Contacts of the helix formed by residues 233 - 242 (chain A) in PDB entry 1R4L
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 233 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A THR 3.3 18.2 - - - +
230A PHE* 3.0 26.7 + - + +
231A GLU 2.6 6.1 + - - -
232A GLU* 1.3 75.8 - - - +
234A LYS* 1.3 64.8 + - - +
235A PRO 3.6 0.2 - - - -
236A LEU* 3.6 8.6 + - + +
237A TYR* 3.2 17.1 + - + +
447A VAL* 4.9 7.9 - - + -
450A LEU* 3.8 39.7 - - + -
451A PRO* 5.4 1.1 - - + -
516A TYR* 4.6 4.9 - - - +
520A LEU* 5.3 2.2 - - + -
581A VAL* 3.5 22.0 - - + -
584A LEU* 4.0 13.5 - - + -
585A LEU* 4.0 15.9 - - + -
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Residues in contact with LYS 234 (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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230A PHE* 3.1 50.0 + - + +
231A GLU* 2.8 22.2 + - - +
233A ILE* 1.3 73.6 - - - +
235A PRO* 1.3 77.8 - - + +
237A TYR* 2.6 21.5 + - + +
238A GLU* 2.9 25.1 + - + +
483A GLU 5.9 0.4 + - - -
484A ILE* 5.6 8.5 - - - +
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Residues in contact with PRO 235 (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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231A GLU 3.1 17.9 - - - +
232A GLU* 4.1 9.4 - - - +
233A ILE 3.9 1.6 - - - -
234A LYS* 1.3 89.5 - - + +
236A LEU* 1.3 63.2 + - - +
237A TYR 2.9 0.5 + - - -
238A GLU* 3.1 20.9 + - - +
239A HIS* 3.2 17.5 + - + +
592A PHE* 3.7 22.9 - - + -
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Residues in contact with LEU 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A GLU 5.0 4.6 + - - +
233A ILE* 3.6 11.8 + - + +
234A LYS 3.3 1.0 - - - -
235A PRO* 1.3 78.6 - - - +
237A TYR* 1.3 59.7 + - - +
239A HIS* 5.0 0.2 - - - -
240A LEU* 3.2 18.4 + - + +
443A ALA* 6.1 0.2 - - + -
447A VAL* 4.0 15.8 - - + +
584A LEU* 4.4 11.0 - - + -
585A LEU* 5.0 9.6 - - + -
588A PHE* 3.5 44.0 - - + +
591A LEU* 5.0 5.6 - - + -
592A PHE* 3.3 44.7 - - + +
595A LEU* 4.3 9.1 - - + +
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Residues in contact with TYR 237 (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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230A PHE* 5.9 3.1 - + + -
233A ILE* 3.2 16.5 + - + +
234A LYS* 2.6 22.7 + - + +
236A LEU* 1.3 69.6 - - - +
238A GLU* 1.3 52.6 + - + +
240A LEU* 2.5 14.6 + - + +
241A HIS* 2.5 41.0 + - + +
275A TRP* 3.3 43.6 - + - -
447A VAL* 4.1 20.6 - - + +
448A GLY 4.4 2.9 - - - -
451A PRO* 3.4 38.3 - - + +
484A ILE 3.9 2.2 - - - -
485A VAL* 2.3 37.2 + - - +
606A TRP* 3.5 26.9 - + - -
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Residues in contact with GLU 238 (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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234A LYS* 2.9 23.7 + - + +
235A PRO* 3.6 18.4 - - - +
237A TYR* 1.3 75.2 - - + +
239A HIS* 1.3 56.9 + - + +
241A HIS* 2.7 8.9 + - - -
242A ALA* 2.6 35.5 + - - +
604A VAL* 3.6 23.9 - - + +
605A GLY* 3.9 20.7 - - - +
606A TRP* 4.3 23.2 - - + -
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Residues in contact with HIS 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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235A PRO* 3.2 17.6 + - + +
238A GLU* 1.3 78.8 - - + +
240A LEU* 1.3 57.7 + - - +
243A TYR* 3.0 28.6 + - - +
592A PHE* 4.5 10.7 - + + -
595A LEU* 3.4 22.2 + - + +
596A LYS* 3.2 52.4 + - + +
599A ASN* 3.0 12.7 + - + +
604A VAL* 3.2 41.4 - - + +
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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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236A LEU* 3.2 16.4 + - + +
237A TYR* 2.5 24.2 + - + +
239A HIS* 1.3 76.0 - - - +
241A HIS* 1.3 55.3 + - - +
243A TYR* 3.6 2.2 + - + +
244A VAL* 3.2 37.6 + - + +
275A TRP* 3.4 32.5 - - + -
440A LEU* 3.7 30.1 - - + -
443A ALA* 4.1 31.4 - - + +
444A LEU* 4.5 6.5 - - + -
447A VAL* 4.8 4.9 - - + -
448A GLY 4.8 4.0 - - - +
591A LEU* 5.7 0.2 - - + -
595A LEU* 3.3 15.3 - - + +
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Residues in contact with HIS 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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237A TYR* 2.5 37.5 + - + +
238A GLU 2.7 5.7 + - - +
240A LEU* 1.3 71.1 - - - +
242A ALA* 1.3 61.5 + - - +
243A TYR 3.1 4.9 + - - -
244A VAL* 3.2 11.0 + - - +
245A ARG* 3.2 44.2 + - - +
261A CYS* 3.7 3.7 - - - -
262A LEU* 3.4 21.9 - - + +
275A TRP* 4.1 6.1 - + - -
486A GLY 2.9 27.3 + - - -
605A GLY 4.6 0.2 + - - -
606A TRP* 3.2 52.6 - + + -
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Residues in contact with ALA 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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238A GLU 2.6 18.7 + - - +
241A HIS* 1.3 74.6 + - - +
243A TYR* 1.3 56.5 + - - +
245A ARG* 3.1 27.7 - - - +
246A ALA* 4.0 1.4 + - - +
599A ASN* 3.4 10.6 - - - +
602A SER* 3.4 16.6 + - - -
603A PHE 2.8 28.9 - - - +
604A VAL* 3.6 16.2 - - + -
605A GLY 4.0 5.2 - - - +
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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