Contacts of the helix formed by residues 198 - 216 (chain A) in PDB entry 1F89
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 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A ASN* 2.8 17.1 + - - +
197A THR* 1.3 85.0 - - - +
199A THR* 1.3 65.2 + - - +
200A GLY 3.3 1.1 - - - -
201A PRO* 3.9 8.2 - - - +
202A LEU* 4.1 20.4 + - + +
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Residues in contact with THR 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ARG* 2.9 29.7 + - - +
195A PHE* 3.4 20.4 - - + -
196A ASN* 2.9 46.5 + - - +
198A VAL* 1.3 74.7 - - - +
200A GLY* 1.3 67.4 + - - +
202A LEU* 3.3 10.3 + - - +
203A HIS* 3.1 22.9 + - - +
232A TYR* 5.1 0.2 - - - +
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Residues in contact with GLY 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A PHE* 4.0 9.4 - - - -
196A ASN 2.7 19.6 + - - -
199A THR* 1.3 74.5 - - - +
201A PRO* 1.3 68.8 - - - +
202A LEU 3.1 1.2 + - - -
204A TRP* 3.1 28.7 + - - +
205A HIS* 4.6 1.7 + - - -
235A TYR* 3.6 23.3 + - - -
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Residues in contact with PRO 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ASN 3.7 0.4 - - - +
197A THR* 3.5 24.2 - - - +
198A VAL 3.9 6.1 - - - +
200A GLY* 1.3 89.5 - - - +
202A LEU* 1.3 63.4 + - + +
205A HIS* 5.5 2.7 + - - +
226A ARG* 5.6 0.2 - - - +
235A TYR* 3.1 37.0 - - + +
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Residues in contact with LEU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A VAL* 4.1 19.0 + - + +
199A THR* 3.3 12.0 + - - +
200A GLY 3.0 1.0 - - - -
201A PRO* 1.3 84.9 - - + +
203A HIS* 1.3 93.6 + - + +
206A LEU* 4.7 2.3 - - - +
509B ARG* 3.9 18.7 + - - -
544B ARG* 4.2 40.3 - - + +
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Residues in contact with HIS 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ARG* 3.2 25.7 + - - +
195A PHE* 4.6 2.0 - - + -
199A THR* 3.1 9.9 + - - +
202A LEU* 1.3 109.2 - - + +
204A TRP* 1.3 60.6 + - - +
205A HIS 3.5 1.8 - - - -
206A LEU* 3.2 11.3 + - + +
207A LEU* 2.9 50.5 + - + +
513B VAL* 3.6 27.1 - - + +
544B ARG* 2.6 39.3 + - + -
574B VAL* 5.4 8.7 - - + -
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Residues in contact with TRP 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A MET* 4.8 1.1 - - - -
193A SER* 3.8 26.0 - - - -
195A PHE* 3.5 55.4 - + + -
199A THR 4.2 1.4 + - - -
200A GLY* 3.1 20.9 + - - +
203A HIS* 1.3 75.2 - - - +
205A HIS* 1.3 74.2 + + - +
207A LEU* 3.5 2.7 + - - +
208A ALA* 3.1 24.9 + - - +
221A LEU* 3.5 39.3 - - + +
223A SER* 3.7 24.2 - - - -
235A TYR* 3.7 22.7 - + + -
236A GLY 3.6 15.3 - - - -
237A HIS* 2.8 28.4 + - + +
239A ILE* 4.1 8.7 - - + +
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Residues in contact with HIS 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A GLY 4.6 1.8 + - - -
201A PRO 5.5 3.0 + - - -
203A HIS 3.5 0.2 - - - -
204A TRP* 1.3 85.1 - + - +
206A LEU* 1.3 63.5 + - - +
208A ALA* 3.5 3.4 + - - +
209A ARG* 3.0 39.4 + - - +
235A TYR* 3.4 35.1 + + - -
237A HIS* 4.2 6.1 - + - -
239A ILE* 4.4 8.3 - - + -
247A ILE* 3.7 23.3 - - + -
250A GLU* 2.6 31.5 + - - -
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Residues in contact with LEU 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A LEU 4.7 1.1 + - - +
203A HIS* 3.2 19.6 + - + +
205A HIS* 1.3 79.7 - - - +
207A LEU* 1.3 56.5 + - + +
209A ARG* 3.6 2.8 - - - +
210A SER* 2.6 38.6 + - - -
506B LEU* 3.3 34.5 - - + +
509B ARG* 3.6 71.3 - - + +
510B SER* 4.3 7.2 - - - +
513B VAL* 3.8 21.5 - - + -
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Residues in contact with LEU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A MET* 3.3 42.6 - - + +
173A ARG* 4.0 27.8 - - + +
195A PHE* 4.2 11.0 - - + -
203A HIS* 2.9 41.0 + - + +
206A LEU* 1.3 75.2 - - + +
208A ALA* 1.3 66.6 + - - +
210A SER* 2.9 5.4 + - - -
211A ARG* 2.9 33.4 + - + +
513B VAL* 4.8 13.7 - - + -
514B ASP* 4.0 20.6 - - - +
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Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A MET* 3.8 3.0 - - - +
204A TRP 3.1 12.7 + - - +
205A HIS 3.6 1.6 - - - +
207A LEU* 1.3 80.5 - - - +
209A ARG* 1.3 62.5 + - - +
211A ARG* 3.4 1.4 + - - +
212A ALA* 3.3 19.8 + - - +
219A VAL* 3.8 19.0 - - + +
221A LEU* 3.5 18.4 - - + -
239A ILE* 3.4 33.4 - - + -
241A VAL* 4.2 8.1 - - + -
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Residues in contact with ARG 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A HIS* 3.0 24.1 + - - +
206A LEU* 3.9 2.3 - - - +
208A ALA* 1.3 74.7 - - + +
210A SER* 1.3 61.5 + - - +
212A ALA* 3.9 0.8 - - - +
213A VAL* 3.2 30.3 + - - +
241A VAL* 4.0 22.7 - - + -
245A GLY* 2.8 33.5 + - - +
247A ILE* 4.2 19.0 - - + +
502B LEU 3.9 16.0 + - - -
506B LEU* 3.6 42.3 - - + +
509B ARG* 6.0 1.6 - - - +
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Residues in contact with SER 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A LEU* 2.6 24.9 + - - -
207A LEU* 2.9 7.4 + - - -
209A ARG* 1.3 75.4 - - - +
211A ARG* 1.3 75.5 + - - +
213A VAL* 4.4 0.8 - - - +
214A ASP* 3.1 35.4 + - - +
506B LEU* 4.2 9.2 - - - +
510B SER* 2.5 36.6 + - - -
514B ASP* 5.1 0.2 - - - -
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Residues in contact with ARG 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A MET* 3.2 27.1 + - + +
173A ARG 3.8 3.4 + - - -
174A PHE 4.1 0.8 + - - -
175A PRO* 3.3 32.0 - - - +
178A ALA* 3.7 27.4 - - + +
189A MET* 5.8 0.2 - - + -
191A TYR* 4.1 17.9 - - + +
207A LEU* 2.9 24.1 + - + +
208A ALA* 4.0 4.3 - - - +
210A SER* 1.3 104.2 + - - +
212A ALA* 1.3 59.7 + - - +
214A ASP* 4.2 5.6 + - - +
215A ASN* 2.7 33.3 + - - +
217A VAL* 4.0 4.5 - - - +
219A VAL* 4.0 12.7 - - + +
514B ASP* 2.6 42.2 + - - -
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Residues in contact with ALA 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A ALA 3.3 4.4 + - - +
209A ARG 3.9 3.8 - - - +
210A SER 3.2 0.6 - - - -
211A ARG* 1.3 78.1 - - - +
213A VAL* 1.3 57.7 + - + +
216A GLN* 2.6 34.0 + - - -
217A VAL* 3.0 21.5 + - - +
219A VAL* 3.6 8.9 - - + +
241A VAL* 3.3 34.3 - - + -
242A ASP 3.7 8.1 - - - +
243A PRO 3.3 4.6 - - - +
245A GLY 5.1 0.2 - - - +
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Residues in contact with VAL 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ARG 3.2 13.8 + - - +
210A SER* 4.4 1.6 - - - +
212A ALA* 1.3 75.2 - - - +
214A ASP* 1.3 66.8 + - - +
216A GLN* 3.5 15.9 - - - +
243A PRO 3.7 6.1 - - - +
244A ARG 3.2 35.4 - - - +
245A GLY* 3.3 13.0 - - - +
473B ARG* 5.7 6.6 - - + +
503B HIS* 3.7 30.7 - - + +
506B LEU* 4.0 8.7 - - + -
507B LEU* 4.7 16.2 - - + -
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Residues in contact with ASP 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A PRO* 5.8 2.3 - - - +
179A MET* 6.3 1.1 - - + -
183A ARG* 5.7 1.0 + - - -
210A SER* 3.1 24.5 + - - +
211A ARG* 4.7 5.3 + - - +
213A VAL* 1.3 81.6 - - - +
215A ASN* 1.3 69.4 + - - +
216A GLN* 4.6 4.2 + - - +
278A LYS* 4.2 17.2 + - - -
473B ARG* 4.6 7.9 - - - +
475B PRO* 3.5 22.0 - - + +
507B LEU* 4.0 12.8 - - - +
510B SER* 5.0 0.3 + - - -
511B ARG* 2.8 47.0 + - - -
514B ASP* 5.4 1.4 - - - +
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Residues in contact with ASN 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A PRO* 6.2 0.2 - - - +
178A ALA* 3.4 16.5 + - - +
179A MET* 2.9 46.5 - - - +
182A ALA* 3.6 21.1 - - + +
183A ARG* 5.2 4.6 - - - +
211A ARG* 2.7 31.6 + - - +
214A ASP* 1.3 84.5 + - - +
216A GLN* 1.3 75.5 + - - +
217A VAL* 3.3 14.4 + - + +
271A ARG* 3.9 8.0 + - - -
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Residues in contact with GLN 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A ALA 2.6 19.1 + - - -
213A VAL 3.5 15.5 + - - +
214A ASP 3.5 3.9 + - - +
215A ASN* 1.3 79.1 + - - +
217A VAL* 1.3 55.6 + - - +
243A PRO* 3.7 20.3 - - + +
267A ILE* 3.9 10.2 - - - +
270A PHE* 3.1 19.7 - - + +
271A ARG* 3.5 33.0 + - + +
274A VAL* 2.8 37.4 + - - +
275A PRO 4.1 1.0 + - - -
276A LEU* 3.6 31.9 - - - +
278A LYS* 5.8 2.0 - - - +
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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
------------------------------------------------------------
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