Contacts of the helix formed by residues 199 - 219 (chain A) in PDB entry 2W99
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 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A GLU* 3.2 30.3 - - + +
39A ALA* 6.3 2.9 - - + -
197A SER 4.1 4.5 - - - +
198A ASN* 1.3 88.9 - - + +
200A PRO* 1.3 71.8 - - + +
201A SER* 2.8 14.9 + - - +
202A MET* 2.9 27.2 + - + -
203A VAL 3.1 8.8 + - - -
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Residues in contact with PRO 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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35A GLU* 3.4 21.3 - - + +
83A ASN* 5.6 8.5 - - - +
155A MET* 3.9 24.0 - - + +
156A THR* 3.4 8.7 - - - +
157A PRO* 3.4 30.2 - - + +
160A PHE* 4.0 5.4 - - + -
195A PHE* 5.7 6.1 - - + -
198A ASN 3.9 1.1 - - - +
199A PRO* 1.3 84.6 - - + +
201A SER* 1.3 52.4 + - - +
203A VAL* 3.7 10.5 - - + -
204A ALA* 2.7 37.4 + - - +
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Residues in contact with SER 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.9 10.2 - - - +
35A GLU* 2.6 41.6 + - - -
160A PHE* 3.8 29.1 - - - -
164A PHE* 3.9 1.4 - - - -
199A PRO* 2.8 7.4 + - - +
200A PRO* 1.3 72.7 - - - +
202A MET* 1.3 65.9 + - - -
204A ALA* 3.6 2.3 - - - +
205A ALA* 3.0 19.1 + - - +
237A ILE* 3.2 29.8 - - - +
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Residues in contact with MET 202 (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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198A ASN* 3.9 17.9 - - + +
199A PRO* 2.9 31.1 + - + +
201A SER* 1.3 78.9 + - - +
203A VAL* 1.3 60.1 + - - +
205A ALA* 3.1 1.8 + - - +
206A GLY* 2.7 32.9 + - - -
237A ILE* 3.8 9.4 - - + +
239A CYS* 4.0 28.9 - - + -
243A CYS* 3.3 22.2 - - + +
244A LEU* 3.8 14.9 - - + +
247A CYS* 3.0 42.0 - - + -
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Residues in contact with VAL 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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157A PRO* 3.9 17.7 - - + -
186A VAL* 4.2 10.1 - - + -
189A CYS* 3.9 29.8 - - + -
194A LYS* 4.3 6.1 - - - +
195A PHE* 4.3 19.1 - - + -
198A ASN* 3.6 34.3 - - + +
199A PRO 3.1 5.0 + - - +
200A PRO* 3.8 9.9 - - + +
202A MET* 1.3 74.3 - - - +
204A ALA* 1.3 57.4 + - - +
206A GLY* 4.0 0.5 - - - -
207A SER* 2.6 35.6 + - - +
247A CYS* 4.6 7.0 - - - -
251A ILE* 4.4 0.7 - - - +
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Residues in contact with ALA 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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157A PRO* 3.1 31.6 - - - +
160A PHE* 3.5 17.7 - - + -
161A ILE* 3.7 14.9 - - + +
164A PHE* 3.9 4.5 - - + -
200A PRO 2.7 20.3 + - - +
201A SER 3.6 1.8 - - - +
203A VAL* 1.3 73.8 - - - +
205A ALA* 1.3 51.0 + - - +
207A SER* 3.3 4.2 + - - -
208A VAL* 2.8 38.7 + - - +
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Residues in contact with ALA 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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164A PHE* 3.5 13.2 - - + -
201A SER 3.0 18.3 + - - +
202A MET 3.7 0.7 - - - +
204A ALA* 1.3 73.7 - - - +
206A GLY* 1.3 56.3 + - - +
208A VAL* 3.9 0.2 - - - +
209A VAL* 2.7 39.2 + - - +
233A LEU* 4.1 12.1 - - + -
237A ILE* 3.6 20.0 - - + -
244A LEU* 3.6 23.6 - - + -
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Residues in contact with GLY 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 MET 2.7 18.9 + - - -
205A ALA* 1.3 72.2 - - - +
207A SER* 1.3 55.4 + - - +
209A VAL* 3.8 3.3 - - - +
210A ALA* 2.9 30.5 + - - +
244A LEU* 3.2 16.8 - - - +
247A CYS* 3.9 6.1 - - - -
248A GLN* 4.1 8.5 - - - +
251A ILE* 3.4 17.8 - - - +
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Residues in contact with SER 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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182A ALA* 3.5 26.9 - - - -
185A PHE* 3.5 21.3 - - - +
186A VAL* 3.4 18.4 + - - +
189A CYS* 4.6 0.2 - - - -
203A VAL* 2.6 25.6 + - - +
204A ALA* 3.6 3.4 - - - -
205A ALA 3.2 0.2 - - - -
206A GLY* 1.3 73.9 - - - +
208A VAL* 1.3 59.2 + - - +
210A ALA 3.3 0.3 + - - -
211A ALA* 2.8 32.4 + - - +
251A ILE* 3.5 9.6 - - - +
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Residues in contact with VAL 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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161A ILE* 4.2 31.6 - - + -
164A PHE* 4.5 5.8 - - + -
165A LEU* 4.3 9.4 - - + -
168A MET* 3.6 32.5 - - + -
178A ILE* 4.5 4.9 - - + -
182A ALA* 4.3 5.8 - - + -
204A ALA 2.8 23.8 + - - +
205A ALA 3.9 2.9 - - - +
207A SER* 1.3 71.2 - - - +
209A VAL* 1.3 55.4 + - - +
211A ALA* 3.2 5.1 + - - -
212A VAL* 2.7 47.1 + - + +
229A LEU* 4.2 2.0 - - + -
233A LEU* 4.0 9.6 - - + -
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Residues in contact with VAL 209 (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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205A ALA 2.7 25.5 + - - +
206A GLY* 3.9 4.5 - - - +
208A VAL* 1.3 73.0 - - - +
210A ALA* 1.3 57.2 + - - +
212A VAL* 4.6 0.2 - - - +
213A GLN* 3.0 36.9 + - + +
228A ARG* 5.6 0.7 - - - +
229A LEU* 3.9 29.9 - - + +
230A THR* 3.8 16.8 - - - +
233A LEU* 3.6 20.9 - - + -
244A LEU* 4.6 6.7 - - + +
248A GLN* 3.3 33.2 - - + +
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Residues in contact with ALA 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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185A PHE* 4.0 27.2 - - + -
206A GLY 2.9 21.6 + - - +
207A SER 3.9 2.7 - - - +
209A VAL* 1.3 73.3 - - - +
211A ALA* 1.3 63.0 + - - +
213A GLN* 4.0 1.4 - - - +
214A GLY* 3.1 20.3 + - - -
248A GLN* 4.1 8.1 - - + +
251A ILE* 4.5 8.5 - - + -
252A GLU* 3.5 27.6 - - + +
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Residues in contact with ALA 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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178A ILE* 4.1 13.5 - - + +
181A HIS* 3.8 27.8 - - + -
182A ALA 3.9 8.5 - - - +
185A PHE* 3.7 9.1 - - + -
207A SER 2.8 23.3 + - - +
208A VAL* 3.6 5.2 - - - +
210A ALA* 1.3 76.0 - - - +
212A VAL* 1.3 64.1 + - - +
214A GLY* 3.2 1.2 + - - -
215A LEU* 3.0 28.3 + - + +
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Residues in contact with VAL 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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168A MET* 5.2 4.3 - - - -
178A ILE* 3.3 39.9 - - + -
208A VAL* 2.7 31.2 + - + +
211A ALA* 1.3 73.4 - - - +
213A GLN* 1.3 56.2 + - - +
215A LEU* 3.3 9.3 + - - +
216A ASN* 2.9 26.5 + - - +
223A PHE* 3.6 14.4 - - + +
225A SER* 4.1 6.3 - - - -
226A TYR* 3.5 34.3 - - - +
229A LEU* 3.8 11.2 - - + -
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Residues in contact with GLN 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 VAL* 3.0 23.8 + - + +
210A ALA 4.0 2.0 - - - +
212A VAL* 1.3 78.8 - - - +
214A GLY* 1.3 60.2 + - - +
216A ASN* 3.1 9.6 + - + +
217A LEU* 3.0 34.7 + - + +
226A TYR* 4.3 20.6 - - + +
228A ARG* 5.1 6.9 + - - -
229A LEU* 5.5 0.2 - - - +
248A GLN* 3.1 35.3 + - - +
252A GLU* 4.1 10.3 + - - -
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Residues in contact with GLY 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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210A ALA 3.1 13.3 + - - -
211A ALA 3.7 3.4 - - - -
213A GLN* 1.3 79.4 - - - +
215A LEU* 1.3 60.8 + - - +
217A LEU* 3.9 12.3 + - - +
218A ARG* 3.7 27.1 + - - +
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Residues in contact with LEU 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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177A ILE* 3.9 22.2 - - + +
178A ILE* 3.6 41.5 - - + +
181A HIS* 4.2 12.1 - - + +
211A ALA* 3.0 23.7 + - + +
212A VAL* 3.6 4.3 - - - +
213A GLN 3.1 0.2 - - - -
214A GLY* 1.3 76.9 - - - +
216A ASN* 1.3 60.7 + - - +
217A LEU 3.2 1.6 - - - -
218A ARG* 3.5 32.1 + - - +
219A SER* 3.0 24.4 + - - +
223A PHE* 3.5 38.4 - - + -
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Residues in contact with ASN 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 VAL 2.9 13.9 + - - +
213A GLN* 3.1 9.8 + - - +
215A LEU* 1.3 78.5 - - - +
217A LEU* 1.3 62.0 + - + +
219A SER 4.0 2.9 - - - -
220A PRO* 3.0 32.1 - - - +
221A ASN 3.9 19.0 - - - +
223A PHE* 3.8 17.6 + - - +
224A LEU* 4.0 1.2 - - - +
226A TYR* 3.0 56.8 + - + -
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Residues in contact with LEU 217 (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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213A GLN* 3.0 32.5 + - + +
214A GLY* 3.9 13.5 - - - +
215A LEU 3.2 0.4 - - - -
216A ASN* 1.3 80.9 - - + +
218A ARG* 1.3 67.5 + - + +
220A PRO* 3.0 19.6 - - - +
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Residues in contact with ARG 218 (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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177A ILE* 5.6 4.9 - - - +
181A HIS* 4.7 8.3 + - - -
214A GLY 3.7 14.4 + - - +
215A LEU* 3.5 35.3 + - - +
217A LEU* 1.3 80.5 - - + +
219A SER* 1.3 62.0 + - - +
220A PRO* 3.5 5.2 - - - +
223A PHE* 5.9 1.4 - - - -
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Residues in contact with SER 219 (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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215A LEU 3.0 15.7 + - - +
216A ASN* 3.2 8.6 - - - +
218A ARG* 1.3 84.2 - - - +
220A PRO* 1.3 66.8 + - - +
221A ASN 3.7 0.2 + - - -
222A ASN* 3.0 41.7 + - - +
223A PHE* 4.0 7.7 + - - -
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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