Contacts of the helix formed by residues 252 - 266 (chain A) in PDB entry 5I73
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 SER 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A VAL 5.0 1.2 + - - -
237A LEU 4.8 3.6 + - - -
238A GLN* 3.7 9.9 + - - +
250A GLY 4.2 0.2 + - - -
251A ILE* 1.3 78.4 - - - +
253A TRP* 1.3 63.8 + - - +
254A GLN* 3.8 12.1 - - - -
255A LEU* 4.4 18.7 - - - -
256A ALA* 3.5 18.9 + - - +
481A LEU* 3.1 20.7 + - - +
482A THR 4.7 0.9 + - - -
483A PHE* 3.4 29.3 + - - -
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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
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251A ILE* 3.7 4.9 + - - +
252A SER* 1.3 72.1 - - - +
254A GLN* 1.3 113.5 + - + +
255A LEU 3.5 0.2 - - - -
256A ALA* 3.2 7.6 + - - +
257A LEU* 2.9 57.9 + - + +
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Residues in contact with GLN 254 (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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185A TYR* 3.5 37.0 + - + +
238A GLN* 5.3 5.9 + - - +
252A SER* 3.8 10.2 - - - -
253A TRP* 1.3 134.0 + - + +
255A LEU* 1.3 62.8 + - + +
257A LEU* 3.1 7.5 + - - +
258A CYS* 2.9 32.7 + - - -
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Residues in contact with LEU 255 (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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181A ALA* 3.4 31.1 - - + +
182A TRP* 3.5 30.3 - - + +
185A TYR* 4.0 15.5 - - + -
236A VAL* 3.2 35.0 - - + +
237A LEU* 6.0 0.2 - - - -
252A SER* 4.0 18.3 + - - +
254A GLN* 1.3 85.6 - - + +
256A ALA* 1.3 58.9 + - - +
258A CYS* 3.7 3.4 - - - +
259A ILE* 2.9 32.2 + - - +
481A LEU* 3.5 21.5 - - + +
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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
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251A ILE* 5.4 2.5 - - + -
252A SER 3.5 14.7 + - - +
253A TRP* 3.2 14.1 + - + +
254A GLN 3.1 0.2 - - - -
255A LEU* 1.3 77.4 - - - +
257A LEU* 1.3 63.6 + - + +
259A ILE* 3.2 3.3 - - - +
260A MET* 2.9 36.0 + - - +
474A PHE* 3.9 8.9 - - + -
478A LEU* 5.3 2.7 - - + -
481A LEU* 3.7 23.1 - - + +
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Residues in contact with LEU 257 (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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253A TRP* 2.9 47.7 + - + +
254A GLN* 3.4 8.5 - - - +
256A ALA* 1.3 79.0 - - + +
258A CYS* 1.3 59.7 + - - +
260A MET* 3.2 18.4 + - + +
261A LEU* 2.9 28.4 + - - +
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Residues in contact with CYS 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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181A ALA* 3.7 18.6 - - + +
184A LEU* 3.5 17.3 - - + +
185A TYR* 3.8 40.6 - - - -
188A ILE* 4.3 10.5 - - - -
254A GLN 2.9 20.9 + - - +
255A LEU* 3.7 6.3 - - - +
257A LEU* 1.3 77.8 - - - +
259A ILE* 1.3 57.2 + - - +
261A LEU* 3.1 6.7 + - - +
262A ILE* 2.9 32.4 + - - +
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Residues in contact with ILE 259 (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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177A ASN* 4.0 21.1 - - + +
178A THR* 3.6 29.8 - - + -
181A ALA* 4.0 8.5 - - + +
255A LEU 2.9 16.8 + - - +
256A ALA 3.2 14.4 - - - +
258A CYS* 1.3 76.6 - - - +
260A MET* 1.3 56.9 + - - +
262A ILE* 3.8 6.1 - - + -
263A PHE* 2.9 61.2 + - + -
474A PHE* 3.8 11.2 - - + -
477A SER* 3.7 14.4 - - - +
481A LEU* 3.7 19.1 - - + -
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Residues in contact with MET 260 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A ALA* 2.9 26.5 + - - +
257A LEU* 3.3 19.1 - - + +
258A CYS 3.1 0.2 - - - -
259A ILE* 1.3 76.7 - - - +
261A LEU* 1.3 54.8 + - - +
263A PHE* 3.2 8.5 + - + +
264A THR* 2.7 38.9 + - - +
474A PHE* 3.5 33.2 - - + -
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Residues in contact with LEU 261 (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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184A LEU* 3.8 28.3 - - + -
188A ILE* 6.1 2.2 - - + -
257A LEU 2.9 12.3 + - - +
258A CYS* 3.1 9.4 + - - +
260A MET* 1.3 75.8 - - - +
262A ILE* 1.3 58.8 + - + +
264A THR* 3.2 14.0 + - + -
265A VAL* 2.9 29.4 + - + +
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Residues in contact with ILE 262 (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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177A ASN* 4.0 14.4 - - + +
180A MET* 3.3 68.2 - - + +
181A ALA* 3.4 12.3 - - + +
184A LEU* 3.8 14.1 - - + -
258A CYS 2.9 18.4 + - - +
259A ILE* 3.8 6.3 - - - +
261A LEU* 1.3 74.1 - - + +
263A PHE* 1.3 56.3 + - - +
264A THR 3.0 4.7 - - - -
265A VAL* 3.2 11.9 - - + +
266A ILE* 3.0 33.4 + - + +
432A ILE* 5.5 6.1 - - + -
436A LEU* 4.0 13.9 - - + -
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Residues in contact with PHE 263 (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 ALA* 4.2 1.3 - - + -
177A ASN* 3.4 35.0 - - + -
259A ILE* 2.9 50.4 + - + +
260A MET* 3.2 6.5 + - - +
262A ILE* 1.3 76.0 - - - +
264A THR* 1.3 58.5 + - - +
266A ILE* 3.5 24.6 - - + +
267A TYR* 3.5 11.6 - - - +
443A LEU* 6.0 0.9 - - + -
470A VAL* 3.4 33.3 - - + +
473A CYS* 4.0 15.9 - - + -
474A PHE* 3.4 44.2 - + + -
477A SER* 3.9 10.3 - - - -
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Residues in contact with THR 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 MET* 2.7 20.3 + - - +
261A LEU* 3.4 17.3 - - + -
262A ILE 3.0 0.2 - - - -
263A PHE* 1.3 77.7 - - - +
265A VAL* 1.3 63.1 + - - +
266A ILE 3.2 1.6 - - - -
267A TYR* 3.2 17.1 + - + +
268A PHE* 3.3 41.8 + - + -
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Residues in contact with VAL 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 LEU* 2.9 16.4 + - + +
262A ILE* 3.2 26.6 + - + +
264A THR* 1.3 77.3 - - - +
266A ILE* 1.3 56.9 + - - +
268A PHE* 4.2 6.4 + - - +
269A SER* 3.0 23.6 + - - +
280A VAL* 6.5 0.4 - - + -
432A ILE* 6.1 0.4 - - + -
436A LEU* 3.7 37.5 - - + -
440A PHE* 4.0 3.6 - - + -
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Residues in contact with ILE 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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177A ASN* 4.4 1.1 - - - +
262A ILE* 3.2 19.3 - - + +
263A PHE* 3.5 37.9 - - + +
265A VAL* 1.3 76.5 - - - +
267A TYR* 1.3 66.1 + - - +
268A PHE 3.4 0.7 - - - -
269A SER* 3.5 1.0 + - - -
270A ILE* 3.3 28.5 + - + +
436A LEU* 3.7 19.1 - - + -
439A SER* 3.9 16.8 - - - +
440A PHE* 3.4 30.1 - - + -
443A LEU* 3.7 29.7 - - + +
466A VAL* 5.3 0.3 - - - +
470A VAL* 4.5 7.2 - - + -
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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