Contacts of the helix formed by residues 196 - 210 (chain B) in PDB entry 1P7D
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 PRO 196 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B ALA 4.8 0.9 - - - +
195B SER* 1.3 93.9 - - - +
197B CYS* 1.3 67.2 + - - +
198B TRP* 3.6 31.2 - - + +
199B LEU* 3.2 16.9 + - + +
200B ARG* 4.2 1.2 + - - +
275B THR* 4.5 12.1 - - - +
288B TYR* 3.8 28.7 - - + -
3E A 4.1 18.4 - - - +
4E T 4.8 3.4 - - - +
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Residues in contact with CYS 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B SER 3.5 2.6 + - - -
196B PRO* 1.3 72.1 - - - +
198B TRP* 1.3 64.8 + - - +
199B LEU 2.7 2.6 + - - -
200B ARG* 3.0 34.7 + - - +
201B LEU* 3.1 17.3 + - + +
265B ILE* 4.1 32.3 - - + -
266B LEU* 4.9 2.5 - - + -
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Residues in contact with TRP 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B PRO* 3.6 23.2 - - + +
197B CYS* 1.3 76.9 - - - +
199B LEU* 1.3 88.5 + - + +
201B LEU* 3.8 6.6 - - - +
202B ALA* 2.6 43.2 + - + +
266B LEU* 3.5 29.4 - - + +
272B ILE* 4.5 4.2 - - + +
273B ALA 3.5 17.5 - - - +
274B SER* 4.0 6.7 - - - -
275B THR* 4.2 7.1 + - - +
280B LEU* 3.4 25.6 - - + +
284B THR* 3.9 18.2 - - + -
285B VAL* 3.8 33.2 - - + -
288B TYR* 3.6 35.4 - + + -
4E T 4.0 22.6 + - - -
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Residues in contact with LEU 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B ALA* 3.8 18.8 - - + +
195B SER* 3.3 31.9 - - - +
196B PRO* 3.2 14.0 + - + +
197B CYS 2.7 4.6 + - - -
198B TRP* 1.3 101.1 - - + +
200B ARG* 1.3 52.4 + - - +
202B ALA* 2.8 9.3 + - + +
203B MET* 2.8 47.7 + - + +
285B VAL* 4.4 4.9 - - + +
288B TYR* 3.6 21.5 - - + +
289B PHE* 3.9 25.4 - - + +
292B ALA* 4.1 5.2 - - + -
307B PHE* 5.5 0.4 - - + -
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Residues in contact with ARG 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B TYR* 3.2 66.5 + - + +
190B GLN* 5.8 0.2 - - - +
192B ALA* 4.0 15.4 + - + -
193B GLU* 2.9 39.2 + - - +
195B SER 5.7 1.7 + - - -
196B PRO 4.2 1.1 + - - +
197B CYS* 3.0 26.5 + - - +
199B LEU* 1.3 80.5 - - - +
201B LEU* 1.3 64.4 + - + +
203B MET* 3.3 9.7 + - - +
204B GLU* 3.1 27.2 + - - +
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Residues in contact with LEU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B CYS* 3.1 16.2 + - + +
198B TRP* 3.8 7.6 - - - +
200B ARG* 1.3 74.6 - - + +
202B ALA* 1.3 66.4 + - - +
204B GLU* 3.2 6.1 + - - +
205B LEU* 3.0 24.3 + - - +
258B THR* 4.3 9.0 - - + +
261B LYS* 3.5 57.4 - - + +
262B CYS* 4.0 18.6 - - - -
265B ILE* 4.4 13.7 - - + -
266B LEU* 3.4 35.2 - - + -
272B ILE* 4.3 2.9 - - + -
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Residues in contact with ALA 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B TRP* 2.6 31.8 + - + +
199B LEU* 3.2 7.0 - - + +
201B LEU* 1.3 73.2 - - - +
203B MET* 1.3 57.9 + - - +
205B LEU* 3.5 2.3 + - - +
206B ALA* 2.9 30.8 + - - +
216B LEU* 4.3 3.3 - - + +
272B ILE* 3.7 24.2 - - + +
285B VAL* 4.4 19.7 - - + -
307B PHE* 3.9 5.2 - - + -
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Residues in contact with MET 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B TYR* 3.5 35.4 - - + +
188B ILE* 4.3 11.4 - - + -
189B TYR* 4.0 34.1 - - + +
192B ALA* 4.4 15.5 - - - -
199B LEU* 2.8 27.8 + - + +
200B ARG* 3.5 13.0 - - - +
202B ALA* 1.3 77.9 - - - +
204B GLU* 1.3 61.2 + - - +
206B ALA* 3.6 1.4 + - - +
207B VAL* 3.2 29.3 + - - +
289B PHE* 4.3 26.5 - - + -
292B ALA* 5.8 0.4 - - - -
307B PHE* 4.4 4.5 - - + -
310B LEU* 3.9 9.3 - - + +
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Residues in contact with GLU 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B TYR* 3.6 15.5 - - - +
189B TYR* 2.5 32.0 + - + -
200B ARG 3.1 14.9 + - - +
201B LEU* 3.2 9.2 + - - +
203B MET* 1.3 74.7 - - - +
205B LEU* 1.3 60.1 + - - +
207B VAL* 3.4 2.9 + - - +
208B VAL* 3.0 32.4 + - - +
253B ILE* 3.8 21.6 - - + +
257B GLU* 3.4 10.7 - - - +
258B THR* 2.7 32.6 + - + +
261B LYS* 2.9 26.1 + - - -
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Residues in contact with LEU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B LEU 3.0 14.9 + - - +
202B ALA* 3.8 5.2 - - - +
204B GLU* 1.3 73.6 - - - +
206B ALA* 1.3 63.7 + - - +
208B VAL* 3.7 9.4 - - + -
209B THR* 2.7 47.7 + - + +
216B LEU* 4.3 16.8 - - + -
219B MET* 4.4 11.2 - - - -
229B LEU* 5.8 0.7 - - + -
255B MET* 4.9 2.9 - - + -
258B THR* 3.4 25.8 - - + -
259B LEU* 3.9 20.6 - - + -
262B CYS* 4.8 1.8 - - - -
271B ILE* 4.2 17.3 - - + -
272B ILE* 4.1 26.7 - - + -
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Residues in contact with ALA 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ALA 2.9 18.6 + - - +
203B MET 3.7 0.7 - - - +
205B LEU* 1.3 76.7 - - - +
207B VAL* 1.3 56.2 + - - +
209B THR* 4.3 0.4 - - - -
210B GLY* 3.1 27.5 + - - -
211B GLN 3.9 6.3 + - - +
216B LEU* 3.3 17.8 - - + +
307B PHE* 3.4 27.4 - - + -
310B LEU* 3.5 23.4 - - + +
311B ARG* 5.1 0.7 - - - +
314B SER* 4.4 1.4 - - - -
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Residues in contact with VAL 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B TYR* 3.5 24.2 - - + -
203B MET 3.2 17.5 + - - +
204B GLU 4.0 2.7 - - - +
205B LEU 3.2 0.4 - - - -
206B ALA* 1.3 77.2 - - - +
208B VAL* 1.3 60.4 + - - +
248B ILE* 4.3 7.7 - - + +
251B LEU* 4.0 20.2 - - + -
253B ILE* 4.6 6.5 - - + -
310B LEU* 3.8 22.4 - - + +
313B LEU* 4.3 5.2 - - + -
314B SER* 2.8 43.4 + - - +
317B LEU* 4.3 9.9 - - + -
318B TYR* 4.0 3.6 - - - -
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Residues in contact with VAL 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B GLU 3.0 22.1 + - - +
205B LEU* 3.4 13.9 - - + +
207B VAL* 1.3 77.2 - - - +
209B THR* 1.3 73.6 + - + +
210B GLY 3.6 0.2 - - - -
246B LEU* 3.6 11.2 - - + +
247B HIS* 4.1 17.9 - - - +
248B ILE* 4.3 7.0 - - + +
253B ILE* 4.1 15.0 - - + -
255B MET* 3.9 36.3 - - + +
258B THR* 5.3 0.7 - - - +
318B TYR* 2.8 38.6 + - - +
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Residues in contact with THR 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B LEU* 2.7 32.4 + - + +
208B VAL* 1.3 89.4 - - + +
210B GLY* 1.3 57.6 + - - +
211B GLN* 2.8 42.5 + - - +
216B LEU* 3.6 14.7 - - - +
219B MET* 4.8 1.6 - - + -
229B LEU* 4.8 6.3 - - + -
242B ILE* 4.0 13.6 - - + +
255B MET* 3.9 24.9 - - + -
330B LEU* 3.6 15.8 - - - +
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Residues in contact with GLY 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B ALA 3.1 13.0 + - - -
209B THR* 1.3 76.9 - - - +
211B GLN* 1.3 56.3 + - - +
311B ARG* 2.5 43.2 + - - +
314B SER* 3.3 28.5 + - - -
330B LEU* 4.6 5.6 - - - -
331B LEU* 3.7 7.5 - - - +
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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
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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