Contacts of the helix formed by residues 195 - 204 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182G PRO* 3.4 12.0 - - - +
193G LEU 3.3 0.2 + - - -
194G PRO* 1.3 92.0 - - + +
196G ILE* 1.3 67.1 + - - +
197G GLY 3.2 8.3 + - - -
198G HIS* 2.9 38.7 + - + +
199G ALA 3.1 9.5 + - - -
221G GLU* 3.7 14.8 - - - +
224G ALA* 4.8 4.7 - - + -
226G LEU* 3.9 17.9 - - + -
195H THR* 4.5 1.1 - - + -
198H HIS* 3.2 14.2 - - - -
226H LEU* 4.2 16.2 - - + -
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Residues in contact with ILE 196 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182G PRO* 3.7 10.3 - - + -
195G THR* 1.3 73.1 - - - +
197G GLY* 1.3 63.7 + - - +
199G ALA* 3.2 3.2 + - - +
200G LEU* 3.0 42.8 + - + +
214G VAL* 4.4 3.5 - - + +
216G PRO* 3.5 35.7 - - + -
221G GLU* 3.0 41.7 + - + +
228G PHE* 4.1 5.2 - - + -
231G GLY* 3.9 38.1 - - - +
232G ILE 4.1 1.1 - - - +
234G GLN* 5.5 0.2 - - + -
235G ALA* 4.7 7.6 - - + -
198H HIS* 4.3 7.0 - - + +
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Residues in contact with GLY 197 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195G THR* 3.1 4.8 + - - -
196G ILE* 1.3 79.8 - - - +
198G HIS* 1.3 56.5 + - - +
200G LEU* 3.2 9.5 + - - +
201G ALA* 2.9 25.6 + - - +
197H GLY 3.2 14.2 - - - +
198H HIS* 3.4 38.2 + - - -
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Residues in contact with HIS 198 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193G LEU* 3.5 21.2 - - - +
194G PRO* 3.5 29.4 - - + +
195G THR* 2.9 29.2 + - + +
197G GLY* 1.3 71.8 - - - +
199G ALA* 1.3 66.0 + - - +
202G PHE* 3.0 21.3 + - - +
195H THR* 3.3 29.3 + - - -
196H ILE* 4.3 9.7 - - + +
197H GLY* 3.6 16.1 + - - -
221H GLU* 4.6 1.8 + - - -
226H LEU* 4.6 5.5 - - + +
231H GLY* 4.6 14.9 - - - -
234H GLN* 3.0 37.8 + - + +
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Residues in contact with ALA 199 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180G ILE* 4.3 19.2 - - + +
182G PRO* 3.7 26.0 - - + -
193G LEU* 4.4 10.4 - - + +
195G THR 3.1 5.3 + - - -
196G ILE 3.2 7.4 + - - +
198G HIS* 1.3 76.6 - - - +
200G LEU* 1.3 59.4 + - - +
202G PHE* 3.1 8.4 + - - +
203G ILE* 2.9 35.0 + - - +
214G VAL* 3.8 13.7 - - + -
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Residues in contact with LEU 200 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196G ILE* 3.0 34.5 + - + +
197G GLY* 3.6 6.7 - - - +
199G ALA* 1.3 76.8 - - - +
201G ALA* 1.3 62.4 + - - +
203G ILE* 3.3 16.5 + - + +
204G GLU* 3.4 18.5 + - - +
214G VAL* 3.7 17.3 - - + -
234G GLN* 4.4 27.8 - - + +
235G ALA* 4.5 4.3 - - - -
238G ALA* 4.6 8.5 - - + -
240G LYS* 3.3 40.8 - - + -
201H ALA* 3.7 20.0 - - + -
205H ARG* 6.0 0.2 - - - +
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Residues in contact with ALA 201 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197G GLY 2.9 16.5 + - - +
198G HIS* 4.6 0.4 - - - -
200G LEU* 1.3 76.9 - - - +
202G PHE* 1.3 63.2 + - - +
204G GLU* 3.3 19.0 + - - +
205G ARG* 3.9 10.4 + - - +
197H GLY 3.8 1.1 - - - +
200H LEU* 3.5 33.9 - - + -
201H ALA* 3.7 11.8 - - - +
204H GLU* 5.6 1.1 - - - +
234H GLN* 3.8 15.9 - - - +
237H TRP* 5.8 0.2 - - - -
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Residues in contact with PHE 202 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155G LEU* 4.0 15.0 - - + -
158G MET* 3.8 22.9 - - + -
159G LYS* 3.7 29.8 - - + -
162G PHE* 3.9 10.8 - + - -
180G ILE* 3.6 32.8 - - + -
193G LEU* 3.7 19.3 - - + -
198G HIS 3.0 19.5 + - - +
199G ALA 3.1 3.6 + - - +
201G ALA* 1.3 77.0 - - - +
203G ILE* 1.3 64.4 + - - +
205G ARG* 3.0 18.2 + - - +
206G LEU* 3.8 25.3 + - + +
234H GLN* 3.9 5.7 - - - +
237H TRP* 3.8 30.5 - + - -
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Residues in contact with ILE 203 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180G ILE* 3.9 18.8 - - + -
199G ALA 2.9 20.2 + - - +
200G LEU* 3.3 13.7 + - + +
202G PHE* 1.3 76.5 - - - +
204G GLU* 1.3 63.5 + - - +
205G ARG 3.0 1.6 + - - -
206G LEU* 3.0 24.0 + - + +
209G PRO* 3.7 24.1 - - + +
212G TYR* 3.7 29.4 - - + +
213G GLY* 3.5 34.3 - - - +
214G VAL* 4.0 12.8 - - + -
240G LYS* 4.2 13.2 - - + +
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Residues in contact with GLU 204 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200G LEU 3.4 13.9 + - - +
201G ALA* 3.3 10.9 + - - +
202G PHE 3.2 1.2 + - - -
203G ILE* 1.3 76.8 - - - +
205G ARG* 1.3 62.5 + - + +
206G LEU 3.4 1.5 + - - +
209G PRO* 4.1 20.0 - - - +
240G LYS* 4.0 10.7 - - - +
201H ALA* 5.2 3.4 - - - +
204H GLU* 3.6 46.8 - - + +
205H ARG* 2.8 32.2 + - - -
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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