Contacts of the helix formed by residues 287 - 302 (chain H) in PDB entry 5MGX
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 HIS 287 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282H GLN* 2.8 26.7 + - + +
285H LEU* 3.0 11.1 - - + +
286H ASP* 1.4 72.5 - - - +
288H TYR* 1.4 52.3 + - - +
289H ARG 3.5 2.9 - - - -
290H ALA* 3.4 12.4 + - + -
291H ALA* 2.9 33.7 + - - +
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Residues in contact with TYR 288 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283H LEU* 4.1 11.0 - - + -
286H ASP* 3.0 49.9 + - + -
287H HIS* 1.4 70.6 - - - +
289H ARG* 1.4 59.4 + - - +
291H ALA* 3.4 2.4 + - - -
292H LEU* 3.0 37.4 + - + +
315H VAL* 3.6 33.3 - - + +
318H GLN* 3.0 50.8 + - + +
319H GLN* 5.1 13.9 - - + -
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Residues in contact with ARG 289 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287H HIS 3.5 0.6 - - - -
288H TYR* 1.4 77.7 - - - +
290H ALA* 1.3 60.7 + - - +
292H LEU* 3.6 11.3 - - - +
293H ARG* 3.4 24.3 + - - +
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Residues in contact with ALA 290 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282H GLN* 3.4 29.7 + - + +
287H HIS* 3.4 17.1 + - + +
289H ARG* 1.3 76.3 - - - +
291H ALA* 1.4 63.8 + - - +
293H ARG* 3.2 10.9 + - - +
294H SER* 3.2 19.2 + - - -
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Residues in contact with ALA 291 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279H ALA* 3.6 24.9 - - + +
282H GLN* 3.4 16.7 + - + -
283H LEU* 3.8 7.0 - - - +
287H HIS 2.9 18.6 + - - +
288H TYR 3.8 3.8 - - - +
290H ALA* 1.4 72.5 - - - +
292H LEU* 1.4 55.7 + - - +
294H SER 3.3 1.2 + - - -
295H CYS* 2.8 39.8 + - - +
315H VAL* 4.1 17.5 - - + -
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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
----------------------------------------------------------
288H TYR* 3.0 24.2 + - + +
289H ARG* 3.6 9.9 - - - +
291H ALA* 1.4 76.8 - - - +
293H ARG* 1.4 51.3 + - - +
295H CYS* 3.4 5.5 + - - +
296H SER* 2.9 41.7 + - - +
312H LYS* 3.8 37.7 - - + -
315H VAL* 3.7 19.7 - - + +
316H LEU* 4.1 26.0 - - + -
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Residues in contact with ARG 293 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289H ARG 3.4 11.9 + - - +
290H ALA* 3.2 12.9 + - - +
292H LEU* 1.4 77.4 - - - +
294H SER* 1.4 57.0 + - - +
296H SER* 3.4 6.0 + - - -
297H LEU* 2.9 41.3 + - + +
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Residues in contact with SER 294 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275H LEU* 3.4 36.6 - - - +
278H LEU* 3.7 15.2 - - - +
279H ALA* 3.8 2.9 - - - -
282H GLN* 3.0 27.4 + - - -
290H ALA 3.2 4.4 + - - -
291H ALA 3.7 3.6 - - - -
293H ARG* 1.4 75.1 - - - +
295H CYS* 1.4 64.0 + - - +
297H LEU* 3.5 3.8 + - - +
298H VAL* 3.1 30.7 + - - +
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Residues in contact with CYS 295 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276H ASN* 5.8 0.7 - - - +
279H ALA* 3.7 12.6 - - - -
291H ALA* 2.8 25.8 + - - +
292H LEU* 3.5 7.4 - - - +
294H SER* 1.4 76.2 - - - +
296H SER* 1.3 55.4 + - - +
298H VAL* 3.3 7.5 + - - +
299H LEU* 3.0 34.9 + - - +
308H ALA* 3.7 10.2 - - - +
311H ARG* 3.7 20.6 - - - -
312H LYS* 3.6 42.6 - - + -
315H VAL* 5.4 0.9 - - - -
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Residues in contact with SER 296 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292H LEU* 2.9 25.1 + - - +
293H ARG* 3.8 6.1 - - - -
295H CYS* 1.3 69.6 - - - +
297H LEU* 1.4 59.3 + - - +
299H LEU* 3.5 6.8 + - - +
300H GLU* 3.1 33.3 + - - +
312H LYS* 3.2 28.2 + - - +
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Residues in contact with LEU 297 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F LEU* 4.4 21.8 - - + -
95F ASP 5.5 5.2 - - - +
275H LEU* 4.1 29.6 - - + -
293H ARG* 2.9 27.7 + - + +
294H SER* 3.8 4.7 - - - +
295H CYS 3.3 0.2 - - - -
296H SER* 1.4 73.0 - - - +
298H VAL* 1.3 59.6 + - - +
300H GLU* 3.3 11.3 + - + +
301H HIS* 2.8 35.7 + - + -
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Residues in contact with VAL 298 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272H VAL* 3.6 19.2 - - + +
275H LEU* 3.6 25.1 - - + -
276H ASN* 3.6 20.9 - - - +
294H SER 3.1 16.8 + - - +
295H CYS* 3.6 7.4 - - - +
297H LEU* 1.3 75.7 - - - +
299H LEU* 1.3 50.6 + - - +
301H HIS* 3.1 11.4 + - - +
302H GLN* 2.8 31.7 + - + +
305H ASN* 3.8 23.8 - - + +
308H ALA* 3.6 22.9 - - + -
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Residues in contact with LEU 299 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F ARG* 4.9 1.4 + - - -
295H CYS 3.0 20.2 + - - +
296H SER* 3.5 6.9 + - - +
297H LEU 3.3 0.2 - - - -
298H VAL* 1.3 73.1 - - - +
300H GLU* 1.3 62.2 + - - +
301H HIS 3.3 0.2 - - - -
302H GLN 3.5 17.0 - - - +
303H PRO* 3.2 34.7 - - + +
305H ASN 3.9 3.1 - - - +
308H ALA* 3.8 29.6 - - + +
309H LEU* 3.8 34.3 - - + -
312H LYS* 3.9 28.3 - - + +
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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
----------------------------------------------------------
94F LEU* 3.9 42.2 - - + +
104F LYS* 5.8 1.7 + - - -
116F ARG* 2.8 47.1 + - - +
162F LEU* 3.7 7.3 - - - +
296H SER* 3.1 19.1 + - - +
297H LEU* 3.5 12.3 - - + +
298H VAL 3.2 0.4 - - - -
299H LEU* 1.3 77.1 - - - +
301H HIS* 1.4 57.2 + - - +
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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
----------------------------------------------------------
94F LEU* 4.6 14.0 - - + +
95F ASP 5.6 0.9 - - - -
96F ILE* 3.6 27.6 + - + -
116F ARG* 4.1 4.3 + - - -
161F PRO 5.5 0.5 - - - +
162F LEU* 3.9 29.6 - - + +
268H LEU* 4.5 12.5 - - + +
271H LYS* 4.6 14.1 - - - -
272H VAL* 3.6 32.0 - - + +
275H LEU* 4.9 4.5 - - + -
297H LEU* 2.8 35.6 + - + -
298H VAL* 3.1 1.8 + - - +
300H GLU* 1.4 80.1 - - - +
302H GLN* 1.3 65.1 + - + +
303H PRO* 3.8 6.9 - - - +
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Residues in contact with GLN 302 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269H GLN* 3.6 25.9 + - - +
272H VAL* 3.5 31.3 - - - +
298H VAL* 2.8 12.8 + - + +
299H LEU* 3.5 13.1 - - - +
301H HIS* 1.3 81.4 - - + +
303H PRO* 1.4 64.8 - - - +
304H ASP 3.2 4.1 + - - -
305H ASN* 3.1 45.8 + - + +
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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