Contacts of the strand formed by residues 238 - 248 (chain A) in PDB entry 4II9
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 LYS 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A GLU* 3.1 6.2 - - - -
235A ARG* 2.9 45.9 + - + +
236A GLU 3.3 2.0 - - - +
237A GLY* 1.3 73.4 - - - +
239A LEU* 1.3 71.6 + - - +
240A LEU* 3.5 13.4 + - + +
265A TYR* 6.5 1.3 - - + -
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Residues in contact with LEU 239 (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 GLU* 3.8 37.2 - - + +
197A LYS* 4.5 19.3 - - + -
198A THR* 3.8 20.9 - - + -
232A VAL* 3.6 31.2 - - + -
233A ALA 4.1 4.7 - - - +
234A GLU* 4.1 10.5 - - + +
237A GLY 3.9 2.6 + - - -
238A LYS* 1.3 76.8 - - - +
240A LEU* 1.4 67.7 + - - +
242A THR* 4.2 2.9 - - + -
260A MET* 3.3 19.2 - - + +
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Residues in contact with LEU 240 (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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181A VAL* 4.0 9.4 - - + -
198A THR* 4.7 1.6 - - - -
233A ALA 2.9 11.3 + - - +
234A GLU 4.2 2.2 - - - -
235A ARG* 3.7 30.5 - - + +
238A LYS* 3.5 24.5 - - + +
239A LEU* 1.4 81.9 - - - +
241A SER* 1.3 66.6 + - - +
259A SER* 3.4 2.1 - - - -
260A MET* 2.9 33.8 + - + +
263A ASN 4.1 19.5 - - - +
264A THR* 3.5 25.1 - - - +
265A TYR* 4.2 12.1 - - + -
267A ALA* 3.7 17.0 - - + -
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Residues in contact with SER 241 (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 THR* 4.4 2.2 - - - +
233A ALA* 2.8 27.9 + - - +
239A LEU* 4.7 0.2 - - - +
240A LEU* 1.3 82.5 - - - +
242A THR* 1.3 69.7 + - - +
258A GLY 3.3 14.8 - - - -
259A SER* 3.7 11.7 - - - +
264A THR* 5.3 0.2 - - - -
267A ALA* 3.4 26.8 - - - +
268A PRO* 3.4 18.0 - - - +
271A VAL* 3.6 9.2 - - - +
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Residues in contact with THR 242 (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 GLU 3.9 2.0 - - - +
195A PHE* 3.4 39.7 - - - +
198A THR* 2.7 33.0 + - + +
230A ILE* 4.8 0.9 - - - -
231A PHE 3.1 11.2 - - - -
232A VAL* 4.0 22.2 - - + -
239A LEU* 4.2 1.1 - - + -
241A SER* 1.3 83.3 + - - +
243A GLY* 1.3 60.8 + - - +
257A ALA* 3.4 7.6 - - - +
258A GLY 2.9 23.7 + - - +
271A VAL* 4.4 10.6 - - - +
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Residues in contact with GLY 243 (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 PHE* 4.9 0.4 - - - -
230A ILE* 3.4 2.9 - - - +
231A PHE 2.8 32.2 + - - -
242A THR* 1.3 80.1 - - - +
244A ILE* 1.4 62.7 + - - -
254A TYR* 4.7 0.7 - - - -
256A TYR 3.2 11.4 - - - -
257A ALA* 4.0 3.6 - - - -
271A VAL* 4.0 5.1 - - - +
275A MET* 3.3 21.1 - - - +
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Residues in contact with ILE 244 (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 LEU* 5.0 0.7 - - + -
195A PHE* 3.7 47.1 - - + -
216A PHE* 3.8 17.9 - - + -
219A MET* 4.9 3.1 - - - -
228A MET* 4.1 26.2 - - + -
229A ARG 3.6 9.0 - - - +
230A ILE* 4.0 14.8 - - + -
243A GLY* 1.4 79.3 - - - +
245A ALA* 1.3 62.4 + - - +
246A LEU* 3.8 21.5 - - + -
254A TYR* 3.8 1.9 - - - -
255A MET* 2.9 27.8 + - + +
256A TYR* 2.8 22.4 + - + +
275A MET* 3.6 1.7 - - - +
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Residues in contact with ALA 245 (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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228A MET* 3.6 0.2 - - - -
229A ARG 2.9 34.3 + - - +
231A PHE* 4.3 0.9 - - + -
244A ILE* 1.3 74.1 - - - +
246A LEU* 1.3 68.5 + - - +
252A ILE* 3.9 12.1 - - + -
253A TRP 3.1 11.4 - - - +
275A MET* 3.9 28.6 - - + +
278A TRP* 3.6 22.0 - - + -
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Residues in contact with LEU 246 (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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26A VAL* 4.0 28.0 - - + -
32A TRP* 5.8 0.7 - - + -
219A MET* 4.3 12.3 - - + -
223A PHE* 4.2 11.7 - - + -
227A THR* 3.2 22.0 - - + +
228A MET* 3.7 24.7 - - + -
244A ILE* 3.8 20.4 - - + -
245A ALA* 1.3 80.5 - - - +
247A LYS* 1.3 60.6 + - - +
248A TYR* 3.9 1.6 + - + +
251A LYS 3.8 1.4 - - - +
252A ILE* 3.4 3.3 - - - -
253A TRP* 2.8 38.7 + - + +
255A MET* 3.5 32.5 - - + -
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Residues in contact with LYS 247 (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 ASP 3.9 15.7 + - - +
227A THR* 2.8 31.3 + - - +
246A LEU* 1.3 68.7 - - - +
248A TYR* 1.3 68.7 - - - +
249A GLY 5.3 6.8 + - - +
251A LYS 3.6 4.5 - - - +
252A ILE* 3.7 17.7 - - + -
278A TRP* 3.6 29.7 - - + +
282A THR* 3.5 38.8 + - + +
284A THR* 3.8 9.1 + - + +
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Residues in contact with TYR 248 (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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18A MET* 3.4 40.0 - - + +
19A ARG* 3.8 16.7 + - + +
24A GLY* 3.7 4.6 - - - +
25A GLN* 3.4 34.0 - - - -
26A VAL* 3.6 36.1 - - + +
29A ASP* 2.6 44.4 + - + +
223A PHE* 4.9 2.2 - + - -
227A THR* 4.6 7.9 - - + -
246A LEU 3.9 2.8 + - - +
247A LYS* 1.3 80.5 - - - +
249A GLY* 1.3 85.0 + - - +
250A ARG 3.3 0.5 + - - -
251A LYS* 3.0 26.9 + - + +
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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