5 0.9 - - + +
332A HIS* 3.8 34.3 - - + -
333A GLU* 5.2 7.9 - - + +
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Residues in contact with PHE 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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161A TYR* 3.4 51.8 - + - -
182A PHE* 2.9 46.1 + + + +
183A MET* 3.6 7.9 - - - +
184A ILE 3.2 0.2 - - - -
185A VAL* 1.3 77.4 - - - +
187A GLN* 1.3 56.4 + - - +
189A GLU* 4.8 0.7 - - - -
190A HIS* 2.8 55.1 + + + +
192A ILE* 3.9 19.2 + - + -
290A ILE* 3.6 29.4 - - + -
293A MET* 3.7 28.5 - - + -
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Residues in contact with GLN 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 MET 3.0 13.1 + - - +
184A ILE* 3.2 10.1 + - - +
186A PHE* 1.3 75.3 - - - +
188A ALA* 1.3 60.5 + - - +
191A ASN* 2.9 49.5 + - - +
192A ILE* 3.1 17.5 + - + +
193A LEU* 3.0 49.3 + - + +
321A ILE* 3.8 9.5 - - - +
325A ASN* 2.9 30.7 + - - +
328A MET* 4.0 13.0 - - + -
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Residues in contact with ALA 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 ILE 3.1 6.9 + - - +
185A VAL* 3.5 11.7 - - + +
187A GLN* 1.3 76.5 - - - +
189A GLU* 1.3 65.7 + - + +
325A ASN* 3.7 19.3 - - - +
328A MET* 3.6 29.1 - - + -
329A GLU* 3.8 18.0 - - - +
332A HIS* 5.7 0.9 - - - +
411C ALA* 3.7 12.5 + - - +
412C THR* 4.1 14.6 - - - +
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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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161A TYR* 3.9 13.0 + - - -
165A GLN* 5.6 0.3 - - - +
170A ASP* 5.5 3.6 - - - +
185A VAL* 3.0 30.8 + - - +
186A PHE* 5.3 0.2 - - - -
188A ALA* 1.3 82.0 - - + +
190A HIS* 1.3 77.7 + - + +
298A ASN* 3.5 10.2 + - - -
329A GLU* 6.2 2.7 - - + -
332A HIS* 2.7 35.2 + - + -
342A ASP* 2.9 16.4 - - + +
344A ALA 4.9 10.0 - - - +
401C LEU* 5.7 3.8 - - - +
410C VAL* 5.5 1.0 - - - +
411C ALA* 3.5 14.9 + - - +
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Residues in contact with HIS 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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161A TYR* 2.5 34.3 + + - -
165A GLN* 4.3 1.3 - - - -
186A PHE* 2.8 39.6 + + + +
189A GLU* 1.3 90.6 + - + +
191A ASN* 1.3 70.6 + - - +
192A ILE* 3.1 1.1 + - - +
293A MET* 3.0 40.7 + - + +
296A ASN* 3.4 17.3 - - - -
298A ASN* 2.7 30.1 + - - +
299A GLY 2.9 24.6 + - - -
411C ALA* 4.0 4.0 - - - -
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Residues in contact with ASN 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 GLN* 2.9 37.5 + - - -
189A GLU 3.8 0.2 - - - -
190A HIS* 1.3 80.0 - - - +
192A ILE* 1.3 65.8 + - - +
193A LEU* 3.1 3.5 - - - +
194A MET* 2.9 32.7 + - - +
299A GLY* 3.5 16.1 - - - +
300A PHE 3.4 21.6 + - - +
301A ASN* 5.1 3.0 - - - +
303A ASN* 5.6 4.2 + - - +
318A ALA 5.9 0.6 + - - -
321A ILE* 3.7 6.7 - - - +
322A ASN* 6.3 0.2 - - - +
325A ASN* 3.4 15.9 + - - +
411C ALA* 3.9 19.2 + - + +
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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