Contacts of the helix formed by residues 252 - 270 (chain A) in PDB entry 4U1D
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 LEU 252 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A LYS* 3.7 45.5 - - + +
199A PHE* 3.7 31.0 - - + -
200A LYS* 4.0 27.1 - - + +
247A SER* 2.9 13.0 + - - +
250A LEU* 3.3 29.6 - - + +
251A GLU* 1.3 75.2 - - - +
253A TRP* 1.3 58.7 + - - +
254A HIS 3.4 2.7 - - - -
255A GLU* 3.2 12.2 + - + -
256A ALA* 2.8 26.5 + - - +
218B SER* 5.1 2.9 - - - -
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Residues in contact with TRP 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A VAL* 3.5 42.6 - - + -
251A GLU* 3.1 50.6 + - + +
252A LEU* 1.3 68.5 - - - +
254A HIS* 1.3 68.7 + - + +
256A ALA* 3.5 4.1 - - + +
257A TYR* 3.2 22.9 + - - +
288A LYS* 3.9 10.5 - - + -
289A VAL* 3.9 41.3 - - + +
292A VAL* 3.5 43.3 - - + +
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Residues in contact with HIS 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A LYS* 5.7 5.8 - - - +
252A LEU 3.4 0.6 - - - -
253A TRP* 1.3 81.4 - - + +
255A GLU* 1.3 60.7 + - - +
257A TYR* 3.6 5.6 + - - +
258A ARG* 3.3 35.0 + - - +
214B ASN* 6.0 4.0 - - - -
227B LEU* 3.6 23.9 + - + -
228B SER* 4.6 8.1 + - - -
233B LEU* 5.4 0.2 - - + -
269B ILE* 3.1 54.9 - - + +
271B LYS* 3.7 25.1 + - - -
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Residues in contact with GLU 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A PHE* 4.2 15.7 - - + -
200A LYS* 4.1 24.3 - - + +
203A ALA* 3.3 13.0 - - + +
204A GLU* 5.4 0.7 - - - +
207A ARG* 2.6 41.4 + - - -
247A SER* 3.7 13.9 - - - +
252A LEU* 3.2 22.4 + - + +
254A HIS* 1.3 78.4 - - - +
256A ALA* 1.3 64.7 + - - +
258A ARG* 3.0 31.8 + - - +
259A SER* 2.9 27.6 + - - +
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Residues in contact with ALA 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A VAL* 4.3 1.3 - - - +
247A SER* 3.5 22.4 - - - -
248A VAL* 4.2 7.9 - - + -
252A LEU 2.8 13.0 + - - +
253A TRP* 3.5 14.1 - - + +
255A GLU* 1.3 76.2 - - - +
257A TYR* 1.3 57.0 + - - +
259A SER* 3.0 6.7 + - - -
260A ILE* 2.8 34.6 + - + +
289A VAL* 3.7 24.9 - - + -
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Residues in contact with TYR 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A TRP 3.2 12.8 + - - +
254A HIS* 3.9 6.5 - - - +
255A GLU 3.2 0.2 - - - -
256A ALA* 1.3 80.6 - - - +
258A ARG* 1.3 63.1 + - + +
260A ILE* 3.2 18.3 + - + +
261A GLU* 3.3 34.2 + - + +
289A VAL* 4.7 8.9 - - + +
290A PHE* 3.9 19.1 - + - -
293A SER* 5.2 0.7 - - - -
347A PRO 4.2 1.4 + - - -
348A HIS* 3.3 61.0 - + + +
350A ARG* 5.3 2.3 + - - +
351A MET* 3.0 39.9 + - + +
268B LYS* 4.0 16.6 - - + -
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Residues in contact with ARG 258 (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 LYS* 5.2 7.5 - - - +
204A GLU* 5.0 6.2 + - - -
207A ARG* 3.2 25.5 + - - +
254A HIS* 3.3 19.0 + - - +
255A GLU* 3.0 47.3 + - - +
257A TYR* 1.3 77.9 - - + +
259A SER* 1.3 59.9 + - - +
261A GLU* 3.1 24.7 - - - +
262A ASP* 3.2 14.7 + - - -
265B HIS* 6.0 7.3 - - - -
268B LYS* 4.5 20.4 - - + +
269B ILE* 4.1 21.0 - - - +
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Residues in contact with SER 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ARG* 3.4 2.9 + - - -
240A ARG* 4.6 0.7 - - - +
243A GLN* 2.7 43.1 + - - +
244A VAL* 3.4 27.7 - - - +
247A SER* 3.8 4.4 + - - -
255A GLU* 2.9 17.0 + - - -
256A ALA* 3.0 9.8 + - - -
258A ARG* 1.3 74.5 - - - +
260A ILE* 1.3 60.3 + - - +
262A ASP* 3.4 4.9 - - - +
263A VAL* 3.0 24.6 + - - +
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Residues in contact with ILE 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A VAL* 3.9 16.4 - - + -
256A ALA 2.8 18.0 + - - +
257A TYR* 3.2 11.8 + - + +
259A SER* 1.3 76.4 - - - +
261A GLU* 1.3 65.9 + - - +
263A VAL* 3.4 1.3 + - - +
264A PHE* 3.2 20.2 + - + -
282A TYR* 3.2 20.7 + - - +
286A LEU* 3.5 29.4 - - + -
289A VAL* 3.7 37.7 - - + -
290A PHE* 5.0 4.9 - - + -
351A MET* 3.9 29.6 - - + -
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Residues in contact with GLU 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A TYR* 3.3 34.8 + - + +
258A ARG* 3.1 22.4 - - - +
260A ILE* 1.3 75.8 - - - +
262A ASP* 1.3 66.3 + - - +
264A PHE* 3.3 8.1 + - - +
265A HIS* 2.8 46.5 + - + +
350A ARG* 4.3 16.0 + - - +
351A MET* 5.2 3.5 - - - -
354A LEU* 4.8 5.6 - - + -
268B LYS* 3.1 31.4 + - - +
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Residues in contact with ASP 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ARG* 2.7 48.0 + - - +
240A ARG* 4.6 18.7 - - + +
243A GLN* 3.6 7.6 + - - +
258A ARG 3.2 10.9 + - - +
259A SER* 3.4 10.1 - - - +
261A GLU* 1.3 78.4 - - - +
263A VAL* 1.3 63.4 + - - +
265A HIS* 3.4 5.7 + - - +
266A LEU* 3.2 32.4 + - + +
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Residues in contact with VAL 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A LEU* 3.7 5.7 - - + +
240A ARG* 3.5 39.3 - - + +
241A PHE* 3.7 27.4 - - + +
244A VAL* 3.9 9.2 - - + -
259A SER 3.0 18.0 + - - +
260A ILE 3.7 7.4 - - - +
261A GLU 3.3 0.2 - - - -
262A ASP* 1.3 75.0 - - - +
264A PHE* 1.3 64.7 + - - +
266A LEU* 3.1 5.7 + - - +
267A MET* 2.9 28.4 + - - +
282A TYR* 3.5 27.1 - - + +
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Residues in contact with PHE 264 (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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260A ILE* 3.2 18.6 + - + -
261A GLU 3.3 4.7 + - - +
263A VAL* 1.3 79.2 - - - +
265A HIS* 1.3 64.4 + - - +
267A MET* 3.0 24.4 + - + +
268A LYS* 3.0 26.2 + - - +
282A TYR* 3.3 33.0 - + - -
283A TYR* 5.2 7.0 - + - -
286A LEU* 4.3 3.1 - - + -
305A LYS* 6.3 0.9 - - - -
351A MET* 3.4 28.3 - - + -
354A LEU* 3.5 52.9 - - + -
355A LEU* 3.5 22.4 - - + -
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Residues in contact with HIS 265 (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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261A GLU* 2.8 39.1 + - + +
262A ASP* 3.8 7.7 + - - +
263A VAL 3.3 0.2 - - - -
264A PHE* 1.3 77.2 - - - +
266A LEU* 1.3 64.9 + - + +
268A LYS* 3.5 27.7 + - - +
269A ILE* 3.4 26.0 + - - +
350A ARG* 3.1 41.1 + - - -
354A LEU* 5.2 4.7 - - + -
353B ARG* 4.1 18.7 - - - -
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Residues in contact with LEU 266 (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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210A LEU* 3.8 27.4 - - + -
233A LEU* 4.5 9.8 - - + +
236A TYR* 3.5 23.8 - - + +
237A LEU* 3.4 43.5 - - + +
240A ARG* 3.9 13.0 - - + +
262A ASP* 3.2 24.8 + - + +
263A VAL 3.1 8.1 + - - +
264A PHE 3.1 0.8 - - - -
265A HIS* 1.3 78.8 - - + +
267A MET* 1.3 60.1 + - - +
268A LYS 3.0 1.6 - - - -
269A ILE* 3.2 6.9 + - + +
270A SER* 2.9 32.3 + - - -
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Residues in contact with MET 267 (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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237A LEU* 3.9 22.0 - - + -
241A PHE* 4.1 10.8 - - + -
263A VAL* 2.9 30.8 + - - +
264A PHE* 3.0 30.0 + - + +
266A LEU* 1.3 76.9 - - - +
268A LYS* 1.3 58.5 + - - +
270A SER* 3.0 28.1 - - - +
274A PRO* 4.2 21.8 - - + -
279A LEU* 4.4 14.4 - - + -
282A TYR* 4.9 2.0 - - - -
283A TYR* 5.1 6.3 - - - +
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Residues in contact with LYS 268 (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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264A PHE 3.0 9.1 + - - +
265A HIS* 3.5 45.7 + - - +
267A MET* 1.3 77.1 - - - +
269A ILE* 1.3 71.8 + - + +
270A SER 3.4 4.0 + - - +
271A LYS* 4.7 7.6 - - - +
350A ARG* 4.6 6.5 - - - +
354A LEU* 5.1 15.6 - - - +
358B ASP 4.8 7.7 + - - -
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Residues in contact with ILE 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LEU* 4.1 12.3 - - + +
233A LEU* 3.5 28.5 - - + +
265A HIS 3.4 15.0 + - - +
266A LEU* 3.2 9.0 + - + +
268A LYS* 1.3 83.6 - - + +
270A SER* 1.3 61.9 + - - +
271A LYS* 3.4 18.7 + - - +
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Residues in contact with SER 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ALA 5.6 0.5 + - - -
233A LEU* 3.8 24.8 - - - +
234A GLN* 5.1 5.0 + - - +
237A LEU* 4.6 11.7 - - - +
266A LEU 2.9 18.0 + - - -
267A MET* 3.0 22.9 - - - +
268A LYS 3.2 4.2 - - - +
269A ILE* 1.3 77.4 - - - +
271A LYS* 1.3 63.3 + - - +
272A ARG* 2.7 32.5 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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