Contacts of the helix formed by residues 234 - 244 (chain A) in PDB entry 5I1U
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 ASN 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A TYR* 3.7 3.5 - - - -
219A ASP* 3.0 36.8 + - - +
222A SER* 3.5 6.7 + - - -
223A PHE* 3.7 14.0 - - - +
226A GLU* 2.6 27.7 + - + +
233A ALA* 1.3 78.9 - - - +
235A LEU* 1.3 65.6 + - - +
236A VAL* 2.8 39.9 + - - +
237A MET* 3.0 26.8 + - + +
238A ILE* 3.1 18.0 + - - +
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Residues in contact with LEU 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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165A ARG* 3.9 39.9 - - + +
168A TYR* 3.8 10.1 - - + -
169A LEU* 4.4 10.3 - - + -
216A PHE* 3.5 47.3 - - + -
219A ASP* 2.8 23.8 + - + +
234A ASN* 1.3 71.6 + - - +
236A VAL* 1.3 57.0 + - - +
238A ILE* 4.1 19.1 - - + -
239A VAL* 2.9 32.4 + - + +
254A VAL* 4.0 17.9 - - + -
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Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ASP 4.1 1.6 - - - +
220A VAL* 3.8 39.9 - - + +
223A PHE* 3.8 22.7 - - + -
234A ASN* 2.8 14.6 + - - +
235A LEU* 1.3 76.7 - - - +
237A MET* 1.3 58.7 + - - +
239A VAL* 4.7 0.2 - - - -
240A ARG* 2.9 29.9 + - + +
247A THR* 4.4 2.2 - - + +
250A ALA* 3.6 8.2 - - + +
251A CYS* 3.7 37.0 - - - +
254A VAL* 3.9 16.6 - - + -
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Residues in contact with MET 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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223A PHE* 3.4 24.2 - - + -
226A GLU 6.5 1.6 - - - -
233A ALA 5.4 4.0 - - - +
234A ASN* 3.0 22.2 + - + +
236A VAL* 1.3 78.0 - - - +
238A ILE* 1.3 57.2 + - + +
240A ARG* 3.3 37.9 + - - +
241A ARG* 3.0 31.3 + - - +
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Residues in contact with ILE 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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163A PRO* 3.8 26.5 - - + +
164A ASP 4.5 1.1 - - - +
165A ARG* 4.0 23.3 - - + +
168A TYR* 3.7 41.7 - - + -
233A ALA 5.9 0.2 - - - +
234A ASN 3.1 17.4 + - - +
235A LEU* 3.6 14.6 - - + +
237A MET* 1.3 77.8 - - + +
239A VAL* 1.3 59.2 + - + +
241A ARG* 3.4 22.0 + - - +
242A ASP* 2.9 51.3 + - - +
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Residues in contact with VAL 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ARG* 4.1 22.4 - - - +
235A LEU* 2.9 23.7 + - + +
236A VAL 3.8 3.6 - - - +
238A ILE* 1.3 75.7 - - + +
240A ARG* 1.3 60.4 + - - +
242A ASP* 4.5 4.9 - - - -
243A ARG* 2.8 59.5 + - + +
245A CYS* 4.5 1.1 - - - -
250A ALA* 4.1 11.9 - - + -
253A VAL* 3.9 23.6 - - + -
254A VAL* 4.0 15.5 - - + -
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Residues in contact with ARG 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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223A PHE* 3.9 11.3 - - - -
236A VAL* 2.9 18.5 + - + +
237A MET* 3.3 39.8 - - - +
239A VAL* 1.3 76.1 - - - +
241A ARG* 1.3 58.6 + - - +
244A CYS* 3.0 23.6 + - - -
245A CYS* 3.1 36.0 + - - +
246A SER 3.7 13.2 - - - +
247A THR* 3.5 24.4 + - - +
250A ALA* 3.7 10.7 - - + +
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Residues in contact with ARG 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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162A PRO* 3.3 33.7 - - - +
163A PRO 2.9 29.9 + - - -
164A ASP* 4.7 4.2 - - - +
237A MET 3.0 17.2 + - - +
238A ILE* 3.7 19.6 - - - +
240A ARG* 1.3 76.2 - - - +
242A ASP* 1.3 105.3 + - - +
244A CYS* 3.2 14.3 + - - +
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Residues in contact with ASP 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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164A ASP* 5.8 0.2 - - - -
165A ARG* 4.9 7.6 + - - +
238A ILE* 2.9 36.9 + - - +
239A VAL* 3.9 4.4 - - - +
241A ARG* 1.3 109.2 + - - +
243A ARG* 1.3 63.7 + - + +
244A CYS* 3.8 0.5 + - - +
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Residues in contact with ARG 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ARG* 6.2 0.2 - - - +
239A VAL* 2.8 37.0 + - + +
242A ASP* 1.3 80.2 - - + +
244A CYS* 1.3 71.0 + - - +
245A CYS* 3.4 18.5 + - + +
249A GLU* 5.6 3.9 + - - -
253A VAL* 3.5 37.2 - - - +
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Residues in contact with CYS 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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240A ARG 3.0 11.1 + - - -
241A ARG* 3.2 9.3 + - - +
242A ASP 5.1 0.9 - - - +
243A ARG* 1.3 81.2 - - - +
245A CYS* 1.3 61.2 + - - +
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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