Contacts of the helix formed by residues 235 - 245 (chain A) in PDB entry 4L3P
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 PRO 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A GLY 3.9 1.9 - - - +
234A GLY* 1.3 88.9 - - - +
236A ALA* 1.3 66.3 + - - +
237A PHE* 3.2 30.2 + - + -
238A ARG* 3.2 32.1 + - - +
239A ILE* 4.1 3.7 + - - +
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Residues in contact with ALA 236 (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* 3.7 12.0 - - + +
235A PRO* 1.3 75.2 - - - +
237A PHE* 1.3 62.0 + - - +
239A ILE* 3.2 21.7 + - - +
240A MET* 3.2 33.8 + - + +
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Residues in contact with PHE 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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235A PRO* 3.6 32.1 - - + -
236A ALA* 1.3 78.4 - - - +
238A ARG* 1.3 79.7 + - + +
239A ILE 3.3 0.2 - - - -
240A MET* 3.6 17.5 - - + +
241A TRP* 2.9 30.5 + - + +
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Residues in contact with ARG 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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232A ILE* 3.2 38.3 + - + +
233A GLY 3.3 17.8 + - - +
234A GLY* 4.0 3.1 - - - +
235A PRO* 3.6 31.0 - - - +
236A ALA 3.2 1.0 - - - -
237A PHE* 1.3 100.9 - - + +
239A ILE* 1.3 63.9 + - - +
241A TRP* 4.0 7.9 - - - +
242A ALA* 3.2 21.7 + - - +
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Residues in contact with ILE 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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192A SER* 6.5 0.2 - - - -
193A ALA* 4.0 22.2 - - + +
194A ALA* 4.5 14.6 - - + +
228A PRO 5.5 0.2 - - - +
229A PHE* 4.0 41.1 - - + +
232A ILE* 4.3 13.9 - - + -
233A GLY* 4.6 8.5 - - - +
234A GLY 5.7 1.6 - - - +
235A PRO 4.8 1.6 - - - +
236A ALA* 3.2 15.7 + - - +
238A ARG* 1.3 75.6 - - - +
240A MET* 1.3 56.1 + - - +
242A ALA* 3.1 5.4 + - - +
243A VAL* 2.7 50.7 + - + +
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Residues in contact with MET 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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193A ALA* 3.7 15.5 - - + +
196A MET* 4.1 15.9 - - + -
201A PHE* 3.5 46.4 - - + +
236A ALA* 3.2 32.1 + - + +
237A PHE* 3.6 15.3 - - + +
238A ARG 3.4 0.2 - - - -
239A ILE* 1.3 78.4 - - - +
241A TRP* 1.3 57.7 + - - +
244A HIS* 2.8 33.4 + - - +
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Residues in contact with TRP 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 PHE* 2.9 19.1 + - + +
238A ARG* 4.0 8.7 - - - +
240A MET* 1.3 76.0 - - - +
242A ALA* 1.3 69.9 + - + +
244A HIS* 3.2 11.6 + - - +
245A ASN* 2.9 56.3 + - - +
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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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232A ILE* 3.7 25.8 - - + -
238A ARG 3.2 17.2 + - - +
239A ILE 3.1 4.4 + - - +
241A TRP* 1.3 86.8 - - + +
243A VAL* 1.3 60.5 + - + +
245A ASN* 3.2 11.4 + - - +
246A GLY 3.4 0.5 + - - -
247A THR* 2.9 39.0 + - + +
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Residues in contact with VAL 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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193A ALA 5.0 2.5 - - - +
196A MET 4.5 2.0 - - - +
198A PRO* 4.3 8.2 - - + +
201A PHE* 3.8 24.0 - - + -
213A PHE* 4.1 18.4 - - + -
229A PHE* 3.7 37.7 - - + -
239A ILE* 2.7 31.8 + - + +
242A ALA* 1.3 69.9 - - + +
244A HIS* 1.3 65.6 + - - +
246A GLY 3.2 5.0 + - - -
247A THR 3.6 7.9 - - - +
248A ARG* 2.8 37.2 + - - +
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Residues in contact with HIS 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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198A PRO* 4.4 17.0 - - + +
201A PHE* 4.3 8.2 - + + -
202A GLU* 3.1 34.6 + - + +
240A MET 2.8 21.7 + - - +
241A TRP* 3.6 11.6 + - - +
243A VAL* 1.3 77.3 - - - +
245A ASN* 1.3 65.7 + - - +
246A GLY 3.6 0.3 + - - -
269A LYS* 4.8 21.4 + - - +
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Residues in contact with ASN 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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241A TRP* 2.9 71.8 + - - +
242A ALA* 3.7 6.0 - - - +
243A VAL 3.2 0.8 - - - -
244A HIS* 1.3 82.0 + - - +
246A GLY* 1.3 56.7 + - - +
247A THR* 3.7 2.9 - - - +
269A LYS* 6.5 0.7 - - - -
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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