Contacts of the helix formed by residues 248 - 263 (chain A) in PDB entry 3HIC
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 GLY 248 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A HIS* 5.9 2.2 - - - -
247A THR* 1.3 81.6 - - - +
249A ALA* 1.3 61.9 + - - +
250A GLY 3.2 2.2 - - - -
251A ASP* 3.3 18.5 + - - +
252A VAL* 3.3 24.9 + - - +
281A LYS* 4.2 19.7 - - - +
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Residues in contact with ALA 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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246A ASP* 4.2 14.8 - - - +
247A THR 2.8 10.2 + - - +
248A GLY* 1.3 73.9 - - - +
250A GLY* 1.3 58.8 + - - +
252A VAL* 3.4 2.6 + - - +
253A PHE* 3.1 23.6 + - - +
278A SER* 3.3 27.7 + - - +
281A LYS* 4.1 12.6 - - + +
282A VAL* 3.9 24.9 - - + -
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Residues in contact with GLY 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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39A LYS* 6.2 0.2 - - - -
167A ASP* 4.9 2.0 - - - -
185A LYS* 3.5 31.2 - - - -
247A THR 4.1 3.8 + - - -
248A GLY* 3.2 1.2 - - - -
249A ALA* 1.3 80.0 - - - +
251A ASP* 1.3 61.9 + - - +
253A PHE* 3.5 2.9 + - - -
254A VAL* 3.2 19.6 + - - +
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Residues in contact with ASP 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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39A LYS* 3.3 41.3 - - - +
42A HIS* 3.0 48.2 - - + -
43A VAL* 4.1 8.7 - - + +
46A VAL* 4.4 4.0 - - - +
167A ASP* 4.0 2.8 - - - +
248A GLY* 3.3 16.2 + - - +
249A ALA 3.3 0.2 - - - -
250A GLY* 1.3 73.9 - - - +
252A VAL* 1.3 62.2 + - + +
254A VAL* 3.5 5.9 + - - +
255A GLY* 2.9 25.8 + - - -
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Residues in contact with VAL 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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46A VAL* 3.9 17.9 - - + +
248A GLY 3.3 14.2 + - - +
249A ALA 3.8 6.5 - - - +
251A ASP* 1.3 74.9 - - + +
253A PHE* 1.3 66.9 + - - +
255A GLY* 3.4 0.5 + - - -
256A ALA* 2.9 23.1 + - - +
277A CYS* 3.6 40.6 - - + +
278A SER* 4.5 0.4 - - - -
281A LYS* 3.7 28.7 - - + -
290A PHE* 3.9 21.3 - - + -
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Residues in contact with PHE 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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183A PHE* 5.5 1.1 - + - -
185A LYS* 3.5 21.8 - - + -
217A VAL* 3.6 32.1 - - + -
225A SER* 4.6 7.6 - - - -
249A ALA 3.1 14.7 + - - +
250A GLY* 3.6 11.0 - - - +
251A ASP 3.2 0.4 - - - -
252A VAL* 1.3 78.7 - - - +
254A VAL* 1.3 53.9 + - + +
256A ALA* 3.6 0.5 - - - -
257A PHE* 2.7 55.2 + + + +
271A LEU* 4.4 9.4 - - + -
274A ALA* 3.4 44.5 - - + +
275A THR* 3.5 24.9 - - + -
278A SER* 4.2 9.1 - - - +
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Residues in contact with VAL 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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43A VAL* 4.1 17.0 - - + -
136A VAL* 4.3 11.7 - - + -
167A ASP* 3.5 27.4 - - + +
183A PHE* 4.1 25.6 - - + -
185A LYS* 3.7 19.3 - - + -
250A GLY 3.2 14.6 + - - +
251A ASP* 3.9 6.7 - - - +
252A VAL 3.3 0.2 - - - -
253A PHE* 1.3 77.0 - - - +
255A GLY* 1.3 65.1 + - - +
257A PHE* 3.2 5.7 + - - +
258A ILE* 2.9 38.6 + - + +
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Residues in contact with GLY 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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43A VAL* 3.8 23.3 - - - +
46A VAL* 3.8 19.5 - - - -
47A LEU* 3.4 8.8 - - - +
251A ASP 2.9 16.9 + - - -
252A VAL 3.8 1.3 - - - -
254A VAL* 1.3 77.4 - - - +
256A ALA* 1.3 56.4 + - - +
258A ILE* 3.7 0.4 - - - +
259A ALA* 2.9 26.3 + - - +
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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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46A VAL* 3.7 2.3 - - + +
50A PHE* 4.1 9.9 - - + -
252A VAL 2.9 17.3 + - - +
255A GLY* 1.3 72.9 - - - +
257A PHE* 1.3 60.8 + - - +
259A ALA* 3.1 8.7 + - - +
260A GLY* 2.8 27.4 + - - -
270A THR* 4.8 0.3 - - - +
273A VAL* 4.2 6.7 - - + +
274A ALA* 3.6 23.7 - - - +
277A CYS* 3.9 26.0 - - + -
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Residues in contact with PHE 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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183A PHE* 3.6 34.8 - + + -
215A TYR* 3.9 22.2 - + + -
217A VAL* 3.8 22.0 - - + -
227A CYS* 4.9 0.9 - - - -
253A PHE* 2.7 43.0 + + + +
254A VAL* 3.6 6.7 - - - +
256A ALA* 1.3 73.3 - - - +
258A ILE* 1.3 67.8 + - + +
260A GLY 3.2 1.9 + - - -
261A LEU* 3.1 40.2 + - + +
267A ILE* 4.1 10.8 - - + -
270A THR* 3.4 29.7 - - + +
271A LEU* 3.9 15.7 - - + -
274A ALA* 3.8 10.0 - - + +
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Residues in contact with ILE 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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2A ILE* 3.7 34.3 - - + -
43A VAL* 5.1 1.3 - - + -
47A LEU* 4.1 7.9 - - + -
134A MSE 4.0 9.5 - - + +
136A VAL* 3.9 27.4 - - + -
163A PHE* 4.2 23.1 - - + -
183A PHE* 4.6 12.6 - - + -
254A VAL* 2.9 29.6 + - + +
255A GLY* 3.7 4.7 - - - +
257A PHE* 1.3 84.7 - - + +
259A ALA* 1.3 61.6 + - - +
261A LEU* 3.2 7.5 + - + +
262A ALA* 2.8 27.4 + - - +
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Residues in contact with ALA 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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47A LEU* 3.7 6.3 - - + -
50A PHE* 4.0 17.5 - - + -
52A ILE* 3.3 28.3 - - + -
255A GLY 2.9 16.1 + - - +
256A ALA* 3.1 14.8 + - - +
258A ILE* 1.3 75.6 - - - +
260A GLY* 1.3 64.4 + - - +
262A ALA* 3.0 4.6 + - - +
263A MSE 3.0 32.8 + - + +
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Residues in contact with GLY 260 (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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256A ALA 2.8 14.7 + - - -
257A PHE 3.2 4.2 + - - -
259A ALA* 1.3 76.6 - - - +
261A LEU* 1.3 61.5 + - - +
263A MSE 3.1 17.9 + - - +
265A MSE 3.1 33.3 + - - +
270A THR* 3.7 20.0 - - - -
273A VAL* 5.5 1.3 - - - -
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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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134A MSE 4.6 9.9 - - - -
163A PHE* 3.8 33.7 - - + -
215A TYR* 3.5 37.0 - - + +
257A PHE* 3.1 37.3 + - + +
258A ILE* 3.6 9.9 - - + +
260A GLY* 1.3 74.9 - - - +
262A ALA* 1.3 64.8 + - - +
264A ASN* 2.9 19.7 + - - +
265A MSE 4.7 7.9 - - - +
267A ILE* 5.0 2.7 - - + -
270A THR* 4.3 16.4 - - + +
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Residues in contact with ALA 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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2A ILE* 3.8 11.7 - - + -
52A ILE* 4.0 16.4 - - + -
134A MSE 3.1 30.0 - - + +
258A ILE 2.8 10.3 + - - +
259A ALA 3.3 10.1 - - - +
261A LEU* 1.3 77.3 - - - +
263A MSE 1.3 57.9 + - + +
264A ASN* 3.1 14.3 + - - +
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Residues in contact with MSE 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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50A PHE* 4.0 33.7 - - + +
52A ILE* 4.3 16.4 - - + -
259A ALA* 3.0 28.2 + - + +
260A GLY 3.1 5.5 + - - +
262A ALA* 1.3 76.6 - - - +
264A ASN* 1.3 72.4 + - - +
265A MSE 3.2 41.1 + - + +
273A VAL* 5.2 2.5 - - + -
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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