Contacts of the helix formed by residues 195 - 204 (chain C) in PDB entry 4HHM
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 THR 195 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182C PRO* 3.3 15.0 - - - +
193C LEU 3.4 0.6 - - - +
194C PRO* 1.3 88.8 - - + +
196C ILE* 1.3 65.5 + - - +
197C GLY 3.1 2.8 + - - -
198C HIS* 2.8 38.9 + - + +
199C ALA* 3.1 9.7 + - - +
221C GLU* 3.5 13.5 - - - +
224C ALA* 4.8 4.7 - - + -
226C LEU* 3.9 19.1 - - + -
195D THR* 4.5 0.4 - - + -
198D HIS* 3.2 21.9 - - + -
226D LEU* 4.3 16.2 - - + -
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Residues in contact with ILE 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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182C PRO* 3.6 10.3 - - + -
195C THR* 1.3 74.5 - - - +
197C GLY* 1.3 58.0 + - - +
199C ALA* 3.5 2.3 + - - +
200C LEU* 2.9 51.6 + - + +
214C VAL* 4.3 15.9 - - + -
216C PRO* 3.5 32.3 - - + -
221C GLU* 3.2 32.3 + - + +
228C PHE* 4.4 4.3 - - + -
231C GLY* 3.8 37.5 - - - +
232C ILE* 4.1 2.7 - - + +
234C GLN* 6.0 0.2 - - + -
235C ALA* 4.4 2.7 - - + -
198D HIS* 4.6 6.3 - - + +
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Residues in contact with GLY 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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195C THR* 3.1 4.8 + - - -
196C ILE* 1.3 77.7 - - - +
198C HIS* 1.3 59.8 + - - +
200C LEU* 3.1 10.8 + - - +
201C ALA 2.9 26.3 + - - -
197D GLY 3.0 27.6 - - - +
198D HIS* 3.7 21.5 + - - -
201D ALA* 4.7 0.2 - - - -
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Residues in contact with HIS 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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193C LEU* 3.7 16.6 - - - -
194C PRO* 3.5 27.8 - - + +
195C THR* 2.8 29.5 + - + +
197C GLY* 1.3 74.8 - - - +
199C ALA* 1.3 58.1 + - - +
202C PHE* 3.0 27.0 + - - +
195D THR* 3.1 30.1 - - - -
196D ILE* 4.6 7.5 - - + +
197D GLY* 3.5 20.3 + - - -
221D GLU* 4.7 2.0 + - - -
226D LEU* 4.3 6.3 - - + +
231D GLY* 4.7 15.2 - - - -
234D GLN* 3.1 37.7 + - + +
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Residues in contact with ALA 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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180C ILE* 4.2 17.3 - - + -
182C PRO* 3.6 31.0 - - + -
193C LEU* 4.3 14.9 - - + +
195C THR 3.1 5.4 + - - +
196C ILE 3.7 4.3 - - - +
198C HIS* 1.3 78.7 - - - +
200C LEU* 1.3 62.1 + - - +
202C PHE* 3.3 2.3 + - - +
203C ILE* 3.1 29.5 + - - +
214C VAL* 3.8 14.4 - - + -
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Residues in contact with LEU 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 ILE* 2.9 37.9 + - + +
197C GLY* 3.1 8.5 + - - +
199C ALA* 1.3 78.0 - - - +
201C ALA* 1.3 63.3 + - - +
202C PHE 3.3 0.5 + - - -
203C ILE* 3.4 12.8 + - + +
204C GLU* 3.4 19.5 + - + +
214C VAL* 3.6 24.9 - - + -
234C GLN* 4.3 22.9 - - + +
235C ALA* 4.4 11.2 - - - -
238C ALA* 5.4 4.7 - - + -
240C LYS* 3.8 30.5 - - + -
198D HIS* 6.1 0.2 - - + -
201D ALA* 3.6 22.2 - - + -
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Residues in contact with ALA 201 (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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197C GLY 2.9 15.6 + - - +
198C HIS* 3.7 4.5 - - - +
200C LEU* 1.3 77.0 - - - +
202C PHE* 1.3 63.3 + - - +
204C GLU* 3.5 16.1 + - - +
205C ARG* 3.7 12.5 + - - +
197D GLY 3.9 2.2 - - - +
200D LEU* 3.6 34.3 - - + -
201D ALA* 3.9 10.0 - - - +
204D GLU* 5.3 3.1 - - + +
234D GLN* 3.8 11.4 - - - +
237D TRP* 5.8 0.2 - - - -
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Residues in contact with PHE 202 (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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155C LEU* 3.8 17.0 - - + -
158C MET* 3.5 27.8 - - + -
159C LYS* 3.6 17.9 - - + -
162C PHE* 3.7 25.4 - + - -
180C ILE* 4.1 11.2 - - + -
193C LEU* 3.5 31.4 - - + -
198C HIS 3.0 18.0 + - - +
199C ALA 3.5 4.0 - - - +
201C ALA* 1.3 74.3 - - - +
203C ILE* 1.3 59.4 + - - +
205C ARG* 2.8 31.2 + - - +
206C LEU* 3.5 14.4 + - + +
234D GLN* 4.0 4.2 - - - +
237D TRP* 3.4 38.6 - + - -
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Residues in contact with ILE 203 (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 ILE* 3.7 22.2 - - + -
199C ALA 3.1 17.0 + - - +
200C LEU* 3.4 7.2 + - + +
202C PHE* 1.3 78.0 - - - +
204C GLU* 1.3 60.1 + - - +
206C LEU* 2.9 32.6 + - + +
209C PRO* 3.6 23.0 - - + +
212C TYR* 3.5 26.0 - - + +
213C GLY* 3.3 42.4 - - - +
214C VAL* 4.1 8.7 - - + -
240C LYS* 4.3 11.4 - - - +
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Residues in contact with GLU 204 (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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200C LEU* 3.4 14.3 + - + +
201C ALA 3.6 9.6 - - - +
202C PHE 3.1 1.4 + - - -
203C ILE* 1.3 76.3 - - - +
205C ARG* 1.3 62.2 + - + +
206C LEU 3.4 0.9 - - - +
209C PRO* 4.1 26.7 - - - +
240C LYS* 4.5 18.9 + - - +
201D ALA* 5.6 1.6 - - - +
204D GLU* 4.0 46.1 - - + +
205D ARG* 6.1 2.4 - - - +
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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