Contacts of the helix formed by residues 252 - 264 (chain D) in PDB entry 4BL5
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 ILE 252 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187D VAL* 4.0 37.2 - - + -
191D LEU* 5.2 1.3 - - + -
207D VAL* 4.0 24.2 - - + -
208D TRP 4.7 6.5 - - - +
211D GLY* 3.2 15.8 + - - +
213D PRO* 3.0 33.2 + - + +
215D ARG* 4.0 25.8 - - + +
217D PHE* 4.5 6.1 - - + -
251D SER* 1.3 69.7 - - - +
253D LYS* 1.3 68.6 + - - +
255D ALA* 3.1 7.5 + - + +
256D ALA* 2.9 21.8 + - - +
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Residues in contact with LYS 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D GLY* 3.0 17.7 + - - +
251D SER* 3.6 8.7 - - - +
252D ILE* 1.3 76.6 - - - +
254D GLU* 1.3 58.7 + - + +
256D ALA* 3.3 4.1 + - - +
257D GLU* 2.9 42.4 + - - +
271D PHE* 4.3 26.1 - - + -
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Residues in contact with GLU 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D ARG* 4.3 7.2 + - - -
249D GLU 4.4 2.1 - - - +
250D VAL* 3.6 21.2 - - + +
251D SER* 3.2 33.1 + - - +
252D ILE 3.1 1.2 - - - -
253D LYS* 1.3 75.0 - - + +
255D ALA* 1.3 61.9 + - - +
257D GLU* 3.3 16.5 + - - +
258D ALA* 2.9 29.6 + - - +
301D PHE* 4.8 2.9 - - + -
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Residues in contact with ALA 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D VAL* 5.6 0.7 - - + -
188D LEU* 3.9 21.4 - - + +
191D LEU* 4.5 3.6 - - + -
217D PHE* 4.1 20.0 - - + -
250D VAL* 4.7 1.3 - - + +
251D SER 3.2 9.1 + - - +
252D ILE* 3.1 13.9 + - + +
254D GLU* 1.3 77.4 - - - +
256D ALA* 1.3 57.9 + - - +
258D ALA* 3.2 4.5 + - - +
259D VAL* 3.0 34.4 + - - +
301D PHE* 4.2 15.3 - - + -
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Residues in contact with ALA 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D LEU* 3.6 24.1 - - + +
205D LEU* 5.1 4.8 - - + +
207D VAL* 4.0 23.8 - - + -
252D ILE 2.9 12.3 + - - +
253D LYS* 3.4 11.2 - - - +
255D ALA* 1.3 74.9 - - - +
257D GLU* 1.3 58.3 + - + +
259D VAL* 3.3 4.2 + - - +
260D VAL* 2.9 35.0 + - - +
269D VAL* 5.3 5.8 - - + -
271D PHE* 5.4 2.2 - - + -
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Residues in contact with GLU 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D LYS* 2.9 30.6 + - - +
254D GLU* 3.6 16.2 - - - +
255D ALA 3.3 0.2 - - - -
256D ALA* 1.3 76.0 - - + +
258D ALA* 1.3 57.3 + - - +
260D VAL* 3.4 10.4 + - - +
261D GLU* 2.9 29.3 + - - +
269D VAL* 6.1 4.7 - - + -
271D PHE* 6.1 1.4 - - + -
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Residues in contact with ALA 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254D GLU 2.9 13.3 + - - +
255D ALA 3.3 9.6 - - - +
257D GLU* 1.3 73.8 - - - +
259D VAL* 1.3 59.6 + - - +
261D GLU* 3.2 6.8 + - - +
262D ALA* 3.0 30.8 + - - +
301D PHE* 4.2 20.2 - - + -
302D LYS* 5.3 9.0 - - + -
305D VAL* 4.4 12.8 - - + -
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Residues in contact with VAL 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D LEU* 4.0 21.8 - - + -
191D LEU* 4.0 22.0 - - + +
192D ILE* 3.9 36.3 - - + -
195D VAL* 4.0 10.7 - - + +
255D ALA 3.0 21.3 + - - +
256D ALA* 3.6 7.2 - - - +
258D ALA* 1.3 70.4 - - - +
260D VAL* 1.3 68.8 + - - +
262D ALA* 3.6 0.8 + - - -
263D MET* 3.3 27.6 + - - +
305D VAL* 4.0 19.0 - - + +
309D CYS* 4.4 0.7 - - - -
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Residues in contact with VAL 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D VAL* 4.4 3.4 - - + -
205D LEU* 3.9 25.4 - - + -
256D ALA 2.9 20.3 + - - +
257D GLU* 3.4 11.7 - - - +
258D ALA 3.2 0.2 - - - -
259D VAL* 1.3 79.8 - - - +
261D GLU* 1.3 66.5 + - - +
262D ALA 3.1 0.2 + - - -
263D MET 3.8 0.3 - - - -
264D ASP 3.1 16.8 + - - -
265D PHE* 3.3 50.4 + - + +
267D GLY 6.0 0.2 - - - +
269D VAL* 4.1 16.8 - - + -
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Residues in contact with GLU 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257D GLU 2.9 19.4 + - - +
258D ALA* 3.2 6.7 + - - +
260D VAL* 1.3 75.0 - - - +
262D ALA* 1.3 62.0 + - - +
264D ASP* 3.2 13.9 + - - +
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Residues in contact with ALA 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258D ALA 3.0 15.8 + - - +
259D VAL 3.9 4.0 - - - +
260D VAL 3.2 0.2 - - - -
261D GLU* 1.3 77.5 - - - +
263D MET* 1.3 60.5 + - - +
264D ASP* 3.4 1.5 + - - +
302D LYS 5.4 1.3 - - - +
305D VAL* 4.3 4.7 - - + -
306D LYS* 4.1 29.8 - - + +
309D CYS* 4.3 16.0 - - + +
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Residues in contact with MET 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D ILE* 3.8 34.3 - - + +
195D VAL* 4.1 19.3 - - + -
196D HIS* 4.0 27.4 - - + +
199D LYS* 4.9 9.6 - - + +
259D VAL* 3.3 17.9 + - - +
260D VAL 3.2 3.2 + - - +
262D ALA* 1.3 75.4 - - - +
264D ASP* 1.3 69.8 + - - +
265D PHE* 3.3 1.5 + - - -
309D CYS* 3.7 34.8 - - + -
312D PHE* 5.2 0.9 - - + -
313D THR* 4.2 18.2 - - - +
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Residues in contact with ASP 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D LYS* 5.4 1.8 - - - +
260D VAL 3.1 3.2 + - - -
261D GLU* 3.2 13.1 + - - +
262D ALA 3.4 1.4 - - - +
263D MET* 1.3 81.9 - - - +
265D PHE* 1.3 60.2 + - - +
266D HIS* 2.7 44.8 + - - -
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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