Contacts of the helix formed by residues 245 - 256 (chain A) in PDB entry 5HI7
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 THR 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A MET* 1.3 76.4 - - - +
246A SER* 1.3 61.9 + - - +
247A GLU* 3.6 13.1 + - - +
248A GLU* 2.9 38.0 + - - +
249A ARG* 2.8 27.6 + - - +
272A ASP* 3.5 16.8 - - - +
275A MET* 4.2 7.6 - - + -
276A LEU* 3.7 42.0 - - + -
325A ILE* 4.2 7.6 - - + +
326A TYR* 4.9 0.7 - - - +
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Residues in contact with SER 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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245A THR* 1.3 70.7 - - - +
247A GLU* 1.3 59.0 + - - +
249A ARG* 3.5 29.3 - - - +
250A ARG* 2.8 41.4 + - - +
266A CYS* 4.5 16.4 - - - -
269A GLN* 3.7 24.0 - - - +
272A ASP* 2.5 33.4 + - - -
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Residues in contact with GLU 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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245A THR* 3.0 10.9 + - - +
246A SER* 1.3 82.8 + - - +
248A GLU* 1.3 63.2 + - + +
250A ARG* 3.4 17.9 + - - +
251A LYS* 3.2 22.1 + - + +
272A ASP* 5.6 0.7 - - - +
276A LEU* 6.0 1.9 - - - +
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Residues in contact with GLU 248 (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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243A LEU 4.7 0.5 - - - +
244A MET* 3.2 34.2 - - + +
245A THR* 2.9 34.5 + - - +
247A GLU* 1.3 77.7 - - + +
249A ARG* 1.3 65.0 + - - +
251A LYS* 3.3 8.0 + - - +
252A GLN* 3.1 18.7 + - - +
287A GLN* 3.3 13.3 + - - -
325A ILE* 3.9 5.0 - - - +
326A TYR* 2.5 34.1 + - - -
329A LYS* 6.2 0.2 - - - -
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Residues in contact with ARG 249 (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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208A CYS* 3.2 26.4 - - - -
238A CYS* 5.6 3.4 - - - -
240A LEU* 3.6 26.7 - - + -
241A ASP 5.0 5.6 - - - -
242A MET 5.4 2.3 + - - -
244A MET* 3.1 41.4 + - + +
245A THR 2.8 17.2 + - - +
246A SER* 3.5 29.3 - - - +
248A GLU* 1.3 71.6 - - - +
250A ARG* 1.3 64.0 + - - +
252A GLN* 3.3 0.5 + - - +
253A LEU* 2.9 35.6 + - + +
265A ARG* 3.8 37.5 + - - +
266A CYS* 3.4 32.5 - - - +
270A ASP 4.9 2.8 + - - +
272A ASP* 4.5 2.8 + - - -
275A MET* 5.1 0.2 - - - +
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Residues in contact with ARG 250 (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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246A SER* 2.8 27.8 + - - +
247A GLU* 3.6 24.3 - - - +
249A ARG* 1.3 75.6 - - - +
251A LYS* 1.3 57.7 + - - +
253A LEU* 3.9 6.2 - - - +
254A ARG* 2.9 73.2 + - - +
259A PHE 4.9 0.3 - - - +
260A GLU* 4.5 6.7 + - - +
261A CYS* 5.6 5.7 + - - +
266A CYS* 4.7 22.4 + - - +
269A GLN* 6.3 0.8 - - - +
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Residues in contact with LYS 251 (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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247A GLU* 3.2 11.4 + - + +
248A GLU* 3.3 10.7 + - - +
250A ARG* 1.3 81.6 - - - +
252A GLN* 1.3 58.3 + - - +
254A ARG* 3.2 7.9 + - - +
255A ASP* 2.8 55.0 + - - +
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Residues in contact with GLN 252 (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 LEU* 3.4 29.6 - - + -
244A MET* 4.2 9.4 - - + -
248A GLU 3.1 15.9 + - - +
249A ARG 4.0 0.9 - - - +
251A LYS* 1.3 78.3 - - - +
253A LEU* 1.3 58.9 + - - +
255A ASP* 4.6 8.2 - - - +
256A GLN* 2.7 67.5 + - - +
257A TYR* 5.4 0.4 - - + -
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Residues in contact with LEU 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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206A HIS* 3.7 29.8 - - + +
208A CYS* 4.8 0.7 - - - -
239A TYR* 4.5 2.2 - - + -
240A LEU* 3.7 27.1 - - + -
249A ARG* 2.9 26.6 + - + +
250A ARG* 4.1 3.8 - - - +
252A GLN* 1.3 75.7 - - - +
254A ARG* 1.3 57.8 + - - +
257A TYR* 3.2 28.6 + - + +
258A CYS 2.9 22.7 + - - -
259A PHE* 3.3 35.9 + - + +
261A CYS* 3.7 26.0 - - + +
266A CYS* 5.6 0.4 - - - -
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Residues in contact with ARG 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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140A LYS* 3.0 14.2 + - - -
250A ARG* 2.9 49.6 + - - +
251A LYS* 3.5 7.8 - - - +
253A LEU* 1.3 75.2 - - - +
255A ASP* 1.3 69.7 + - - +
258A CYS* 3.1 16.7 + - - +
259A PHE 3.9 7.9 - - - +
260A GLU* 2.7 44.5 + - - +
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Residues in contact with ASP 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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136A LEU* 5.6 0.2 - - - +
140A LYS* 2.7 36.7 + - - +
251A LYS* 2.8 52.9 + - - +
252A GLN* 4.0 10.8 - - - +
254A ARG* 1.3 76.5 - - - +
256A GLN* 1.3 63.3 + - + +
258A CYS* 4.5 0.5 - - - -
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Residues in contact with GLN 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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132A ASN* 5.0 0.7 + - - -
136A LEU* 5.9 1.0 - - - +
179A ILE* 3.1 40.8 + - + +
180A CYS* 4.3 12.6 + - - +
182A SER* 4.9 7.5 + - - -
252A GLN* 2.7 51.6 + - - +
255A ASP* 1.3 77.5 - - - +
257A TYR* 1.3 94.7 + - + +
258A CYS* 3.6 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