Contacts of the helix formed by residues 196 - 212 (chain G) in PDB entry 3TMP
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 VAL 196 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195G THR* 1.3 80.0 - - + +
197G GLU* 1.3 72.9 + - - +
198G GLN 3.1 0.5 + - - -
199G GLN* 3.2 10.4 + - - +
200G GLU* 3.1 29.3 + - + +
331G ARG* 4.0 28.5 - - + -
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Residues in contact with GLU 197 (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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195G THR 4.3 5.5 - - - +
196G VAL* 1.3 83.3 - - - +
198G GLN* 1.3 62.4 + - + +
200G GLU* 3.2 7.2 + - - +
201G HIS* 3.1 33.6 + - - +
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Residues in contact with GLN 198 (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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18D GLU* 4.5 4.2 - - - +
20D SER* 2.8 49.2 + - - +
21D ASP* 3.0 29.3 + - - +
22D THR* 4.1 9.2 + - - +
25D ASN* 3.9 15.1 + - - +
195G THR* 3.3 9.3 + - - +
196G VAL 3.2 0.8 - - - -
197G GLU* 1.3 80.6 - - + +
199G GLN* 1.3 65.2 + - - +
200G GLU 3.1 2.0 - - - -
201G HIS* 3.5 10.2 + - + +
202G TRP* 3.1 24.1 + - - +
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Residues in contact with GLN 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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24D GLU* 4.9 1.2 + - - +
25D ASN* 3.2 27.4 + - - +
28D ALA* 3.6 14.6 - - - +
195G THR* 2.9 39.3 + - - +
196G VAL* 3.2 10.4 + - - +
198G GLN* 1.3 76.6 - - - +
200G GLU* 1.3 58.9 + - + +
202G TRP* 4.0 6.6 - - + +
203G PHE* 3.1 25.3 + - - +
301G TYR* 3.1 60.8 + - + +
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Residues in contact with GLU 200 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196G VAL* 3.1 23.6 + - + +
197G GLU* 3.4 11.2 - - - +
198G GLN 3.1 0.4 - - - -
199G GLN* 1.3 79.0 - - + +
201G HIS* 1.3 65.5 + - - +
202G TRP 3.2 1.1 - - - -
203G PHE* 3.3 17.5 - - - +
204G GLU* 3.0 26.2 + - - +
301G TYR* 4.9 12.1 + - - +
329G TYR 5.0 1.3 - - - +
330G HIS* 3.1 30.4 + - - +
331G ARG* 3.5 33.4 + - - +
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Residues in contact with HIS 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 GLU* 3.1 24.0 + - + +
198G GLN* 3.5 10.5 + - + +
200G GLU* 1.3 76.7 - - - +
202G TRP* 1.3 64.0 + - + +
204G GLU* 3.7 7.1 + - - +
205G LYS* 3.2 35.8 + - + +
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Residues in contact with TRP 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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29D LYS* 4.9 16.6 - - - +
198G GLN 3.1 17.3 + - - +
199G GLN* 4.0 7.4 - - + +
201G HIS* 1.3 79.1 - - + +
203G PHE* 1.3 68.9 + - - +
205G LYS* 3.2 28.7 + - + -
206G ALA* 2.9 50.8 + - + +
209G ASP* 5.2 3.1 - - + -
301G TYR* 5.8 8.3 - + - -
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Residues in contact with PHE 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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199G GLN 3.1 15.0 + - - +
200G GLU* 3.3 26.9 - - - +
202G TRP* 1.3 81.7 - - - +
204G GLU* 1.3 65.7 + - + +
206G ALA* 3.3 6.6 + - - +
207G LEU* 3.0 44.6 + - + +
215G ILE* 4.1 7.0 - - + -
299G TYR* 3.8 13.9 - + + -
300G GLN* 3.7 34.1 - - - -
301G TYR* 3.8 23.1 - - + -
308G VAL* 4.9 9.1 - - + +
328G SER* 4.1 7.2 - - - -
329G TYR 5.4 1.3 - - - -
330G HIS* 3.6 25.8 - + - -
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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 GLU 3.0 14.4 + - - +
201G HIS* 4.0 7.0 - - - +
202G TRP 3.2 0.4 - - - -
203G PHE* 1.3 85.2 - - + +
205G LYS* 1.3 62.3 + - - +
207G LEU* 3.1 16.9 + - - +
208G ARG* 3.1 40.9 + - - +
213G PHE 4.7 0.4 - - - +
215G ILE* 3.9 38.9 - - + +
217G GLN* 4.9 8.6 + - - -
330G HIS* 5.7 3.1 - - - -
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Residues in contact with LYS 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 HIS* 3.2 31.6 + - + +
202G TRP* 3.9 22.6 - - + +
204G GLU* 1.3 77.8 - - - +
206G ALA* 1.3 57.3 + - - +
208G ARG* 3.4 9.9 + - + +
209G ASP* 2.8 59.6 + - - +
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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
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202G TRP* 2.9 45.1 + - + +
203G PHE* 3.5 7.2 - - + +
205G LYS* 1.3 76.6 - - - +
207G LEU* 1.3 54.8 + - - +
209G ASP* 4.4 4.7 - - - -
210G LYS* 2.8 43.5 + - + +
308G VAL* 4.2 14.4 - - + +
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Residues in contact with LEU 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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203G PHE* 3.0 33.9 + - + +
204G GLU* 3.1 10.5 + - - +
206G ALA* 1.3 73.2 - - - +
208G ARG* 1.3 66.3 - - - +
211G LYS* 3.1 23.9 + - + +
212G GLY 2.9 17.5 + - - -
213G PHE* 3.3 30.8 + - + +
215G ILE* 3.5 34.3 - - + -
299G TYR* 4.3 14.4 - - + -
308G VAL* 3.6 22.2 - - + -
338G VAL* 4.7 8.7 - - + -
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Residues in contact with ARG 208 (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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204G GLU* 3.1 43.9 + - - +
205G LYS* 3.6 11.6 - - - +
207G LEU* 1.3 75.6 - - - +
209G ASP* 1.3 68.1 + - - +
212G GLY* 2.8 29.8 + - - +
213G PHE 3.2 6.0 + - - +
214G ILE* 3.1 56.3 - - + +
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Residues in contact with ASP 209 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202G TRP* 5.2 4.0 - - + -
205G LYS* 2.8 56.3 + - - +
206G ALA* 4.0 5.3 - - - +
208G ARG* 1.3 81.7 - - - +
210G LYS* 1.3 66.4 + - + +
212G GLY 4.9 0.2 + - - -
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Residues in contact with LYS 210 (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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206G ALA* 2.8 26.1 + - + +
209G ASP* 1.3 80.9 - - + +
211G LYS* 1.3 64.3 + - + +
308G VAL* 4.0 22.2 - - + -
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Residues in contact with LYS 211 (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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207G LEU* 3.1 26.5 + - + +
210G LYS* 1.3 89.3 - - + +
212G GLY* 1.3 64.2 + - - +
213G PHE* 3.3 44.2 + - + -
299G TYR* 4.7 7.6 - - - -
308G VAL* 3.7 25.1 - - + +
309G GLU* 2.5 36.5 + - - -
310G PRO* 5.4 0.9 - - - +
340G ASN* 5.4 0.5 - - - +
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Residues in contact with GLY 212 (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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207G LEU 2.9 0.6 + - - -
208G ARG* 2.8 23.7 + - - -
210G LYS 3.8 0.2 - - - -
211G LYS* 1.3 79.5 - - - +
213G PHE* 1.3 61.9 + - - +
214G ILE* 4.2 3.7 - - - +
340G ASN* 4.9 0.4 - - - +
341G PRO* 3.1 26.7 - - - +
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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