Contacts of the helix formed by residues 279 - 294 (chain A) in PDB entry 3MAG
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 279 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264A TYR* 3.6 20.0 - - + +
268A ARG* 3.7 49.9 + - + +
278A THR* 1.3 73.6 - - - +
280A LYS* 1.3 64.0 + - - +
282A LYS* 3.0 12.7 + - - +
283A VAL* 2.9 23.2 + - + +
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Residues in contact with LYS 280 (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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252A ASP* 3.1 45.3 + - - +
253A TYR* 4.3 19.0 - - + +
254A PRO* 4.7 3.5 - - - +
264A TYR* 3.6 20.4 + - + +
278A THR* 3.1 10.9 - - - +
279A THR* 1.3 80.7 - - - +
281A ALA* 1.3 55.6 + - - +
283A VAL* 3.9 1.2 - - - +
284A LEU* 3.0 50.3 + - + +
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Residues in contact with ALA 281 (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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276A PHE* 3.8 20.0 - - + -
277A PRO* 4.2 13.7 - - + -
278A THR* 3.0 22.4 + - - +
280A LYS* 1.3 75.6 - - - +
282A LYS* 1.3 65.5 + - - +
284A LEU* 3.5 8.5 + - - +
285A PHE* 3.0 23.4 + - - +
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Residues in contact with LYS 282 (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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267A LEU 4.0 9.9 - - - -
268A ARG* 3.0 29.6 + - - +
269A THR 4.7 0.4 - - - -
270A VAL 2.9 28.3 + - - +
271A TYR* 5.1 0.4 - - - +
272A CYS* 4.4 11.0 - - + +
276A PHE* 3.6 38.3 - - + -
278A THR 3.2 5.8 + - - +
279A THR* 3.0 14.8 + - - +
281A ALA* 1.3 79.7 - - - +
283A VAL* 1.3 57.4 - - - +
285A PHE* 3.0 5.2 + - - +
286A LEU* 2.8 38.1 + - + +
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A TYR* 3.6 13.0 - - + +
263A MET* 5.8 0.9 - - + -
264A TYR* 3.5 61.5 - - + +
267A LEU* 4.1 14.9 - - + +
268A ARG* 4.0 13.2 - - - +
279A THR* 2.9 29.8 + - + +
280A LYS 3.9 2.9 - - - +
282A LYS* 1.3 73.5 - - + +
284A LEU* 1.3 61.7 + - - +
286A LEU* 3.3 6.8 + - - +
287A GLN* 2.8 28.6 + - - +
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Residues in contact with LEU 284 (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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253A TYR* 3.6 28.7 - - + +
254A PRO* 3.7 24.9 - - + -
280A LYS* 3.0 47.0 + - + +
281A ALA* 3.9 7.4 - - - +
283A VAL* 1.3 76.1 - - - +
285A PHE* 1.3 63.9 + - - +
287A GLN* 3.5 5.6 + - - +
288A GLN* 2.9 27.0 + - - +
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Residues in contact with PHE 285 (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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272A CYS* 4.5 15.9 - - - -
274A LYS* 4.1 29.2 - - + -
276A PHE* 3.5 29.6 - + + -
281A ALA 3.0 14.0 + - - +
282A LYS 3.0 9.7 + - - +
284A LEU* 1.3 77.7 - - - +
286A LEU* 1.3 65.7 + - + +
288A GLN* 2.8 39.2 + - - +
289A SER* 2.9 23.5 + - - -
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Residues in contact with LEU 286 (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* 5.4 3.8 - - + -
77A TYR* 4.3 14.4 - - - +
81A HIS* 4.4 7.9 - - + +
267A LEU* 3.4 43.5 - - + +
270A VAL* 3.7 28.7 - - + +
272A CYS* 3.9 23.3 - - - -
282A LYS* 2.8 36.5 + - + +
283A VAL 3.8 3.4 - - - +
285A PHE* 1.3 78.6 - - + +
287A GLN* 1.3 57.1 + - - +
289A SER* 3.4 4.1 + - - -
290A ILE* 2.9 36.8 + - + +
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Residues in contact with GLN 287 (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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253A TYR* 2.6 42.1 + - - +
254A PRO* 5.9 2.0 - - - +
260A TYR* 4.2 7.2 - - - -
263A MET* 3.3 27.5 - - + +
267A LEU* 4.0 12.2 - - + +
283A VAL 2.8 21.8 + - - +
284A LEU* 3.8 8.3 - - - +
286A LEU* 1.3 70.7 - - - +
288A GLN* 1.3 62.0 + - - +
290A ILE* 3.2 4.6 + - - +
291A PHE* 2.8 66.2 + - + +
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Residues in contact with GLN 288 (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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284A LEU 2.9 17.1 + - - +
285A PHE* 2.8 44.8 + - - +
287A GLN* 1.3 79.2 - - - +
289A SER* 1.3 74.8 + - - +
291A PHE* 3.4 4.0 + - - +
292A ARG* 2.9 51.3 + - + +
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Residues in contact with SER 289 (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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77A TYR* 2.8 25.6 + - - -
285A PHE* 2.9 29.5 + - - -
286A LEU* 3.4 7.0 - - - -
288A GLN* 1.3 91.0 - - - +
290A ILE* 1.3 62.1 + - - +
292A ARG* 3.9 2.9 - - - +
293A PHE* 3.1 23.9 + - - +
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Residues in contact with ILE 290 (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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40A LEU* 3.7 29.8 - - + -
43A LEU* 3.9 17.7 - - + -
44A LEU* 4.1 10.3 - - + -
47A LEU* 4.0 16.4 - - + -
77A TYR* 3.6 28.3 - - + +
263A MET* 6.1 0.7 - - - -
267A LEU* 4.0 28.9 - - + -
286A LEU* 2.9 24.5 + - + +
287A GLN* 3.6 4.0 - - - +
289A SER* 1.3 76.8 - - - +
291A PHE* 1.3 68.2 + - + +
293A PHE* 3.3 3.5 + - - +
294A LEU* 3.0 25.9 + - + +
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Residues in contact with PHE 291 (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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34A LEU* 4.4 4.0 - - + -
40A LEU* 3.8 36.6 - - + -
200A PHE* 4.8 0.7 - + - -
260A TYR* 4.1 28.5 - + - -
263A MET* 4.3 7.6 - - + -
287A GLN* 2.8 53.6 + - + +
288A GLN* 4.0 4.7 - - - +
290A ILE* 1.3 76.9 - - + +
292A ARG* 1.3 64.8 + - - +
294A LEU 3.4 0.7 + - - -
295A ASN 2.9 4.5 + - - -
296A ILE* 2.9 71.5 + - + +
297A PRO 4.1 9.4 - - - -
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Residues in contact with ARG 292 (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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288A GLN* 2.9 34.0 + - + +
289A SER* 3.9 4.3 - - - +
291A PHE* 1.3 77.3 - - - +
293A PHE* 1.3 65.0 + - - +
295A ASN* 3.0 15.6 + - - +
296A ILE 5.1 0.7 - - - -
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Residues in contact with PHE 293 (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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73A THR* 3.6 31.7 - - + +
74A HIS* 4.4 0.4 - - - -
76A ARG* 3.8 18.8 - - + -
77A TYR* 3.7 48.0 - + + -
80A ASP* 4.7 5.6 - - - -
102A ILE* 4.0 10.3 - - + -
289A SER 3.1 19.3 + - - +
290A ILE 3.6 3.6 - - - +
291A PHE 3.3 0.2 - - - -
292A ARG* 1.3 79.3 - - - +
294A LEU* 1.3 82.2 + - + +
295A ASN* 3.3 1.7 + - - +
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Residues in contact with LEU 294 (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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36A TYR* 3.0 28.7 - - + +
39A GLN* 3.8 23.8 - - + -
40A LEU* 3.7 33.7 - - + +
43A LEU* 4.1 9.2 - - + -
73A THR* 4.8 7.0 - - + -
74A HIS* 4.3 11.9 - - + +
290A ILE* 3.0 31.0 + - + +
293A PHE* 1.3 93.9 - - + +
295A ASN* 1.3 67.0 + - - +
296A ILE* 3.8 23.3 - - + -
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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
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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