Contacts of the helix formed by residues 210 - 225 (chain A) in PDB entry 4NKU
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 SER 210 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ASN* 3.5 0.7 - - - +
204A PRO* 3.5 20.3 - - - +
209A LEU* 1.3 81.7 - - - +
211A SER* 1.3 64.4 + - - +
212A TYR* 3.6 6.1 + - - +
213A GLY* 3.0 26.0 + - - -
214A TYR* 3.2 12.3 + - - -
338A VAL* 3.9 14.1 + - - +
341A THR* 4.5 2.1 + - - -
58D A 3.7 18.6 - - - -
59D U 3.5 17.1 + - - -
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Residues in contact with SER 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LYS* 4.1 28.2 - - - +
202A ASN* 3.2 28.4 + - - +
210A SER* 1.3 72.8 - - - +
212A TYR* 1.3 63.6 + - - +
214A TYR* 3.0 18.4 + - - +
215A VAL* 3.0 17.7 + - - +
58D A 5.6 0.2 + - - -
59D U 3.3 20.3 + - - -
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Residues in contact with TYR 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ASN* 3.3 31.4 - - - +
175A LEU* 3.9 27.5 - - + +
210A SER* 3.9 0.9 - - - +
211A SER* 1.3 77.5 - - - +
213A GLY* 1.3 60.8 + - - +
215A VAL* 3.2 4.2 + - - +
216A LEU* 3.0 47.0 + - + +
330A ASP* 2.7 29.8 + - - -
331A PRO* 3.6 12.1 - - - +
338A VAL* 3.7 15.5 - - + -
59D U 3.1 77.8 + + + +
101D BR 4.3 7.4 - - + -
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Residues in contact with GLY 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LEU* 3.8 19.1 - - - -
210A SER* 3.0 14.1 + - - -
212A TYR* 1.3 80.1 - - - +
214A TYR* 1.3 58.7 + - - +
216A LEU* 3.4 6.5 + - - +
217A MET* 3.0 25.6 + - - +
328A ILE* 4.2 4.9 - - - +
338A VAL* 3.7 19.4 - - - +
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Residues in contact with TYR 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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192A VAL* 4.1 25.1 - - + +
193A LYS* 5.4 6.7 - - + -
195A TRP* 4.1 17.9 - + - -
196A ALA* 3.6 22.4 - - + -
201A ILE* 2.7 46.2 + - + +
202A ASN* 4.3 4.7 - - - -
209A LEU* 3.6 30.7 - - + -
210A SER 3.2 20.7 + - - -
211A SER* 3.0 10.2 + - - +
213A GLY* 1.3 72.4 - - - +
215A VAL* 1.3 61.0 + - + +
217A MET* 3.1 16.6 + - + +
218A VAL* 2.9 32.8 + - - +
275A PHE* 5.3 0.2 - + - -
350A ILE* 3.6 12.2 - - + +
354A PHE* 4.5 12.1 - + - -
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Residues in contact with VAL 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 4.3 10.1 - - + -
175A LEU* 3.6 33.0 - - + -
185A LEU* 6.5 0.4 - - + -
189A VAL* 3.7 20.2 - - + -
193A LYS* 3.7 26.2 - - + -
211A SER 3.0 13.3 + - - +
212A TYR* 3.2 9.2 + - - +
214A TYR* 1.3 77.1 - - - +
216A LEU* 1.3 57.6 + - + +
218A VAL* 3.2 9.0 + - - +
219A LEU* 2.9 35.7 + - + +
101D BR 4.0 10.8 - - + -
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Residues in contact with LEU 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 6.1 0.2 - - + -
175A LEU* 4.5 4.7 - - + -
212A TYR* 3.0 44.2 + - + +
213A GLY 3.7 7.2 - - - +
215A VAL* 1.3 77.1 - - + +
217A MET* 1.3 57.1 + - - +
219A LEU* 4.5 13.7 - - + +
220A TYR* 2.9 27.2 + - - +
290A VAL* 4.8 1.8 - - - -
292A PHE* 3.3 30.2 - - + -
328A ILE* 3.9 18.4 - - + -
330A ASP* 4.4 0.7 - - - -
331A PRO* 3.9 24.5 - - + -
338A VAL* 3.7 30.1 - - + -
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Residues in contact with MET 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LEU* 3.5 30.3 - - - -
213A GLY 3.0 13.3 + - - +
214A TYR* 3.1 16.1 + - - +
216A LEU* 1.3 76.3 - - - +
218A VAL* 1.3 63.6 + - - +
220A TYR* 4.5 1.1 - - - -
221A TYR* 3.2 11.6 + - - +
275A PHE* 3.9 6.7 - - + -
279A TYR* 2.7 69.3 + - + +
290A VAL* 4.7 5.4 - - + -
326A LEU* 4.6 13.0 - - + -
328A ILE* 4.0 18.4 - - + -
350A ILE* 5.5 1.8 - - + -
354A PHE* 3.8 21.8 - - + -
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Residues in contact with VAL 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU* 4.1 12.6 - - + -
188A MET* 3.9 19.1 - - + -
189A VAL* 4.3 9.6 - - + -
192A VAL* 4.0 22.2 - - + -
214A TYR 2.9 17.5 + - - +
215A VAL* 3.5 10.1 - - - +
217A MET* 1.3 74.1 - - - +
219A LEU* 1.3 66.4 + - - +
221A TYR* 3.2 4.0 + - - +
222A LEU* 3.0 43.0 + - + +
275A PHE* 3.6 27.1 - - + -
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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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174A LEU* 5.7 2.7 - - + -
175A LEU* 3.8 32.8 - - + -
178A TYR* 3.8 42.0 - - + -
185A LEU* 4.0 14.6 - - + -
215A VAL* 2.9 27.0 + - + +
216A LEU* 4.0 9.9 - - + +
218A VAL* 1.3 73.4 - - - +
220A TYR* 1.3 62.8 + - - +
222A LEU* 3.2 3.2 + - - +
223A ILE* 2.9 32.8 + - + +
231A PHE* 3.8 21.5 - - + -
292A PHE* 3.9 15.9 - - + -
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Residues in contact with TYR 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 LEU 2.9 18.7 + - - +
217A MET 3.8 3.4 - - - +
218A VAL 3.2 0.2 - - - -
219A LEU* 1.3 76.6 - - - +
221A TYR* 1.3 58.8 + - - +
223A ILE* 4.8 1.6 - - - -
224A HIS* 2.8 51.5 + + + +
225A VAL* 3.6 20.6 + - + +
278A PHE* 4.0 14.6 - + - -
279A TYR* 3.4 15.5 - - - +
283A PHE* 5.0 5.0 - + - -
289A VAL 4.7 1.7 + - - -
290A VAL* 3.6 24.5 - - + -
291A THR 3.2 39.7 - - - -
292A PHE* 3.6 8.9 - + + -
296A ASP 4.9 0.3 + - - -
297A GLY* 2.5 31.3 + - - -
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Residues in contact with TYR 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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188A MET* 4.3 1.6 - - + -
217A MET 3.2 11.5 + - - +
218A VAL 3.2 6.7 + - - +
220A TYR* 1.3 81.2 - - - +
222A LEU* 1.3 79.2 + - + +
225A VAL* 3.2 41.2 + - + -
226A ILE* 3.0 64.0 + - + +
270A SER 4.8 0.7 + - - -
271A LEU 3.6 17.2 + - - -
274A GLY* 3.1 38.6 - - - -
275A PHE* 3.7 22.0 - - + -
278A PHE* 3.9 14.1 - - + -
279A TYR* 4.4 5.4 - - + -
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Residues in contact with LEU 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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185A LEU* 3.7 22.0 - - + -
188A MET* 3.8 19.3 - - - -
218A VAL* 3.0 39.9 + - + +
219A LEU* 3.2 3.6 + - - +
221A TYR* 1.3 95.5 - - + +
223A ILE* 1.3 61.1 + - - +
226A ILE* 3.5 7.5 - - + +
229A PRO 3.8 0.7 - - - -
230A VAL* 2.9 54.8 + - + -
231A PHE* 3.5 24.1 + - + -
271A LEU* 4.2 11.0 - - + -
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Residues in contact with ILE 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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178A TYR* 3.5 30.1 - - + +
219A LEU* 2.9 30.3 + - + +
222A LEU* 1.3 79.4 - - - +
224A HIS* 1.3 91.2 + - + +
225A VAL 3.7 0.4 - - - -
226A ILE 4.9 1.0 - - - +
227A LYS* 5.0 1.7 + - - -
229A PRO* 3.8 21.8 - - - +
231A PHE* 3.7 29.1 - - + +
232A PRO 4.0 0.7 - - - +
233A ASN* 3.9 22.7 - - + +
292A PHE* 4.2 17.9 - - + -
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Residues in contact with HIS 224 (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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220A TYR* 2.8 34.2 + + + +
223A ILE* 1.3 95.9 + - + +
225A VAL* 1.3 63.4 + - - +
227A LYS* 3.9 17.3 + - - +
233A ASN* 2.9 33.0 + - + -
236A LEU* 4.7 0.2 - - + -
291A THR 3.9 20.6 + - - -
292A PHE* 4.5 3.6 - + - -
294A ARG 3.2 23.4 + - - -
295A PRO* 3.6 15.7 + - + -
296A ASP* 4.0 8.0 - - - +
297A GLY* 3.6 17.8 + - - +
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Residues in contact with VAL 225 (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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220A TYR* 3.8 18.4 - - + +
221A TYR* 3.2 33.2 + - + +
223A ILE 3.7 0.2 - - - -
224A HIS* 1.3 82.1 - - - +
226A ILE* 1.3 71.0 + - - +
227A LYS* 3.5 16.8 + - - +
278A PHE* 3.5 51.4 - - + -
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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