Contacts of the helix formed by residues 184 - 199 (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 ARG 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A TYR* 4.4 14.1 - - - +
182A ASP* 2.9 37.2 + - - +
183A ALA* 1.3 80.4 - - + +
185A LEU* 1.3 63.4 + - - +
186A LYS 3.5 0.2 - - - -
187A PRO* 3.4 9.3 - - - +
188A MET* 3.3 23.7 + - - +
230A VAL* 3.8 9.6 - - + +
262A SER* 3.7 11.9 + - - -
264A ASN* 2.9 34.9 + - - -
265A TYR* 3.8 2.2 - - - +
266A SER* 2.6 46.0 + - - +
267A SER* 5.1 0.4 - - - +
268A LEU* 3.9 12.3 - - + +
271A LEU* 4.0 28.7 - - + +
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Residues in contact with LEU 185 (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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95A LEU* 5.5 2.0 - - + -
175A LEU 4.8 0.2 - - - +
178A TYR* 3.6 42.0 - - + +
179A THR* 3.7 16.4 - - + +
182A ASP* 3.2 15.7 + - - +
184A ARG* 1.3 76.8 - - - +
186A LYS* 1.3 67.4 + - - +
188A MET* 3.2 3.8 + - + +
189A VAL* 2.9 42.7 + - + +
215A VAL* 6.3 0.9 - - + -
218A VAL* 4.1 6.3 - - + -
219A LEU* 4.0 10.8 - - + -
222A LEU* 3.7 28.7 - - + -
231A PHE* 3.8 15.5 - - + -
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Residues in contact with LYS 186 (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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52A TYR* 3.3 31.1 + - + +
56A LYS* 5.1 9.1 - - - +
57A ILE* 6.0 4.5 + - - +
94A GLY* 3.3 29.6 - - - +
95A LEU* 3.9 15.5 - - + +
96A ALA 5.8 1.3 - - - -
179A THR* 5.3 10.6 - - - +
182A ASP 4.5 1.6 + - - +
183A ALA 4.2 3.7 + - - +
185A LEU* 1.3 79.1 - - - +
187A PRO* 1.4 69.7 - - + +
189A VAL* 3.3 2.1 + - - +
190A LEU* 3.1 35.0 + - + +
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Residues in contact with PRO 187 (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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49A TYR* 4.0 20.6 - - + -
52A TYR* 3.5 38.8 - - + +
183A ALA 3.3 19.5 - - - +
184A ARG* 3.4 14.8 - - - +
186A LYS* 1.4 93.0 - - + +
188A MET* 1.3 59.8 + - - +
190A LEU* 3.4 0.9 + - - +
191A LEU* 3.0 31.9 + - + +
268A LEU* 3.7 19.3 - - + -
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Residues in contact with MET 188 (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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184A ARG 3.3 17.4 + - - +
185A LEU 3.2 6.1 + - - +
187A PRO* 1.3 78.4 - - - +
189A VAL* 1.3 62.6 + - - +
191A LEU* 3.4 2.7 + - - +
192A VAL* 3.0 30.6 + - + +
218A VAL* 3.9 16.8 - - + -
221A TYR* 4.3 2.2 - - + -
222A LEU* 3.8 37.0 - - + -
268A LEU* 3.7 12.3 - - + +
271A LEU* 3.7 30.3 - - + +
272A LEU* 3.7 20.4 - - + +
275A PHE* 3.5 36.6 - - + -
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Residues in contact with VAL 189 (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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95A LEU* 3.9 26.9 - - + -
185A LEU* 2.9 42.5 + - + +
186A LYS 3.8 3.6 - - - +
188A MET* 1.3 75.2 - - - +
190A LEU* 1.3 61.1 + - + +
192A VAL* 3.3 5.7 + - - +
193A LYS* 2.9 41.9 + - + +
215A VAL* 3.7 33.9 - - + -
218A VAL* 4.3 16.2 - - + -
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Residues in contact with LEU 190 (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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52A TYR* 3.7 16.8 - - + -
55A ILE* 3.5 9.2 - - + +
56A LYS* 3.6 39.0 - - + +
94A GLY 5.0 0.2 - - - +
95A LEU* 3.3 41.5 - - + +
96A ALA 3.8 11.9 - - - +
97A LEU* 3.8 17.0 - - + +
186A LYS* 3.1 27.7 + - + +
187A PRO 3.9 3.4 - - - +
189A VAL* 1.3 77.7 - - + +
191A LEU* 1.3 58.1 + - - +
193A LYS* 3.4 3.4 + - + +
194A HIS* 2.9 30.7 + - - +
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Residues in contact with LEU 191 (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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48A CYS* 3.6 44.6 - - + +
51A VAL* 3.7 31.9 - - + -
52A TYR* 3.9 9.9 - - + +
55A ILE* 4.0 5.2 - - + -
187A PRO 3.0 22.8 + - - +
188A MET 3.9 3.1 - - - +
190A LEU* 1.3 76.7 - - - +
192A VAL* 1.3 59.3 + - - +
194A HIS* 3.4 2.8 + - - +
195A TRP* 2.9 29.8 + - - +
268A LEU* 4.0 9.0 - - + -
272A LEU* 3.7 22.9 - - + -
276A PHE* 6.2 0.7 - - - -
374A PHE* 3.4 19.8 - - + -
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Residues in contact with VAL 192 (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* 3.0 20.0 + - + +
189A VAL 3.8 3.1 - - - +
191A LEU* 1.3 73.8 - - - +
193A LYS* 1.3 60.0 + - + +
195A TRP* 3.4 13.8 + - + +
196A ALA* 2.9 28.2 + - - +
214A TYR* 4.1 28.5 - - + -
218A VAL* 4.0 15.9 - - + -
272A LEU* 3.6 21.5 - - + -
275A PHE* 3.7 34.3 - - + -
276A PHE* 4.9 4.5 - - + -
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Residues in contact with LYS 193 (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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90A SER* 3.6 18.6 + - - -
95A LEU* 2.8 30.5 + - - +
96A ALA* 4.9 0.4 - - - +
97A LEU* 3.9 22.4 - - + +
189A VAL* 2.9 27.9 + - + +
190A LEU* 3.6 5.4 - - + +
192A VAL* 1.3 78.2 - - - +
194A HIS* 1.3 55.9 + - - +
196A ALA* 3.4 5.7 + - - +
197A LYS* 3.0 29.5 + - - +
202A ASN* 4.6 4.7 - - - +
211A SER* 4.1 34.4 - - - +
214A TYR* 5.4 5.8 - - + -
215A VAL* 3.7 25.8 - - + -
59D U 5.2 1.2 + - - -
101D BR 3.7 9.8 - - - +
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Residues in contact with HIS 194 (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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51A VAL* 3.9 17.4 - - + +
55A ILE* 3.7 31.1 - - + +
97A LEU* 4.2 11.8 - - + +
190A LEU 2.9 18.9 + - - +
191A LEU 3.6 4.0 - - - +
193A LYS* 1.3 74.5 - - - +
195A TRP* 1.3 59.4 + - - +
197A LYS* 3.3 12.0 + - + +
198A ARG* 2.9 79.7 + - + +
374A PHE* 3.3 33.6 - + + +
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Residues in contact with TRP 195 (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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191A LEU 2.9 18.6 + - - +
192A VAL* 3.6 17.0 - - + +
194A HIS* 1.3 76.8 - - - +
196A ALA* 1.3 75.1 + - + +
198A ARG* 3.2 2.9 + - - -
199A LYS* 2.9 48.0 + - + +
201A ILE* 3.8 19.1 - - + -
214A TYR* 4.1 13.0 - + - -
276A PHE* 3.5 36.1 - + + -
353A GLU* 3.7 32.8 + - + -
354A PHE* 3.8 34.1 - + - -
357A ALA* 4.1 10.1 - - - +
373A LEU* 3.3 35.1 - - + +
374A PHE* 3.8 16.9 - - + -
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Residues in contact with ALA 196 (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 2.9 20.2 + - - +
193A LYS* 3.8 5.2 - - - +
195A TRP* 1.3 79.0 - - + +
197A LYS* 1.3 62.6 + - - +
200A GLN 3.2 3.5 + - - -
201A ILE* 2.9 38.2 + - + +
202A ASN* 3.5 11.0 + - + -
214A TYR* 3.6 40.2 - - + -
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Residues in contact with LYS 197 (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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97A LEU* 3.6 35.5 - - - +
98A LYS 5.0 4.9 + - - -
193A LYS 3.0 13.5 + - - +
194A HIS* 3.6 13.3 + - + +
196A ALA* 1.3 77.2 - - - +
198A ARG* 1.3 69.5 + - + +
200A GLN* 3.1 18.2 + - - +
202A ASN* 3.9 19.2 - - - +
376A GLU* 5.4 1.0 - - - +
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Residues in contact with ARG 198 (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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194A HIS* 2.9 57.5 + - + +
195A TRP* 3.9 3.1 - - - +
197A LYS* 1.3 81.4 - - + +
199A LYS* 1.3 61.1 + - + +
200A GLN* 3.1 9.4 - - - +
374A PHE* 2.8 48.3 + - - +
375A GLU* 4.3 3.7 - - - +
376A GLU* 3.4 25.5 - - - +
377A ALA 2.9 22.3 + - - -
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Residues in contact with LYS 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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195A TRP* 2.9 34.5 + - - +
196A ALA 4.2 2.0 - - - +
198A ARG* 1.3 75.7 - - - +
200A GLN* 1.3 69.7 + - - +
201A ILE* 3.3 10.4 + - + +
349A ARG* 3.1 11.6 + - - -
353A GLU* 3.5 42.2 + - + +
372A SER 2.9 20.7 + - - -
373A LEU 3.2 20.6 - - - -
374A PHE* 4.9 0.4 - - - +
375A GLU* 2.8 27.6 + - - +
376A GLU 4.8 1.8 + - - -
377A ALA* 4.0 20.6 + - - +
401A MG 3.8 12.0 - - - -
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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
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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