Contacts of the helix formed by residues 288 - 303 (chain H) in PDB entry 3MQT
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 288 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103H SER* 3.2 14.8 + - - -
106H ASP* 3.7 4.0 - - - -
107H MET* 5.9 0.4 - - - -
283H TYR 3.3 21.5 + - - -
286H CYS* 3.8 2.4 - - - -
287H GLY* 1.3 78.8 - - - +
289H VAL* 1.3 61.5 + - - -
290H THR 3.2 2.5 - - - -
291H GLU* 3.3 1.9 + - - +
292H LEU* 2.9 35.0 + - - +
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Residues in contact with VAL 289 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H ASP* 2.9 5.0 + - - +
107H MET* 5.2 10.9 - - + +
110H TYR* 3.7 27.8 - - + -
125H MET* 3.9 42.6 - - + -
283H TYR* 4.9 12.6 - - + +
288H GLY* 1.3 70.8 - - - -
290H THR* 1.3 57.9 + - - +
292H LEU* 3.1 8.2 + - + +
293H LEU* 2.8 38.0 + - + +
319H ALA* 4.7 19.3 - - + +
323H PHE* 4.3 8.5 - - + -
369H LEU* 6.2 0.7 - - + -
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Residues in contact with THR 290 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78H PHE* 3.6 27.0 - - + +
79H ARG* 4.4 13.9 - - + +
82H TYR* 4.1 16.6 - - + -
106H ASP* 2.5 31.6 + - - -
110H TYR* 2.7 24.8 + - - +
289H VAL* 1.3 78.7 - - - +
291H GLU* 1.3 60.0 + - - +
293H LEU* 3.6 7.9 + - + +
294H ARG* 3.6 27.4 + - - +
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Residues in contact with GLU 291 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H TYR* 3.4 29.3 + - + +
86H TYR* 6.1 0.2 - - - -
263H THR* 3.3 9.3 - - - +
264H ARG* 2.7 67.4 + - - +
265H PHE* 4.8 1.6 - - - -
286H CYS* 3.8 14.6 - - - +
287H GLY* 3.9 11.6 + - - -
288H GLY 3.3 7.4 + - - +
289H VAL 3.2 0.2 - - - -
290H THR* 1.3 76.6 - - - +
292H LEU* 1.3 66.8 + - - +
294H ARG* 3.0 13.6 + - - +
295H ILE* 2.9 26.5 + - + +
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Residues in contact with LEU 292 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281H SER* 3.7 22.2 - - - +
283H TYR* 3.3 52.0 - - + -
286H CYS* 3.6 21.1 - - - -
288H GLY 2.9 22.4 + - - +
289H VAL* 3.1 8.0 + - - +
291H GLU* 1.3 76.3 - - - +
293H LEU* 1.3 50.8 + - - +
295H ILE* 3.0 7.8 + - + +
296H MET* 2.7 34.8 + - - +
306H LEU* 3.5 14.6 - - + +
308H PRO* 4.2 12.6 - - + -
323H PHE* 3.8 16.2 - - + -
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Residues in contact with LEU 293 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F ARG* 4.1 13.0 + - - +
110H TYR* 4.0 18.4 - - + +
124H LEU 5.3 1.1 - - - +
125H MET* 3.9 35.0 - - + +
289H VAL* 2.8 31.3 + - + +
290H THR* 3.8 7.4 - - + +
291H GLU 3.2 0.2 - - - -
292H LEU* 1.3 71.8 - - - +
294H ARG* 1.3 61.5 + - + +
296H MET* 3.4 31.0 - - + +
297H ASP* 3.4 27.0 + - - +
323H PHE* 3.8 17.7 - - + -
326H VAL* 4.2 5.8 - - + -
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Residues in contact with ARG 294 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297F ASP* 3.2 47.4 + - - +
300F GLU* 3.0 28.7 + - - +
328F HIS* 5.9 0.2 - - - -
79H ARG* 3.8 18.2 - - - +
82H TYR* 6.1 2.4 - - - -
83H ASN* 5.5 3.8 + - - -
264H ARG* 3.3 45.1 - - - +
290H THR* 3.6 19.5 + - - +
291H GLU* 3.0 23.6 + - - +
293H LEU* 1.3 75.3 - - + +
295H ILE* 1.3 65.4 + - - +
297H ASP* 3.5 10.2 + - - +
298H ILE* 3.3 28.5 + - - +
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Residues in contact with ILE 295 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263H THR 4.0 9.2 - - - +
264H ARG* 3.6 33.7 - - - +
267H ALA* 4.1 16.6 - - + -
271H LEU* 5.7 0.9 - - + -
279H VAL* 4.2 3.1 - - + -
281H SER* 3.8 24.5 - - - +
286H CYS* 4.3 7.9 - - + -
291H GLU* 2.9 24.1 + - + +
292H LEU* 3.0 9.4 + - + +
294H ARG* 1.3 74.0 - - - +
296H MET* 1.3 60.0 + - - +
298H ILE* 3.3 8.1 + - + +
299H CYS* 2.9 42.1 + - - -
306H LEU* 4.0 17.3 - - + -
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Residues in contact with MET 296 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F ARG* 3.9 18.6 - - - +
129H GLN* 6.1 0.4 - - - +
292H LEU 2.7 15.9 + - - +
293H LEU* 3.4 39.0 - - + +
294H ARG 3.2 0.2 - - - -
295H ILE* 1.3 72.3 - - - +
297H ASP* 1.3 67.8 + - - +
299H CYS* 3.3 4.7 + - - +
300H GLU* 2.9 27.9 + - + +
306H LEU* 3.8 11.9 - - + -
323H PHE* 4.4 5.8 - - + -
326H VAL* 4.3 9.0 - - + +
327H CYS* 3.8 44.2 - - - -
328H HIS* 4.9 11.2 - - + +
329H ILE* 3.6 17.3 - - + +
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Residues in contact with ASP 297 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F ARG* 2.7 44.2 + - - -
294F ARG* 3.2 44.9 + - - +
297F ASP* 4.6 9.4 - - + +
293H LEU 3.4 9.4 + - - +
294H ARG* 3.7 10.5 - - - +
295H ILE 3.3 0.2 - - - -
296H MET* 1.3 81.4 - - - +
298H ILE* 1.3 61.0 + - + +
300H GLU* 3.4 6.8 + - - +
301H HIS* 3.2 20.1 + - - +
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Residues in contact with ILE 298 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264H ARG* 4.1 29.2 - - + +
267H ALA* 5.6 1.1 - - + -
268H GLN* 3.1 44.9 - - + +
271H LEU* 3.9 13.9 - - + -
294H ARG* 3.3 16.8 + - - +
295H ILE* 3.3 9.9 + - + +
297H ASP* 1.3 73.5 - - + +
299H CYS* 1.3 66.6 + - - +
301H HIS* 3.3 7.3 + - + +
302H HIS* 3.1 48.1 + - + +
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Residues in contact with CYS 299 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271H LEU* 4.1 9.6 - - - -
279H VAL* 3.6 37.5 - - - -
295H ILE* 2.9 29.2 + - - +
296H MET 3.4 9.0 - - - +
298H ILE* 1.3 71.9 - - - +
300H GLU* 1.3 58.2 + - - +
302H HIS 3.1 2.5 + - - +
303H ASN 2.8 9.7 + - - -
304H ALA* 2.8 35.1 + - - +
305H GLN 4.1 3.6 - - - -
306H LEU* 3.9 15.7 - - - -
329H ILE* 3.5 15.7 - - + -
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Residues in contact with GLU 300 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C ASP* 4.5 5.4 - - - +
79F ARG* 5.8 0.2 + - - -
264F ARG* 3.2 23.7 + - - -
265F PHE* 5.8 0.5 - - - -
294F ARG* 2.9 21.8 + - - +
296H MET* 2.9 14.8 + - - +
297H ASP* 3.6 11.8 - - - +
298H ILE 3.3 0.2 - - - -
299H CYS* 1.3 75.7 - - - +
301H HIS* 1.3 64.0 + - - +
303H ASN* 3.0 15.2 + - - +
304H ALA 4.8 0.4 - - - -
328H HIS* 3.9 28.1 + - - +
329H ILE* 3.8 20.7 - - + +
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Residues in contact with HIS 301 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C ASP* 4.2 4.5 - - - +
242C ILE* 3.5 40.9 + - + +
273C LYS* 4.2 15.0 + - - -
265F PHE* 6.0 3.6 - - - -
268F GLN* 2.8 41.7 + - - +
272F GLU* 4.5 2.8 + - - -
297H ASP 3.2 10.8 + - - +
298H ILE* 3.3 11.4 + - - +
300H GLU* 1.3 80.0 - - - +
302H HIS* 1.3 80.6 + + - +
303H ASN 3.4 0.3 + - - -
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Residues in contact with HIS 302 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C ILE* 3.7 20.7 - - + +
246C LYS* 3.3 29.7 + - - +
268H GLN* 5.1 2.7 - - + -
271H LEU* 3.9 39.7 - - + +
272H GLU* 3.0 33.5 + - - -
298H ILE* 3.1 37.9 + - + +
299H CYS 3.1 4.7 + - - +
301H HIS* 1.3 92.9 - + - +
303H ASN* 1.3 69.5 + - - +
304H ALA* 3.3 3.5 + - + +
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Residues in contact with ASN 303 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C THR 2.7 21.7 + - - +
213C ASP* 4.1 7.4 - - - +
214C TRP* 2.8 63.5 + - + +
240C ASP* 3.1 32.8 + - - +
243C GLY* 3.5 7.0 - - - -
277H SER* 4.9 2.1 - - - +
299H CYS 2.8 5.2 + - - -
300H GLU* 3.0 12.0 + - - +
301H HIS 3.2 0.8 - - - -
302H HIS* 1.3 81.0 - - - +
304H ALA* 1.3 59.3 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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