Contacts of the helix formed by residues 207 - 223 (chain A) in PDB entry 4K71
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 GLY 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A SER 2.9 14.5 + - - +
203A LEU* 3.2 17.0 + - - -
204A GLN 4.6 0.6 - - - -
205A LYS 3.7 0.8 - - - -
206A PHE* 1.3 78.4 - - - +
208A GLU* 1.3 65.9 + - - +
209A ARG 3.3 2.7 - - - -
210A ALA* 3.1 12.5 + - - +
211A PHE 3.8 1.7 + - - -
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Residues in contact with GLU 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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203A LEU* 4.1 15.7 + - + -
207A GLY* 1.3 72.2 - - - -
209A ARG* 1.3 75.5 + - + +
211A PHE* 3.2 5.0 + - - +
212A LYS* 3.0 51.8 + - + +
239A THR* 3.7 26.2 - - + +
243A THR* 5.4 1.1 - - - +
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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
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206A PHE 5.8 0.9 - - - +
207A GLY 3.3 0.8 - - - -
208A GLU* 1.3 95.1 + - + +
210A ALA* 1.3 57.5 + - - +
212A LYS* 3.7 24.0 - - - +
213A ALA* 2.9 32.6 + - - +
324A ASP* 2.9 55.4 + - + +
325A VAL* 6.1 2.2 - - - +
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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
----------------------------------------------------------
202A SER* 3.9 13.3 - - - +
206A PHE* 3.7 30.5 + - + +
207A GLY 3.1 14.0 + - - +
209A ARG* 1.3 78.3 - - - +
211A PHE* 1.3 59.8 + - - +
213A ALA* 3.9 4.7 - - - +
214A TRP* 3.3 20.3 + - - +
347A LEU* 4.9 4.0 - - - +
481A LEU* 4.7 6.9 - - + +
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Residues in contact with PHE 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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199A LYS* 3.9 28.9 - - + -
202A SER* 4.0 17.4 + - - +
203A LEU* 3.4 37.0 - - + +
207A GLY 3.8 1.0 + - - -
208A GLU 3.2 2.8 + - - +
210A ALA* 1.3 75.8 - - - +
212A LYS* 1.3 66.1 + - - +
213A ALA 3.2 0.2 - - - -
214A TRP* 3.2 24.6 + + + +
215A ALA* 2.9 29.3 + - + +
238A LEU* 4.0 4.7 - - + -
239A THR* 3.5 41.5 - - + -
242A HIS* 3.6 37.2 - + + -
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Residues in contact with LYS 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 GLU* 3.0 42.5 + - - +
209A ARG* 3.7 32.4 - - - +
211A PHE* 1.3 77.4 - - - +
213A ALA* 1.3 56.0 + - - +
215A ALA* 3.2 2.6 + - - +
216A VAL* 2.9 34.9 + - + +
235A VAL* 3.9 17.9 - - + -
236A THR* 4.2 24.9 + - - +
239A THR* 3.6 23.6 - - + +
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Residues in contact with ALA 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 2.9 17.4 + - - +
210A ALA* 3.9 5.4 - - - +
212A LYS* 1.3 75.9 - - - +
214A TRP* 1.3 62.6 + - - +
216A VAL* 3.5 2.6 + - - +
217A ALA* 3.1 20.3 + - - +
331A LEU* 3.2 22.9 - - + +
347A LEU* 3.5 19.7 - - + -
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Residues in contact with TRP 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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195A LYS* 5.9 0.7 - - + -
198A LEU* 6.5 1.6 - - + -
199A LYS* 3.0 45.5 - - + +
202A SER* 5.9 1.3 - - - +
210A ALA 3.3 12.3 + - - +
211A PHE* 3.2 31.1 + + + +
213A ALA* 1.3 76.7 - - - +
215A ALA* 1.3 91.3 + - + +
217A ALA* 3.4 3.3 + - - +
218A ARG* 3.0 49.6 + - + +
219A LEU* 6.3 0.4 - - + -
222A ARG* 6.0 1.1 - - - -
238A LEU* 4.5 11.4 - - + -
242A HIS* 5.9 0.2 - - - -
343A VAL* 3.3 35.6 - - + +
347A LEU* 3.8 16.8 - - + +
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Residues in contact with ALA 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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211A PHE* 2.9 27.2 + - + +
212A LYS 3.6 4.0 - - - +
214A TRP* 1.3 95.0 - - + +
216A VAL* 1.3 66.9 + - - +
218A ARG* 3.3 0.6 + - - +
219A LEU* 2.9 31.0 + - - +
235A VAL* 3.9 21.5 - - + -
238A LEU* 4.3 11.4 - - + -
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Residues in contact with VAL 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 LYS* 2.9 22.4 + - + +
213A ALA* 4.0 4.7 - - - +
214A TRP 3.4 0.2 - - - -
215A ALA* 1.3 74.7 - - - +
217A ALA* 1.3 56.6 + - - +
219A LEU* 4.1 0.3 - - - +
220A SER* 2.6 46.8 + - - +
228A PHE* 4.8 8.5 - - + -
231A VAL* 4.5 8.3 - - + -
232A SER* 5.5 3.8 - - - +
235A VAL* 3.6 25.6 - - + -
328A GLY* 3.6 31.2 - - - +
331A LEU* 4.3 7.4 - - + -
332A TYR* 3.9 13.0 - - + +
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Residues in contact with ALA 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 ALA 3.1 18.4 + - - +
214A TRP 3.5 5.2 - - - +
216A VAL* 1.3 80.0 - - - +
218A ARG* 1.3 62.2 + - - +
221A GLN* 3.2 27.5 + - - +
331A LEU* 4.2 17.0 - - + +
335A ALA* 3.4 12.5 - - - +
343A VAL* 4.0 17.9 - - + -
346A LEU* 4.2 15.7 - - + -
347A LEU* 4.7 2.0 - - + -
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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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214A TRP* 3.0 44.0 + - + +
215A ALA 4.1 1.8 - - - +
217A ALA* 1.3 76.7 - - - +
219A LEU* 1.3 60.2 + - + +
221A GLN* 3.4 25.8 + - - +
222A ARG* 3.1 61.8 + - - +
293A VAL 5.7 1.0 + - - -
295A ASN* 3.8 23.6 + - - +
343A VAL* 3.9 16.2 - - + -
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Residues in contact with LEU 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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214A TRP* 6.3 0.4 - - + -
215A ALA* 2.9 21.0 + - - +
216A VAL 4.1 1.3 - - - +
218A ARG* 1.3 76.9 - - + +
220A SER* 1.3 53.8 + - - +
222A ARG* 3.9 22.2 - - - +
223A PHE* 2.6 71.2 + - + +
231A VAL* 4.3 12.8 - - + -
234A LEU* 4.3 20.2 - - + -
235A VAL* 4.0 18.2 - - + +
238A LEU* 4.0 28.0 - - + -
264A ILE* 6.4 0.2 - - + -
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Residues in contact with SER 220 (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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216A VAL 2.6 27.1 + - - -
217A ALA 3.8 3.6 - - - -
219A LEU* 1.3 70.0 - - - +
221A GLN* 1.3 64.5 + - - +
223A PHE 4.6 4.9 - - - -
224A PRO* 3.1 26.6 - - - +
231A VAL* 3.8 8.9 - - - +
332A TYR* 3.4 50.7 - - - +
335A ALA* 3.9 7.2 - - - -
336A ARG* 3.3 8.2 - - - +
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Residues in contact with GLN 221 (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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217A ALA 3.2 12.7 + - - +
218A ARG* 3.4 37.6 + - - +
219A LEU 3.3 0.2 - - - -
220A SER* 1.3 78.4 - - - +
222A ARG* 1.3 61.1 + - - +
224A PRO* 3.4 12.8 - - - +
295A ASN* 3.5 18.5 + - - +
296A ASP 4.7 0.2 - - - +
335A ALA* 3.6 23.8 - - + +
336A ARG* 4.2 2.3 - - - +
338A HIS 2.9 20.7 + - - +
339A PRO* 3.1 26.4 + - + +
341A TYR 2.9 27.6 + - - +
343A VAL* 4.1 4.5 - - - +
346A LEU* 3.9 10.8 - - - +
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Residues in contact with ARG 222 (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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214A TRP* 6.0 1.0 - - - -
218A ARG* 3.1 60.7 + - - +
219A LEU* 3.7 25.1 - - - +
221A GLN* 1.3 75.8 - - - +
223A PHE* 1.3 83.8 + - + +
224A PRO* 3.1 1.9 - - - +
272A SER* 4.8 0.2 + - - -
290A ILE 4.0 3.6 + - - -
291A ALA* 3.2 33.3 + - - +
292A GLU* 5.0 2.2 + - - +
293A VAL* 3.6 40.1 + - + +
294A GLU 4.4 1.7 - - - +
295A ASN* 3.4 13.2 + - - +
296A ASP* 3.0 27.0 + - - +
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Residues in contact with PHE 223 (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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219A LEU* 2.6 50.8 + - + +
220A SER* 3.6 4.0 - - - +
222A ARG* 1.3 103.9 - - + +
224A PRO* 1.3 58.2 - - - +
225A LYS 3.2 2.5 - - - -
226A ALA* 3.0 29.0 + - + +
231A VAL* 4.5 7.3 - - + +
234A LEU* 4.1 16.6 - - + -
264A ILE* 5.1 7.2 - - + -
271A ILE* 3.7 36.3 - - + +
272A SER* 3.8 19.1 - - - -
275A LEU* 4.6 5.2 - - + -
290A ILE* 4.4 18.6 - - + -
293A VAL* 3.9 12.3 - - + -
296A ASP* 4.9 1.6 - - - -
332A TYR* 5.3 0.5 - - - -
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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
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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