Contacts of the helix formed by residues 235 - 247 (chain A) in PDB entry 5I7L
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 ASP 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A LEU* 1.3 74.1 - - - +
236A ILE* 1.3 54.4 + - - +
237A THR* 2.7 31.9 + - - +
238A LEU* 2.9 24.2 + - + +
239A VAL* 2.8 32.6 + - - +
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Residues in contact with ILE 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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232A ARG 5.4 5.2 - - - +
234A LEU 3.1 12.9 + - - +
235A ASP* 1.3 72.2 + - - +
237A THR* 1.3 64.3 + - + +
239A VAL* 3.1 12.2 + - + +
240A HIS* 2.8 29.4 + - + +
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Residues in contact with THR 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 ASP* 2.7 20.2 + - - +
236A ILE* 1.3 78.2 - - + +
238A LEU* 1.3 64.7 + - - +
240A HIS* 3.3 7.4 + - - +
241A ASP* 3.1 33.0 + - - +
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Residues in contact with LEU 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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47A LEU* 3.7 23.1 - - + +
50A SER* 4.1 25.8 - - - +
51A LEU* 4.2 9.6 - - + +
54A ALA* 3.9 27.6 - - + -
234A LEU* 4.8 6.3 - - + -
235A ASP* 2.9 29.8 + - + +
237A THR* 1.3 76.7 + - - +
239A VAL* 1.3 65.2 + - - +
241A ASP* 3.3 4.0 + - - -
242A ILE* 3.0 46.6 + - + +
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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
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175A LEU* 4.4 24.0 - - + +
231A LEU 4.4 5.2 - - - +
232A ARG 5.6 1.8 - - - +
234A LEU* 3.4 42.8 - - + +
235A ASP 2.8 10.5 + - - +
236A ILE* 3.1 14.6 + - + +
238A LEU* 1.3 74.3 - - - +
240A HIS* 1.3 64.8 + - - +
242A ILE* 3.4 6.9 + - - +
243A VAL* 3.0 28.2 + - + +
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Residues in contact with HIS 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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173A ILE* 5.9 3.4 - - + -
236A ILE* 2.8 19.0 + - + +
237A THR* 3.3 9.4 + - - +
238A LEU 3.2 0.4 - - - -
239A VAL* 1.3 80.3 - - + +
241A ASP* 1.3 67.7 + - - +
243A VAL* 4.1 4.7 - - + +
244A ASN* 2.8 58.6 + - - +
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Residues in contact with ASP 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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47A LEU* 3.5 29.1 - - + +
237A THR* 3.1 21.1 + - - +
238A LEU* 4.0 1.1 - - - +
240A HIS* 1.3 88.9 + - - +
242A ILE* 1.3 64.2 + - - +
244A ASN* 4.0 4.0 - - - +
245A MET* 3.1 29.7 + - + +
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Residues in contact with ILE 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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47A LEU* 4.2 16.8 - - + -
51A LEU* 3.6 35.0 - - + -
129A LEU* 4.4 12.6 - - + -
163A ILE* 5.4 0.4 - - + -
175A LEU* 4.0 16.8 - - + -
234A LEU* 5.1 2.7 - - + -
238A LEU* 3.0 50.3 + - + +
239A VAL* 3.8 6.7 - - - +
241A ASP* 1.3 77.5 - - - +
243A VAL* 1.3 57.6 + - - +
245A MET* 3.9 1.6 - - - +
246A LEU* 3.0 48.7 + - + +
252A PHE* 4.3 6.4 - - + -
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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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165A ALA* 3.6 20.3 - - + +
173A ILE* 3.4 37.2 - - + +
174A HIS* 3.8 3.6 - - - -
175A LEU* 3.5 46.2 - - + +
239A VAL* 3.0 15.0 + - + +
240A HIS* 4.1 5.2 - - + +
242A ILE* 1.3 80.9 - - - +
244A ASN* 1.3 68.6 + - - +
247A ILE* 3.1 29.8 + - - +
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Residues in contact with ASN 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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173A ILE* 4.6 6.9 - - - +
240A HIS* 2.8 54.0 + - + +
241A ASP* 4.0 5.4 - - - +
242A ILE 3.3 0.6 - - - -
243A VAL* 1.3 86.8 - - - +
245A MET* 1.3 66.2 + - + +
247A ILE* 3.4 9.3 - - - +
248A HIS* 2.8 43.5 + - - +
250A LEU* 5.0 0.7 - - - +
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Residues in contact with MET 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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47A LEU* 3.5 22.0 - - + -
241A ASP* 3.1 20.8 + - + +
244A ASN* 1.3 76.3 - - + +
246A LEU* 1.3 64.0 + - - +
248A HIS 3.2 2.3 + - - -
249A GLY 3.1 4.3 + - - -
250A LEU* 3.0 65.2 + - + +
251A GLN 3.7 17.3 - - - +
252A PHE* 3.7 27.1 - - + -
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Residues in contact with LEU 246 (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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122A GLN* 3.5 14.8 - - - +
126A GLY 3.1 25.5 - - - +
127A HIS* 3.3 37.0 - - - +
128A ARG 3.8 10.5 - - - +
129A LEU* 4.0 13.7 - - + -
163A ILE* 4.3 10.5 - - + +
165A ALA* 3.8 20.9 - - + +
175A LEU* 4.4 9.0 - - + -
242A ILE* 3.0 36.9 + - + +
244A ASN 3.5 0.2 - - - -
245A MET* 1.3 76.4 - - - +
247A ILE* 1.3 57.4 + - - +
249A GLY 3.0 14.6 + - - -
252A PHE* 4.1 11.9 - - + -
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Residues in contact with ILE 247 (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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127A HIS* 3.9 19.2 + - + -
165A ALA* 3.4 32.6 - - + +
166A VAL* 4.0 7.4 - - - +
167A ARG* 3.6 36.3 + - + +
173A ILE* 3.3 33.0 - - + -
243A VAL 3.1 7.1 + - - +
244A ASN* 3.4 16.2 - - - +
246A LEU* 1.3 75.2 - - - +
248A HIS* 1.3 74.6 + - + +
249A GLY 3.3 1.3 - - - -
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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