Contacts of the helix formed by residues 185 - 197 (chain A) in PDB entry 5CXV
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 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A LEU 4.4 1.0 - - - +
184A SER* 1.4 80.4 + - - +
186A PRO* 1.3 73.8 - - + +
187A ILE* 4.1 11.2 - - + +
188A ILE* 3.0 37.7 + - + +
189A THR* 3.0 13.8 + - - +
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Residues in contact with PRO 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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184A SER 4.0 5.2 - - - +
185A GLN* 1.3 86.7 - - + +
187A ILE* 1.3 65.2 + - + +
189A THR* 3.1 14.9 - - + +
190A PHE* 3.0 29.1 + - - +
385A VAL* 4.6 0.2 - - - +
388A SER* 3.8 34.3 - - - +
389A THR* 3.6 9.8 - - - +
392A LYS* 6.6 0.2 - - - -
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Residues in contact with ILE 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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185A GLN* 3.1 8.9 - - + -
186A PRO* 1.3 87.8 - - + +
188A ILE* 1.3 66.1 + - + +
190A PHE* 3.9 12.1 - - + +
191A GLY* 2.9 20.8 + - - -
389A THR* 4.7 18.6 - - - +
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Residues in contact with ILE 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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182A PHE* 3.7 17.5 - - + +
183A LEU* 3.6 22.4 - - + -
184A SER* 3.4 25.6 - - - +
185A GLN* 3.0 23.4 + - + +
187A ILE* 1.3 77.8 - - - +
189A THR* 1.3 63.6 + - - +
191A GLY* 3.1 4.7 + - - -
192A THR* 3.0 28.5 + - + +
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Residues in contact with THR 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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183A LEU* 3.7 25.0 - - - +
185A GLN 3.0 6.9 + - - +
186A PRO* 3.1 31.6 - - + +
188A ILE* 1.3 75.2 - - - +
190A PHE* 1.3 56.1 + - - +
192A THR* 2.8 21.2 + - - -
193A ALA* 2.9 15.1 + - - +
381A TYR* 5.6 0.3 + - - -
385A VAL* 4.0 16.9 - - + +
388A SER* 5.4 2.0 - - - +
400A TRP* 6.5 0.7 - - + -
501A 0HK 3.3 22.3 - - - +
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Residues in contact with PHE 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 PRO 3.0 18.3 + - - +
187A ILE* 3.9 11.7 - - + +
188A ILE 3.1 0.4 - - - -
189A THR* 1.3 75.9 - - - +
191A GLY* 1.3 62.2 + - - +
193A ALA* 3.2 5.5 + - + +
194A MET* 2.9 60.7 + - + +
198A TYR* 5.0 8.1 - + - -
385A VAL* 3.6 10.5 - - + -
386A LEU* 3.5 50.9 - - + -
389A THR* 3.3 23.1 - - + -
390A PHE* 5.6 4.0 - + - -
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Residues in contact with GLY 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 ILE 2.9 15.0 + - - -
188A ILE 3.6 3.6 - - - -
190A PHE* 1.3 78.4 - - - +
192A THR* 1.3 61.6 + - - +
194A MET* 3.0 10.8 + - - +
195A ALA* 3.0 22.2 + - - +
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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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157A TRP* 4.6 10.5 - - + -
182A PHE* 5.0 7.2 - - + -
183A LEU* 3.8 18.7 - - + +
188A ILE* 3.0 19.6 + - + +
189A THR* 2.8 16.6 + - - -
191A GLY* 1.3 74.1 - - - +
193A ALA* 1.3 56.2 + - - +
195A ALA* 4.0 5.5 - - - +
196A ALA* 2.9 34.3 + - - +
501A 0HK 2.9 20.6 - - - +
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Residues in contact with ALA 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 THR 2.9 19.6 + - - +
190A PHE* 3.5 11.7 - - + +
191A GLY 3.2 0.4 - - - -
192A THR* 1.3 75.9 + - - +
194A MET* 1.3 58.2 + - - +
197A PHE* 2.9 25.8 + - - +
198A TYR* 3.1 19.7 + - + -
382A ASN* 3.7 18.8 - - - +
385A VAL* 4.3 11.0 - - + -
501A 0HK 3.5 15.7 - - + -
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Residues in contact with MET 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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190A PHE* 2.9 54.0 + - + +
191A GLY* 3.0 11.0 + - - +
193A ALA* 1.3 74.5 - - - +
195A ALA* 1.3 65.7 + - - +
196A ALA 3.4 0.3 + - - -
198A TYR* 3.4 27.5 + - + -
199A LEU* 3.1 32.1 + - + +
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Residues in contact with ALA 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 GLY 3.0 14.8 + - - +
192A THR* 4.0 6.7 - - - +
194A MET* 1.3 77.4 - - - +
196A ALA* 1.3 60.4 + - - +
199A LEU* 4.4 5.0 - - - +
200A PRO* 3.4 14.4 - - - +
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Residues in contact with ALA 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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110A GLN* 3.3 37.5 + - - +
113A VAL* 3.7 6.2 - - - +
157A TRP* 4.5 7.6 - - + -
192A THR 2.9 19.1 + - - +
195A ALA* 1.3 78.5 - - + +
197A PHE* 1.3 57.4 + - - +
200A PRO* 3.3 14.5 - - - +
501A 0HK 3.7 28.5 - - + -
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Residues in contact with PHE 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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113A VAL* 5.1 0.9 - - + -
193A ALA 2.9 13.8 + - - +
195A ALA 3.6 0.4 - - - -
196A ALA* 1.3 78.3 - - - +
198A TYR* 1.3 82.8 + + - +
199A LEU 3.4 1.6 - - - -
200A PRO* 3.2 5.2 - - - +
201A VAL* 2.9 44.4 + - + +
374A PHE* 3.6 23.1 - + - -
375A ILE* 4.8 2.2 - - - -
378A TRP* 3.5 48.9 - + + -
379A THR* 4.1 16.8 - - + -
382A ASN* 3.3 37.9 - - + +
501A 0HK 3.4 18.2 - - - +
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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