Contacts of the helix formed by residues 318 - 334 (chain G) in PDB entry 3MQ6
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 318 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G ASN 3.3 14.1 + - - -
61G GLY* 3.2 28.0 - - - +
62G MET 3.6 9.0 - - - +
63G ASP* 4.7 0.7 - - - +
64G TYR* 3.9 8.1 - - - -
316G PRO* 4.1 4.9 - - - +
317G PRO* 1.3 87.8 - - + +
319G ALA* 1.3 62.7 + - - +
320G ALA* 3.3 5.0 + - - +
321G ASP* 2.9 30.7 + - - +
322G LEU* 3.3 12.1 + - - +
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Residues in contact with ALA 319 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G PRO* 3.4 45.8 - - + +
53G GLY* 3.6 3.7 - - - +
59G ILE 4.9 2.6 + - - +
60G ASN* 3.6 7.1 + - - +
62G MET 4.4 1.4 + - - -
64G TYR* 3.8 24.4 - - + -
67G VAL* 5.7 0.9 - - + +
109G VAL* 4.2 6.7 - - + +
318G THR* 1.3 70.8 - - - +
320G ALA* 1.3 65.2 + - - +
322G LEU* 3.2 8.6 + - - +
323G ALA* 3.1 21.8 + - - +
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Residues in contact with ALA 320 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G GLY* 4.3 1.3 - - - -
60G ASN* 3.2 28.7 + - + +
61G GLY* 5.3 1.3 - - - -
132G TYR* 3.5 30.1 - - + +
318G THR* 3.2 4.4 - - - +
319G ALA* 1.3 77.8 - - - +
321G ASP* 1.3 56.6 + - - +
323G ALA 3.2 0.9 + - - -
324G ARG* 2.8 29.4 + - - +
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Residues in contact with ASP 321 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314G TYR* 2.6 28.4 + - - +
317G PRO* 3.2 25.2 - - + +
318G THR* 2.9 22.8 + - - +
319G ALA 3.2 0.2 - - - -
320G ALA* 1.3 74.3 - - - +
322G LEU* 1.3 62.2 + - - +
324G ARG* 2.9 37.9 + - - +
325G ARG* 2.9 28.9 + - - +
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Residues in contact with LEU 322 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G TYR* 3.9 28.9 - - + +
106G SER* 4.0 27.1 - - - +
109G VAL* 4.1 14.6 - - + -
110G MET* 4.4 16.4 - - + -
278G HIS* 3.7 29.8 - - + +
314G TYR* 3.4 16.1 + - + +
316G PRO* 4.4 7.0 - - + -
318G THR 3.3 9.1 + - - +
319G ALA* 3.2 9.6 + - - +
320G ALA 3.2 0.6 - - - -
321G ASP* 1.3 79.0 - - - +
323G ALA* 1.3 63.4 + - - +
325G ARG* 3.3 3.6 + - + +
326G PHE* 3.1 21.7 + - + +
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Residues in contact with ALA 323 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G GLY* 5.4 0.2 - - - -
54G PHE* 4.4 3.1 - - + -
109G VAL* 4.2 9.2 - - + -
113G CYS* 3.6 26.0 - - - -
132G TYR* 3.6 31.6 - - + +
319G ALA 3.1 10.7 + - - +
320G ALA 3.6 2.0 - - - +
322G LEU* 1.3 75.3 - - - +
324G ARG* 1.3 64.6 + - - +
326G PHE* 3.2 2.4 + - - +
327G PHE* 3.0 31.8 + - + -
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Residues in contact with ARG 324 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G TYR* 4.2 10.7 - - + -
133G SER* 5.7 5.6 - - - +
314G TYR* 5.2 0.8 - - - -
320G ALA 2.8 20.1 + - - +
321G ASP* 2.9 41.2 + - - +
323G ALA* 1.3 73.2 - - - +
325G ARG* 1.3 89.5 + - - +
327G PHE* 3.4 8.9 + - - +
328G ALA* 3.1 32.2 + - + +
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Residues in contact with ARG 325 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276G GLU* 2.7 44.4 + - - -
278G HIS* 4.0 2.4 + - - -
311G ARG* 3.5 10.0 - - - +
312G GLU* 2.6 39.0 + - - +
314G TYR* 3.4 49.0 - - + +
321G ASP 2.9 17.3 + - - +
322G LEU* 3.6 7.3 - - + +
324G ARG* 1.3 98.9 - - - +
326G PHE* 1.3 58.8 + - - +
328G ALA* 3.4 4.0 + - - +
329G PHE* 3.0 29.3 + - + +
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Residues in contact with PHE 326 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110G MET* 3.6 61.9 - - + -
113G CYS* 3.5 24.2 - - + -
114G ALA* 4.5 3.1 - - + -
145G VAL* 5.0 1.1 - - + -
147G VAL* 4.1 6.5 - - + -
191G VAL* 3.7 25.8 - - + -
237G LEU* 4.3 11.2 - - + -
322G LEU* 3.1 15.6 + - + +
323G ALA 3.8 4.0 - - - +
325G ARG* 1.3 80.0 - - - +
327G PHE* 1.3 65.7 + - - +
329G PHE* 3.6 10.7 - + + +
330G LEU* 2.9 59.6 + - + +
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Residues in contact with PHE 327 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G PHE* 4.3 3.4 - + - -
113G CYS* 3.4 52.3 - - + -
116G ARG* 4.3 13.7 - - + -
117G TRP* 4.2 11.9 - + + -
126G TRP* 3.7 29.8 - + + -
132G TYR* 3.7 43.7 - + + -
133G SER 5.1 6.3 - - - +
135G PRO* 5.3 4.7 - - + +
323G ALA* 3.0 27.3 + - + +
324G ARG* 3.8 5.4 - - - +
326G PHE* 1.3 76.6 - - - +
328G ALA* 1.3 56.9 + - - +
330G LEU* 3.3 12.4 + - + +
331G ASN* 3.0 27.6 + - - +
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Residues in contact with ALA 328 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324G ARG* 3.1 27.1 + - + +
325G ARG* 3.7 7.0 - - - +
327G PHE* 1.3 75.3 - - - +
329G PHE* 1.3 64.5 + - - +
331G ASN* 3.3 15.5 + - - +
332G GLU* 3.5 19.2 + - - +
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Residues in contact with PHE 329 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191G VAL* 5.8 0.9 - - + -
236G SER* 3.4 23.6 - - - -
237G LEU* 3.8 33.7 - - + -
274G GLU* 4.2 13.5 - - + -
276G GLU* 5.4 0.2 - - - -
311G ARG* 3.6 41.7 - - - +
325G ARG* 3.0 22.0 + - + +
326G PHE* 3.2 17.2 + + + +
328G ALA* 1.3 72.8 - - - +
330G LEU* 1.3 72.3 + - + +
332G GLU* 3.2 4.7 + - - +
333G ARG* 2.8 55.6 + - + +
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Residues in contact with LEU 330 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113G CYS 5.2 0.4 - - - +
114G ALA* 5.2 1.8 - - - -
117G TRP* 3.5 43.6 - - + -
145G VAL* 4.1 28.0 - - + -
191G VAL* 4.6 4.9 - - + -
236G SER* 6.3 0.9 - - - -
326G PHE* 2.9 58.9 + - + +
327G PHE* 3.5 12.3 - - + +
329G PHE* 1.3 83.9 - - + +
331G ASN* 1.3 63.8 + - - +
333G ARG* 4.5 0.9 - - + +
334G MET* 3.0 38.8 + - + +
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Residues in contact with ASN 331 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G TRP* 3.8 8.9 - - + -
135G PRO* 3.5 12.3 - - + +
136G THR* 2.8 45.2 + - - +
137G LEU* 3.0 30.0 + - - +
327G PHE 3.0 13.5 + - - +
328G ALA* 3.5 14.6 - - - +
329G PHE 3.2 0.4 - - - -
330G LEU* 1.3 77.5 - - - +
332G GLU* 1.3 65.6 + - - +
335G GLU* 4.4 3.6 + - - +
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Residues in contact with GLU 332 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328G ALA 3.5 13.0 + - - +
329G PHE* 3.2 5.9 + - + +
330G LEU 3.1 0.4 - - - -
331G ASN* 1.3 85.0 - - + +
333G ARG* 1.3 64.7 + - - +
334G MET 3.2 2.7 + - - -
335G GLU* 3.2 22.7 + - - +
336G LEU* 4.2 7.3 + - - +
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Residues in contact with ARG 333 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233G GLY 4.2 14.1 + - - -
235G ILE 3.7 20.8 + - - -
236G SER* 3.8 28.4 + - - +
271G PRO* 4.2 11.9 + - - +
272G LYS* 3.2 27.5 + - - +
273G VAL* 5.4 0.2 - - - +
274G GLU* 3.3 22.6 + - - +
329G PHE* 2.8 52.6 + - + +
330G LEU* 4.5 2.5 - - + +
332G GLU* 1.3 73.9 - - - +
334G MET* 1.3 67.2 + - - +
336G LEU* 3.5 39.2 + - - +
337G VAL* 4.4 2.6 - - - +
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Residues in contact with MET 334 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G TRP* 3.8 16.4 - - + -
137G LEU* 3.5 15.3 - - + -
143G ARG* 3.0 54.2 + - + +
144G GLN 4.2 0.7 - - - +
145G VAL* 3.8 20.6 - - + -
193G VAL* 3.7 23.3 - - + -
236G SER* 4.5 8.1 - - - -
330G LEU* 3.0 29.2 + - + +
333G ARG* 1.3 82.9 - - + +
335G GLU* 1.3 63.7 + - - +
336G LEU 3.1 2.0 - - - -
337G VAL* 3.1 35.4 + - + +
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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