Contacts of the helix formed by residues 194 - 206 (chain G) in PDB entry 3B4V
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 SER 194 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175G PRO* 4.3 3.3 + - - +
177G PRO* 4.2 10.1 - - - -
182G GLN* 3.6 26.7 - - - -
184G LEU* 4.0 6.5 - - - -
192G TYR* 3.2 4.0 - - - +
193G ILE* 1.3 79.9 - - - +
195G SER* 1.3 63.4 + - - +
196G CYS* 3.7 9.7 + - - +
197G HIS* 2.7 36.1 + - - +
198G MET* 3.0 22.0 + - - +
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Residues in contact with SER 195 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F GLN* 3.9 13.2 + - - +
182G GLN* 4.5 5.3 + - - +
184G LEU* 3.8 17.4 - - - +
194G SER* 1.3 70.4 - - - +
196G CYS* 1.3 56.2 + - - +
198G MET* 3.1 3.4 + - - +
199G ARG* 2.7 69.7 + - - +
239G EDO 3.3 21.2 - - - -
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Residues in contact with CYS 196 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F ASP* 6.3 2.5 - - + -
170G ARG* 3.6 27.6 - - - -
174G CYS* 2.1 52.8 - - + -
175G PRO* 4.2 7.6 - - + -
194G SER* 3.7 9.1 + - - +
195G SER* 1.3 79.0 - - - +
197G HIS* 1.3 63.5 + - - +
199G ARG* 3.2 17.3 + - - +
200G GLN* 3.0 19.9 + - - +
239G EDO 5.6 0.6 + - - +
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Residues in contact with HIS 197 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D HIS* 5.3 13.3 - + - -
174G CYS* 3.3 36.2 + - + +
175G PRO 3.3 21.1 - - - -
176G VAL* 4.6 5.8 - - + +
177G PRO* 4.8 0.4 - - + -
192G TYR* 4.1 9.2 - - + -
193G ILE* 3.7 41.7 - - + +
194G SER* 2.7 32.6 + - - +
196G CYS* 1.3 76.4 - - - +
198G MET* 1.3 62.4 - - - +
200G GLN* 3.6 8.9 + - - +
201G ALA* 3.2 22.2 + - - +
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Residues in contact with MET 198 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F GLN* 3.8 18.2 - - + -
184G LEU* 4.4 12.8 - - + -
186G GLY* 4.2 6.1 - - - -
192G TYR* 3.8 33.8 - - + +
194G SER 3.0 13.1 + - - +
195G SER 3.1 7.6 + - - +
197G HIS* 1.3 76.1 - - - +
199G ARG* 1.3 55.6 + - - +
201G ALA* 3.6 1.2 + - - +
202G THR* 2.7 41.2 + - - +
209G ILE* 4.0 14.5 - - + +
210G GLY* 3.3 49.1 - - - +
211G VAL* 3.6 22.2 - - + +
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Residues in contact with ARG 199 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F ASP* 3.6 33.0 + - - +
28F TRP* 3.0 30.9 - - - +
94F TYR* 3.0 48.9 + - + +
95F ASP 5.3 2.0 + - - -
98F GLN* 3.0 29.3 + - + +
195G SER* 2.7 37.3 + - - +
196G CYS* 3.5 13.7 - - - +
198G MET* 1.3 70.9 - - - +
200G GLN* 1.3 60.3 + - - +
202G THR* 3.4 1.6 + - - -
203G CYS* 2.9 26.2 + - - +
239G EDO 3.0 32.9 + - - -
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Residues in contact with GLN 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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128D ARG* 3.7 24.0 - - - +
170G ARG* 2.8 38.3 + - + +
172G ALA 2.8 25.3 + - - +
173G PRO* 4.9 0.7 - - - +
174G CYS* 4.1 15.7 + - - +
196G CYS 3.0 16.0 + - - +
197G HIS* 3.7 10.3 - - - +
199G ARG* 1.3 76.3 - - - +
201G ALA* 1.3 56.2 + - - +
203G CYS* 3.3 5.5 + - - +
204G PHE* 3.0 53.4 + - + -
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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
----------------------------------------------------------
116D TYR* 5.9 8.3 - - + +
192G TYR* 3.6 35.9 - - + +
197G HIS 3.2 10.1 + - - +
198G MET 4.0 2.2 - - - +
200G GLN* 1.3 76.5 - - - +
202G THR* 1.3 66.6 + - - +
204G PHE* 3.5 5.0 + - - +
205G LEU* 2.9 24.9 + - - +
209G ILE* 4.3 3.4 - - + -
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Residues in contact with THR 202 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F TYR* 4.3 3.8 - - + -
98F GLN 4.1 16.2 + - - +
100F ILE* 3.9 17.7 - - + +
198G MET* 2.7 30.0 + - - +
199G ARG* 3.6 8.0 - - - -
201G ALA* 1.3 75.9 - - - +
203G CYS* 1.3 63.3 + - - +
205G LEU* 3.1 10.8 + - - +
206G GLY 3.1 10.7 + - - -
207G ARG 3.4 23.5 + - - +
208G SER* 3.9 13.9 - - - -
209G ILE* 4.0 23.2 - - - +
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Residues in contact with CYS 203 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ARG* 4.3 0.2 + - - -
30F ILE* 4.7 4.7 - - - -
94F TYR* 3.4 15.3 - - - +
100F ILE* 5.3 1.8 - - - -
155G SER* 4.1 5.0 - - - -
157G VAL* 3.5 26.8 - - - +
167G VAL* 4.0 17.5 - - - -
169G CYS* 2.0 55.1 - - + -
199G ARG 2.9 19.3 + - - +
200G GLN* 3.7 4.7 - - - +
202G THR* 1.3 77.9 - - - +
204G PHE* 1.3 60.2 + - - +
206G GLY* 3.4 9.4 + - - -
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Residues in contact with PHE 204 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D TYR* 6.2 2.5 - - + -
117D ARG* 3.2 28.9 + - - +
121D GLU* 3.3 41.8 - - + +
128D ARG* 3.1 45.8 - - - -
153G PRO 5.6 3.4 - - - -
155G SER* 3.9 14.6 - - - -
169G CYS* 3.7 23.3 - - + -
170G ARG 3.5 20.4 - - - -
171G ALA* 4.7 2.2 - - + -
200G GLN* 3.0 33.8 + - + +
201G ALA* 4.1 4.5 - - - +
203G CYS* 1.3 73.9 - - - +
205G LEU* 1.3 58.5 + - - +
206G GLY 3.4 0.2 - - - -
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Residues in contact with LEU 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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107D GLN* 4.2 4.0 - - - +
115D THR* 3.6 28.5 - - + +
116D TYR* 4.1 2.2 - - - -
117D ARG* 3.5 34.7 - - - +
188G ASN* 5.7 1.1 - - - +
201G ALA 2.9 18.9 + - - +
202G THR 3.1 5.8 + - - +
204G PHE* 1.3 78.7 - - - +
206G GLY* 1.3 59.2 + - - +
207G ARG* 3.7 51.5 + - + +
209G ILE* 3.6 32.3 - - + -
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Residues in contact with GLY 206 (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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105D ARG* 6.2 0.2 - - - -
117D ARG* 3.7 4.5 - - - -
145G CYS* 4.6 2.8 - - - -
156G CYS 3.2 23.3 - - - +
157G VAL* 3.2 9.6 - - - -
158G VAL* 3.0 27.9 + - - +
202G THR 3.1 5.1 + - - -
203G CYS 3.4 7.6 + - - -
204G PHE 3.4 0.2 - - - -
205G LEU* 1.3 78.1 - - - +
207G ARG* 1.3 61.1 + - - +
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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