Contacts of the helix formed by residues 195 - 207 (chain G) in PDB entry 1RZR
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 LYS 195 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148G ILE* 4.4 28.7 - - + +
161G TYR* 3.5 32.6 - - + +
162G GLU* 3.4 26.9 - - + +
190G PRO 3.4 6.9 + - - +
191G ILE* 4.4 3.4 - - - +
194G ALA* 1.3 99.4 - - + +
196G LYS* 1.3 62.1 + - - +
197G VAL 3.6 1.1 - - - -
198G LYS* 4.1 10.6 - - - +
199G GLY* 3.1 21.1 + - - -
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Residues in contact with LYS 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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161G TYR* 4.7 4.5 - - + +
165G ALA* 3.7 16.3 - - + +
182G PHE* 3.7 25.7 - - + -
191G ILE* 2.7 52.2 + - + +
192G ASN* 3.1 20.0 + - - +
195G LYS* 1.3 74.7 - - - +
197G VAL* 1.3 65.7 + - - +
199G GLY 3.4 0.7 + - - -
200G TYR* 3.0 23.0 + - - +
221G TYR* 5.8 3.8 - - - -
244G PHE* 4.9 0.9 - - + -
246G GLY* 3.4 27.2 + - - -
274G PHE* 4.0 40.8 - - + -
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Residues in contact with VAL 197 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182G PHE* 3.6 25.4 - - + -
187G LEU* 3.7 25.1 - - + -
192G ASN 2.9 22.5 + - - +
193G HIS* 4.2 9.0 - - - +
196G LYS* 1.3 69.8 - - - +
198G LYS* 1.3 57.3 + - - +
200G TYR* 3.4 4.8 - - + +
201G LYS* 2.6 72.4 + - + +
216G ILE* 4.3 13.0 - - + -
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Residues in contact with LYS 198 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162G GLU* 3.7 22.6 - - + +
193G HIS 4.0 7.3 + - - +
194G ALA* 2.2 44.8 + - - +
195G LYS* 4.0 16.8 - - - +
196G LYS 3.3 0.2 - - - -
197G VAL* 1.3 76.7 - - - +
199G GLY* 1.3 69.7 + - - +
201G LYS* 4.4 7.6 - - + -
202G ARG* 2.9 25.6 + - - +
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Residues in contact with GLY 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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162G GLU* 3.3 34.5 + - - -
165G ALA* 4.2 0.4 - - - -
166G PHE* 3.6 14.9 - - - +
195G LYS 3.1 13.0 + - - -
196G LYS 3.8 0.9 - - - -
197G VAL 3.3 0.2 - - - -
198G LYS* 1.3 82.0 - - - +
200G TYR* 1.3 62.6 + - - +
202G ARG* 5.1 0.4 - - - -
203G ALA* 3.1 21.8 + - - +
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Residues in contact with TYR 200 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165G ALA* 4.2 2.4 - - - +
169G VAL* 3.6 27.6 - - + -
180G ILE* 2.5 44.8 + - + -
181G ALA* 3.5 23.5 - - - -
182G PHE* 4.1 22.6 + + + -
196G LYS 3.0 15.1 + - - +
197G VAL* 3.4 12.8 - - + +
199G GLY* 1.3 76.7 - - - +
201G LYS* 1.3 76.7 + - + +
203G ALA* 3.2 13.3 - - - +
204G LEU* 3.4 19.2 + - + +
211G VAL* 3.8 24.3 - - + +
215G TYR* 4.1 7.3 - - + +
216G ILE* 5.6 7.2 - - + -
244G PHE* 4.4 13.5 - + + -
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Residues in contact with LYS 201 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197G VAL* 2.6 48.6 + - + +
198G LYS* 3.7 6.5 - - + +
200G TYR* 1.3 81.7 - - + +
202G ARG* 1.3 55.2 + - - +
204G LEU* 2.5 32.3 + - - +
205G THR* 3.1 15.0 + - + +
211G VAL* 4.3 22.4 - - + -
213G ASP* 5.1 4.3 - - - -
216G ILE* 6.1 3.1 - - - -
646G SO4 3.5 35.5 + - - +
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Residues in contact with ARG 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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162G GLU* 2.3 38.2 + - - +
163G GLN* 3.8 25.5 + - - +
166G PHE* 3.3 37.6 - - + +
198G LYS 2.9 14.5 + - - +
199G GLY 4.0 0.7 - - - +
201G LYS* 1.3 75.1 - - - +
203G ALA* 1.3 55.1 + - - +
205G THR* 3.4 11.7 - - - +
206G GLU* 2.7 45.7 + - + +
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Residues in contact with ALA 203 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166G PHE* 3.6 28.7 - - + +
169G VAL* 3.6 26.9 - - + -
170G GLN* 3.0 23.3 + - - +
173G ILE* 4.1 3.3 - - - +
199G GLY 3.1 12.3 + - - +
200G TYR 3.2 14.1 - - - +
201G LYS 2.8 2.4 + - - -
202G ARG* 1.3 77.3 - - - +
204G LEU* 1.3 58.8 - - - +
206G GLU* 3.5 6.1 - - - +
207G SER* 3.6 5.7 + - - -
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Residues in contact with LEU 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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169G VAL* 3.6 8.5 - - + -
173G ILE* 3.0 31.6 - - + -
180G ILE* 3.1 31.6 - - + -
200G TYR* 3.6 24.5 - - + +
201G LYS 2.5 14.0 + - - +
203G ALA* 1.3 69.6 - - - +
205G THR* 1.3 56.1 + - + +
206G GLU 2.8 5.5 + - - -
207G SER* 3.1 2.6 + - - -
208G GLY 2.8 9.5 + - - -
209G LEU* 2.6 47.9 + - + +
210G PRO 4.6 0.4 - - - +
211G VAL* 2.9 36.6 - - + -
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Residues in contact with THR 205 (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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201G LYS* 3.1 13.2 + - + +
202G ARG* 3.3 19.1 + - - +
204G LEU* 1.3 73.7 - - + +
206G GLU* 1.3 61.8 + - - +
208G GLY* 3.6 11.6 + - - +
209G LEU 4.5 2.0 - - - +
210G PRO* 5.1 8.7 - - + -
211G VAL* 4.6 16.8 - - + +
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Residues in contact with GLU 206 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166G PHE* 4.1 20.6 - - + -
170G GLN* 4.1 13.2 + - - +
202G ARG* 2.7 27.0 + - + +
203G ALA* 3.5 9.6 - - - +
204G LEU 2.8 1.8 - - - -
205G THR* 1.3 78.1 - - - +
207G SER* 1.3 61.6 + - - +
208G GLY 3.0 6.9 + - - -
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Residues in contact with SER 207 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170G GLN* 3.7 14.9 + - - -
173G ILE* 3.4 31.5 - - - +
174G ASP* 5.1 1.9 + - - -
203G ALA 3.6 3.5 + - - -
204G LEU 3.1 3.7 + - - -
206G GLU* 1.3 79.2 + - - +
208G GLY* 1.3 63.0 + - - +
209G LEU* 3.1 20.1 - - - +
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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