Contacts of the helix formed by residues 189 - 200 (chain C) in PDB entry 4BVH
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 189 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185C PHE* 3.3 40.8 - - + +
186C PHE* 5.5 0.2 - - - -
187C HIS 4.0 6.7 - - - +
188C ASN* 1.4 88.3 - - - +
190C LYS* 1.4 66.6 + - + +
191C PRO 3.4 1.1 - - - -
192C PHE* 3.4 7.0 + - + +
193C PHE* 3.1 32.1 + - + -
277C VAL* 4.3 22.4 - - + -
286C VAL* 4.7 11.7 - - + -
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Residues in contact with LYS 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C ASN* 3.2 21.1 + - - +
189C PRO* 1.4 80.9 - - + +
191C PRO* 1.4 65.4 - - + +
193C PHE* 3.1 7.6 + - - +
194C THR* 2.8 34.1 + - - +
277C VAL* 4.1 21.1 - - + -
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Residues in contact with PRO 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C PHE* 4.4 20.0 - - + -
188C ASN* 3.6 29.8 - - - +
190C LYS* 1.4 90.5 - - + +
192C PHE* 1.3 67.7 + - - +
194C THR* 3.1 9.9 + - - +
195C LEU* 2.9 22.6 + - - +
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Residues in contact with PHE 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C PHE* 4.6 11.4 - + - -
184C PHE* 5.6 2.7 - - + -
185C PHE* 3.7 29.2 - + + -
188C ASN 5.2 0.8 + - - +
189C PRO* 3.4 9.3 + - + +
190C LYS 3.4 0.4 - - - -
191C PRO* 1.3 79.6 - - - +
193C PHE* 1.3 65.0 + + - +
195C LEU* 3.1 26.5 + - + +
196C ALA* 2.8 24.7 + - + -
230C ILE* 5.2 2.0 - - + -
251C PHE* 4.1 23.3 - + - -
289C PRO* 3.9 28.0 - - + -
291C ILE* 4.2 19.5 - - + -
293C PHE* 3.5 36.3 - + + -
1394C OCZ 5.2 0.4 - - + -
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Residues in contact with PHE 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C PHE* 3.8 29.4 - + - -
189C PRO* 3.1 35.4 + - + -
190C LYS* 3.1 7.6 + - - +
192C PHE* 1.3 77.8 - + - +
194C THR* 1.3 58.8 + - - +
196C ALA* 3.2 8.9 + - + +
197C LYS* 2.9 26.9 + - - +
268C ILE* 4.5 0.2 - - + -
272C VAL* 4.0 23.8 - - + +
275C ASP* 5.3 2.9 - - - -
276C ARG 5.5 1.8 - - - +
277C VAL* 4.0 24.0 - - + -
278C PRO* 3.4 32.8 - - + -
286C VAL* 4.0 2.7 - - + -
287C VAL 3.2 24.2 - - - -
289C PRO* 3.8 20.9 - - + -
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Residues in contact with THR 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C LYS* 2.8 21.1 + - - +
191C PRO* 3.1 10.8 + - - +
193C PHE* 1.3 71.6 - - - +
195C LEU* 1.3 62.6 + - - +
197C LYS* 3.4 22.6 + - - +
198C GLU* 3.3 18.9 + - - +
275C ASP* 4.1 18.2 + - - +
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Residues in contact with LEU 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C PHE* 3.4 37.7 - - + -
191C PRO 2.9 12.6 + - - +
192C PHE* 3.3 23.1 - - + +
194C THR* 1.3 74.6 - - - +
196C ALA* 1.3 64.7 + - - +
198C GLU* 2.9 15.3 + - + +
199C LEU* 2.9 48.3 + - + +
230C ILE* 5.4 2.7 - - + -
251C PHE* 5.8 0.7 - - + -
1394C OCZ 5.4 2.5 - - + -
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Residues in contact with ALA 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C PHE* 2.8 20.8 + - + +
193C PHE* 3.2 21.7 + - + +
195C LEU* 1.3 71.3 - - - +
197C LYS* 1.3 54.5 + - - +
199C LEU 4.3 0.2 - - - +
200C TYR* 2.7 40.8 + - + +
251C PHE* 3.6 34.5 - - + -
272C VAL* 3.9 12.8 - - + -
289C PRO* 4.9 1.6 - - + -
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Residues in contact with LYS 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C PHE 2.9 12.5 + - - +
194C THR* 3.5 24.6 - - - +
195C LEU 3.1 0.2 - - - -
196C ALA* 1.3 77.0 - - - +
198C GLU* 1.3 64.2 + - - +
200C TYR* 4.0 6.4 + - - +
203C ASN* 4.8 3.8 + - - +
272C VAL* 3.6 28.2 - - - +
273C MET* 4.1 41.5 - - + +
275C ASP* 3.2 34.4 + - - +
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Residues in contact with GLU 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C THR 3.3 9.0 + - - +
195C LEU* 2.9 17.1 + - + +
197C LYS* 1.3 82.5 - - - +
199C LEU* 1.3 61.5 + - + +
203C ASN* 2.8 51.9 + - - +
204C TYR* 2.4 36.7 + - + +
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Residues in contact with LEU 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C ILE* 4.0 34.8 - - + -
195C LEU* 2.9 40.6 + - + +
196C ALA 3.1 0.4 + - - -
198C GLU* 1.3 77.2 - - + +
200C TYR* 1.3 68.2 + - - +
201C PRO* 3.6 4.5 - - - +
204C TYR* 4.2 18.2 - - + -
230C ILE* 4.1 28.9 - - + -
231C ASP* 4.3 19.4 - - + +
251C PHE* 3.9 21.9 - - + -
1394C OCZ 4.4 15.9 - - + -
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Residues in contact with TYR 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C ALA* 2.7 30.5 + - + +
197C LYS* 4.3 8.8 - - - +
198C GLU 3.6 1.0 - - - -
199C LEU* 1.3 74.3 - - - +
201C PRO* 1.4 84.1 - - + +
202C GLY 3.3 2.1 + - - -
203C ASN* 3.6 14.7 + - - +
204C TYR 5.1 0.5 + - - -
251C PHE* 3.6 39.8 + + + -
265C GLY* 2.6 39.5 + - - -
266C GLU* 5.3 0.7 - - - -
268C ILE* 3.2 22.7 - - + +
269C ARG* 3.8 35.7 - - + +
272C VAL* 4.3 16.8 - - + -
273C MET* 5.0 8.7 - - - -
289C PRO* 5.2 0.6 - - + +
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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