Contacts of the strand formed by residues 215 - 228 (chain A) in PDB entry 3K6R
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 ALA 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A ASN* 3.4 13.5 - - - +
193A ALA 3.8 4.3 - - - -
196A ILE* 3.7 13.7 - - + +
211A ALA 2.9 17.5 + - - +
212A LEU* 3.7 14.8 - - - +
213A SER 3.3 1.3 - - - +
214A ILE* 1.3 80.1 - - - +
216A LYS* 1.3 64.8 + - - +
219A ALA* 3.7 19.1 - - + -
221A ILE* 4.7 1.6 - - + -
249A TYR* 4.7 6.0 + - + -
275A VAL* 4.0 16.2 - - + -
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Residues in contact with LYS 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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191A ASN* 3.3 31.4 - - - +
192A ILE* 3.3 25.1 + - - +
193A ALA 2.9 14.3 + - - +
194A ASP* 2.6 32.8 + - - +
215A ALA* 1.3 77.9 - - - +
217A ASP* 1.3 71.1 + - - +
218A GLY 3.3 0.3 + - - -
219A ALA* 3.1 18.7 + - + +
249A TYR* 5.8 2.3 - - - -
275A VAL* 4.3 3.1 - - - +
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Residues in contact with ASP 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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191A ASN* 4.1 5.6 + - - +
215A ALA 4.1 0.2 + - - -
216A LYS* 1.3 79.6 - - - +
218A GLY* 1.3 61.0 + - - +
219A ALA 3.6 0.2 + - - -
249A TYR* 5.9 3.5 - - - -
275A VAL 4.3 1.8 - - - -
276A PHE* 3.2 18.4 - - - +
277A LYS* 3.1 48.2 + - + +
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Residues in contact with GLY 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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194A ASP 4.9 0.3 - - - +
217A ASP* 1.3 76.5 + - - +
219A ALA* 1.3 62.5 + - - +
220A ILE* 3.8 0.3 + - - +
274A ARG* 3.0 32.4 + - - +
275A VAL 2.8 17.5 + - - -
276A PHE* 4.1 18.6 - - - -
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Residues in contact with ALA 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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193A ALA 3.3 22.9 - - - +
194A ASP* 3.4 12.3 - - - +
195A ARG* 5.0 0.4 - - - -
196A ILE* 5.4 1.1 - - + -
215A ALA* 3.7 16.4 - - + -
216A LYS* 3.1 19.6 + - + +
217A ASP 3.4 0.6 - - - -
218A GLY* 1.3 79.8 - - - +
220A ILE* 1.3 63.7 + - - +
221A ILE* 5.2 1.3 - - + -
273A LEU 3.6 0.7 - - - +
274A ARG* 3.3 3.1 - - - -
275A VAL* 3.0 30.4 + - + +
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Residues in contact with ILE 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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194A ASP 3.1 10.1 + - - +
195A ARG* 3.1 47.4 - - - +
196A ILE 2.8 31.0 + - - -
218A GLY 4.4 0.2 - - - +
219A ALA* 1.3 76.8 - - - +
221A ILE* 1.3 61.4 + - - +
222A HIS* 4.0 16.8 - - + +
254A LEU* 4.4 14.8 - - + -
272A ASP* 4.8 2.0 - - + -
273A LEU 3.2 12.3 - - - +
274A ARG* 3.6 41.3 - - + +
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Residues in contact with ILE 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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196A ILE* 3.4 23.3 - - + +
198A MSE 3.5 33.7 - - + -
211A ALA* 4.1 24.5 - - + +
212A LEU* 4.7 3.4 - - + -
215A ALA* 4.7 1.3 - - + -
219A ALA 5.0 0.7 - - - -
220A ILE* 1.3 78.9 - - - +
222A HIS* 1.3 66.8 + - - +
223A TYR* 3.7 7.4 + - + +
240A PHE* 4.4 11.9 - - + -
271A LEU 3.4 4.0 - - - +
272A ASP* 3.5 1.7 - - - -
273A LEU* 2.8 42.4 + - + +
275A VAL* 3.9 35.2 - - + -
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Residues in contact with HIS 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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118A ARG* 3.9 3.8 + - - -
119A MSE 4.0 23.6 - - + +
122A VAL* 4.2 7.9 - - + +
139A LEU* 6.3 0.4 - - + -
195A ARG* 3.0 42.5 + - + -
196A ILE 2.8 11.0 + - - +
197A LEU* 3.5 31.0 - - + -
198A MSE 2.8 32.7 + - - +
220A ILE* 4.0 8.0 - - + +
221A ILE* 1.3 72.9 - - - +
223A TYR* 1.3 59.5 + - - +
224A HIS* 3.7 9.1 + - + +
270A VAL* 4.2 9.4 - - + -
271A LEU 3.5 4.3 - - - -
272A ASP* 2.6 37.2 + - - +
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Residues in contact with TYR 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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198A MSE 4.0 16.6 - - - -
204A THR* 3.8 22.0 - - + -
205A HIS* 3.3 25.4 + - - +
208A ILE* 4.1 5.2 - - + +
221A ILE* 4.3 4.7 - - + -
222A HIS* 1.3 70.2 - - - +
224A HIS* 1.3 63.2 + - - +
225A ASN* 3.0 30.0 + - + -
236A PRO* 4.1 29.9 + - + +
239A THR* 5.4 1.2 - - - +
240A PHE* 3.7 37.8 + + + +
269A VAL 3.9 0.5 - - - +
270A VAL* 3.5 1.0 - - - -
271A LEU* 2.8 49.4 + - + +
273A LEU* 3.8 18.8 - - + -
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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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115A GLU* 4.0 14.9 + - + -
119A MSE 6.0 0.8 - - - -
139A LEU* 3.8 25.4 - - + +
198A MSE 3.0 22.3 + - - +
199A GLY* 3.7 12.7 - - - -
200A TYR 3.2 20.8 - - - +
204A THR* 3.2 14.4 - - - +
222A HIS* 3.8 12.8 - - - +
223A TYR* 1.3 77.6 - - - +
225A ASN* 1.3 64.5 + - - +
259A ILE* 3.8 21.7 - - + +
268A HIS* 3.0 29.5 + + + +
269A VAL 3.3 4.5 - - - -
270A VAL* 3.5 21.7 - - + +
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Residues in contact with ASN 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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200A TYR 4.3 2.0 - - - -
201A VAL* 3.6 15.4 - - - +
203A ARG* 3.9 5.6 + - - +
204A THR* 3.7 26.5 + - - +
205A HIS* 4.1 9.3 + - - +
223A TYR* 3.0 33.7 + - + -
224A HIS* 1.3 75.0 - - - +
226A THR* 1.3 85.3 + - - +
236A PRO* 4.5 18.1 - - + +
267A TRP 3.4 1.2 - - - +
268A HIS* 3.4 4.8 - - - -
269A VAL* 3.0 36.0 + - - +
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Residues in contact with THR 226 (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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201A VAL* 3.1 33.3 + - - +
225A ASN* 1.3 89.6 + - - +
227A VAL* 1.3 63.0 + - - +
228A PRO* 4.3 4.0 - - + +
262A TYR* 6.1 1.3 - - + -
266A VAL* 3.9 31.2 - - + -
267A TRP 3.2 7.6 - - - +
268A HIS* 4.5 4.9 - - - +
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Residues in contact with VAL 227 (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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226A THR* 1.3 76.6 - - - +
228A PRO* 1.3 85.5 - - + +
229A GLU 3.3 0.5 + - - -
231A LEU* 4.4 2.2 - - + -
232A MSE 3.6 26.0 - - + -
235A GLU* 3.8 35.7 - - + +
236A PRO* 4.2 13.9 - - + -
266A VAL* 3.3 3.8 - - - -
267A TRP* 2.7 46.2 + - - +
269A VAL* 4.1 20.0 - - + -
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Residues in contact with PRO 228 (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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226A THR* 4.3 4.3 - - + +
227A VAL* 1.3 102.1 - - + +
229A GLU* 1.3 65.6 + - - +
230A LYS* 3.3 6.3 - - + +
231A LEU* 3.1 36.8 + - + -
232A MSE 3.6 2.4 - - - +
265A GLY 3.7 6.7 - - - +
266A VAL* 4.1 13.0 - - + -
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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