Contacts of the helix formed by residues 194 - 212 (chain G) in PDB entry 2JG7
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 194 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106G GLU* 3.3 20.0 - - + -
107G MET* 4.6 4.5 - - + -
164G ALA 4.8 0.3 + - - -
165G PHE* 3.7 24.4 - - + +
168G PRO* 3.6 25.2 - - + +
190G GLY* 5.4 0.2 - - - -
191G ALA* 3.1 22.7 + - - +
193G THR* 1.3 85.9 + - - +
195G PRO* 1.4 63.3 - - - +
197G THR* 3.4 3.6 + - - -
198G SER* 3.3 19.8 + - - -
344G HIS* 4.0 17.9 - - + +
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Residues in contact with PRO 195 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G ILE* 3.8 20.9 - - + -
39G SER* 4.2 10.1 - - - +
51G VAL* 3.8 28.7 - - + -
53G GLN* 5.9 0.4 - - + -
106G GLU* 3.3 8.7 - - - +
191G ALA 3.8 3.7 - - - +
192G PRO* 3.0 20.0 - - + +
193G THR 3.3 3.6 - - - +
194G THR* 1.4 90.1 - - - +
196G LEU* 1.3 56.8 + - - +
198G SER* 3.2 9.5 + - - +
199G VAL* 2.9 33.1 + - - +
223G CYS* 4.4 13.0 - - + -
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Residues in contact with LEU 196 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G ILE* 6.0 0.2 - - + -
18G LEU* 4.0 19.8 - - + +
22G ASN* 3.5 28.5 - - - +
39G SER* 3.7 26.7 - - - +
48G ILE* 3.8 31.6 - - + -
49G ALA* 4.0 14.1 - - + +
50G ARG 4.4 0.4 - - - +
51G VAL* 3.8 14.4 - - + -
102G LEU* 3.6 17.2 - - + +
106G GLU* 3.0 15.6 + - - +
195G PRO* 1.3 76.3 - - - +
197G THR* 1.3 57.3 + - - +
199G VAL* 3.4 3.9 + - - +
200G ALA* 2.9 30.8 + - - +
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Residues in contact with THR 197 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G LEU* 4.8 4.0 - - + -
102G LEU* 3.7 20.1 - - - +
103G VAL* 4.2 11.8 - - + -
106G GLU* 2.8 31.6 + - - +
168G PRO* 3.7 29.0 - - + +
169G VAL* 3.4 31.9 - - + -
194G THR* 3.7 6.0 - - - -
195G PRO 3.3 0.2 - - - -
196G LEU* 1.3 69.3 - - - +
198G SER* 1.3 67.0 + - - +
200G ALA* 3.7 0.6 - - - +
201G VAL* 3.0 25.2 + - + +
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Residues in contact with SER 198 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168G PRO* 5.2 1.0 + - - +
188G TRP* 3.5 33.2 - - - -
190G GLY* 3.8 17.8 - - - -
194G THR* 3.3 12.8 + - - -
195G PRO* 3.2 14.9 + - - +
197G THR* 1.3 80.0 - - - +
199G VAL* 1.3 58.2 + - - +
202G THR* 2.9 34.6 + - - -
221G MET* 3.9 13.5 - - - -
223G CYS* 4.4 6.7 - - - -
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Residues in contact with VAL 199 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G LEU* 3.8 20.2 - - + -
22G ASN* 4.6 7.0 - - + -
23G PRO 3.6 21.3 - - - +
30G TRP* 4.1 8.9 - - + -
51G VAL* 4.3 20.0 - - + -
195G PRO 2.9 19.9 + - - +
196G LEU* 3.7 4.7 - - - +
198G SER* 1.3 76.7 - - - +
200G ALA* 1.3 53.3 + - - +
202G THR* 3.4 2.4 + - - -
203G LYS* 2.8 53.6 + - - +
221G MET* 3.9 17.5 - - + -
223G CYS* 4.6 2.2 - - - -
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Residues in contact with ALA 200 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G LEU* 4.2 27.6 - - + +
18G LEU* 4.6 3.4 - - + -
99G LEU* 4.0 11.9 - - + -
102G LEU* 3.6 21.3 - - + -
196G LEU 2.9 17.1 + - - +
197G THR 3.7 3.1 - - - +
199G VAL* 1.3 78.4 - - - +
201G VAL* 1.3 60.5 + - - +
203G LYS* 3.3 4.9 + - - +
204G ILE* 3.2 28.2 + - - +
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Residues in contact with VAL 201 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G LEU* 5.2 3.1 - - + -
99G LEU* 4.2 13.9 - - + -
121G TYR* 4.0 15.0 - - + -
169G VAL* 3.9 33.7 - - + -
172G TYR* 3.9 20.9 - - + -
188G TRP* 3.7 21.3 - - + -
197G THR* 3.0 21.1 + - + +
198G SER 3.7 2.9 - - - +
200G ALA* 1.3 72.0 - - - +
202G THR* 1.3 66.6 + - - +
204G ILE* 3.0 13.4 + - - +
205G VAL* 3.0 24.9 + - + +
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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
----------------------------------------------------------
26G TYR* 3.8 28.0 - - + -
30G TRP* 3.8 15.9 - - + -
172G TYR* 5.7 1.5 + - - -
188G TRP* 3.7 10.7 - - - -
198G SER 2.9 18.5 + - - -
199G VAL 3.7 4.3 - - - -
201G VAL* 1.3 76.4 - - - +
203G LYS* 1.3 53.0 + - - +
205G VAL* 3.3 6.9 + - + +
206G ALA* 2.7 37.1 + - - +
219G CYS 4.3 8.1 - - - +
221G MET* 3.1 32.6 - - + +
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Residues in contact with LYS 203 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G LEU 3.7 16.2 - - - +
17G GLY* 3.3 31.4 + - - +
22G ASN* 5.4 1.8 - - - -
23G PRO* 5.6 8.2 - - - +
30G TRP* 3.5 38.6 - - + +
199G VAL* 2.8 39.2 + - + +
200G ALA 3.4 7.0 - - - +
201G VAL 3.1 0.4 - - - -
202G THR* 1.3 72.5 - - - +
204G ILE* 1.3 62.8 + - + +
206G ALA* 3.5 1.4 + - - +
207G GLU* 3.1 24.3 + - - +
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Residues in contact with ILE 204 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G LEU* 4.4 11.4 - - + +
88G ILE* 4.9 1.6 - - + +
91G ALA* 3.7 34.4 - - + +
92G LEU* 4.0 17.0 - - + +
95G LYS* 4.1 32.3 - - + -
99G LEU* 3.9 27.4 - - + -
200G ALA 3.2 18.2 + - - +
201G VAL* 3.0 9.5 + - - +
203G LYS* 1.3 75.8 - - + +
205G VAL* 1.3 67.2 + - + +
207G GLU* 3.5 11.3 + - - +
208G VAL* 3.5 14.6 + - - +
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Residues in contact with VAL 205 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G ILE* 3.9 28.0 - - + -
92G LEU* 5.9 0.7 - - + -
121G TYR* 3.8 21.8 - - + +
172G TYR* 4.8 5.6 - - + +
176G ASN* 4.9 0.2 - - - +
201G VAL* 3.0 28.5 + - + +
202G THR* 3.9 6.1 - - + +
204G ILE* 1.3 74.6 - - + +
206G ALA* 1.3 67.9 + - - +
208G VAL* 3.1 17.9 + - - +
209G LEU* 3.1 15.9 + - + +
219G CYS* 3.7 39.7 - - + -
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Residues in contact with ALA 206 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G TYR* 3.6 40.6 - - + +
30G TRP* 4.2 11.2 - - + +
202G THR 2.7 22.3 + - - +
203G LYS 3.7 4.3 - - - +
205G VAL* 1.3 73.7 - - - +
207G GLU* 1.3 63.3 + - - +
209G LEU* 3.3 8.8 + - - +
210G GLU* 3.0 32.5 + - - +
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Residues in contact with GLU 207 (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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95G LYS* 6.0 1.9 - - - -
203G LYS 3.1 14.8 + - - +
204G ILE* 3.7 7.2 - - - +
205G VAL 3.2 0.2 - - - -
206G ALA* 1.3 77.8 - - - +
208G VAL* 1.3 54.0 + - + +
210G GLU* 3.3 10.5 + - + +
211G GLN* 2.8 63.4 + - + +
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Residues in contact with VAL 208 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G ILE* 4.2 10.8 - - + +
87G GLN* 3.8 33.4 - - + +
88G ILE* 4.0 22.9 - - + -
91G ALA* 3.6 31.0 - - + -
204G ILE 3.5 8.7 + - - +
205G VAL 3.1 8.8 + - - +
207G GLU* 1.3 73.9 - - + +
209G LEU* 1.3 64.3 + - + +
211G GLN* 3.4 8.4 + - + +
212G ASN* 2.7 38.4 + - - +
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Residues in contact with LEU 209 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G TYR* 5.3 0.2 - - + -
73G TRP* 5.3 0.9 - - + -
84G ILE* 4.1 17.0 - - + -
88G ILE* 5.6 1.6 - - + -
180G LEU* 5.7 0.4 - - + -
205G VAL* 3.1 20.9 + - + +
206G ALA* 3.6 11.0 - - - +
208G VAL* 1.3 76.2 - - + +
210G GLU* 1.3 60.3 + - - +
212G ASN* 3.2 7.8 + - - -
214G LEU* 2.9 63.6 + - + +
215G PRO 4.3 1.3 - - - +
216G GLY* 3.7 31.2 - - - +
218G ILE* 4.3 16.8 - - + -
219G CYS* 3.9 30.3 - - + +
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Residues in contact with GLU 210 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G TYR* 2.8 32.2 + - - +
28G GLY 4.2 6.8 - - - +
30G TRP* 4.9 3.1 + - - -
206G ALA* 3.0 24.3 + - - +
207G GLU* 3.7 10.9 - - - +
209G LEU* 1.3 73.0 - - + +
211G GLN* 1.3 66.8 + - - +
212G ASN 3.0 1.3 - - - -
213G ASN* 3.0 17.8 + - - +
214G LEU 4.5 7.9 - - - +
216G GLY* 5.4 1.3 - - - +
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Residues in contact with GLN 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G GLN* 5.4 1.6 - - - +
207G GLU* 2.8 58.0 + - + +
208G VAL* 3.6 9.2 - - + +
210G GLU* 1.3 73.4 - - - +
212G ASN* 1.3 64.8 + - - +
213G ASN* 3.3 11.0 + - - +
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Residues in contact with ASN 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G GLU* 5.8 0.2 - - - +
84G ILE* 3.6 29.6 - - + +
87G GLN* 3.0 34.5 + - - -
208G VAL* 2.7 30.3 + - - +
209G LEU 3.7 4.3 - - - +
210G GLU 3.0 1.0 - - - -
211G GLN* 1.3 80.9 - - - +
213G ASN* 1.3 72.9 + - - +
214G LEU* 3.2 12.8 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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