Contacts of the helix formed by residues 331 - 341 (chain A) in PDB entry 2MX7
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 PRO 331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329A GLY 4.7 0.7 - - - +
330A LEU* 1.3 92.8 - - + +
332A ARG* 1.3 59.0 + - - +
333A GLU* 2.9 23.2 + - + +
334A THR* 3.1 34.5 - - + +
335A LEU* 2.8 32.0 + - + +
365A THR* 4.6 4.9 - - + -
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Residues in contact with ARG 332 (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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322A TYR* 4.3 14.2 - - + -
326A MET* 3.6 33.6 - - + +
330A LEU 3.6 3.8 + - - -
331A PRO* 1.3 70.8 - - - +
333A GLU* 1.3 101.2 + - - +
335A LEU* 3.8 12.0 - - - +
336A GLY* 3.3 16.5 + - - -
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Residues in contact with GLU 333 (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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331A PRO* 2.9 21.2 - - + +
332A ARG* 1.3 119.4 + - - +
334A THR* 1.3 66.9 + - - +
336A GLY* 3.2 3.8 + - - -
337A GLN* 3.1 20.4 + - - +
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Residues in contact with THR 334 (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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331A PRO* 3.1 30.9 + - + +
333A GLU* 1.3 78.6 - - - +
335A LEU* 1.3 55.4 + - + +
337A GLN* 3.0 13.1 + - - +
338A ILE* 2.7 55.2 + - + +
365A THR* 4.2 22.7 - - + +
371A ALA* 6.1 2.5 - - + +
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Residues in contact with LEU 335 (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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318A THR* 5.2 0.5 + - - -
321A LEU* 4.4 13.2 - - + +
322A TYR* 4.0 16.2 - - + +
325A LEU* 3.7 13.9 - - + -
326A MET* 3.6 20.2 - - - +
330A LEU* 3.5 33.4 - - + +
331A PRO* 2.8 38.3 + - + +
332A ARG* 3.7 10.3 - - - +
334A THR* 1.3 76.2 - - + +
336A GLY* 1.3 61.7 + - - +
338A ILE* 3.4 7.8 + - - +
339A TRP* 3.2 24.8 + - - +
362A ILE* 3.6 23.1 - - + -
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Residues in contact with GLY 336 (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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322A TYR* 4.1 18.9 - - - -
332A ARG 3.3 9.8 + - - -
333A GLU 3.2 7.3 + - - -
335A LEU* 1.3 74.7 - - - +
337A GLN* 1.3 64.9 + - - +
339A TRP* 3.3 8.7 + - - +
340A ALA* 3.2 21.5 + - - +
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Residues in contact with GLN 337 (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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333A GLU 3.1 13.1 + - - +
334A THR* 3.0 16.1 + - - +
336A GLY* 1.3 75.1 - - - +
338A ILE* 1.3 63.0 + - - +
340A ALA* 2.8 26.9 + - + +
341A LEU* 2.8 52.4 + - + +
371A ALA* 4.5 14.5 + - - +
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Residues in contact with ILE 338 (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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334A THR* 2.7 43.4 + - + +
335A LEU 3.6 3.1 - - - +
336A GLY 3.3 0.2 - - - -
337A GLN* 1.3 79.0 - - - +
339A TRP* 1.3 83.1 + - + +
340A ALA 3.3 0.2 + - - -
341A LEU* 3.6 16.0 + - + -
358A VAL* 3.3 29.8 - - - +
361A MET* 3.2 49.9 - - + +
362A ILE* 3.8 19.1 - - + -
365A THR* 4.8 1.6 - - - +
371A ALA* 4.5 7.9 - - + -
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Residues in contact with TRP 339 (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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306A ILE* 5.4 6.1 - - + -
310A THR* 5.2 4.7 - - + -
316A ILE* 3.5 21.9 - - + +
317A ASP 5.5 0.2 - - - -
318A THR* 3.1 42.6 - - + +
321A LEU* 3.5 39.5 - - + -
322A TYR* 6.0 0.4 - - - +
335A LEU 3.2 14.2 + - - +
336A GLY* 3.7 9.2 - - - +
337A GLN 3.2 0.4 - - - -
338A ILE* 1.3 87.6 - - + +
340A ALA* 1.3 61.6 + - + +
341A LEU 3.7 0.2 + - - -
342A ALA* 4.1 2.6 + - - +
346A THR 4.9 1.9 - - - +
350A LEU* 3.3 45.0 - - + +
355A LEU* 3.9 17.5 - - + -
358A VAL* 3.0 42.4 - - + -
359A LEU* 5.9 1.8 - - + -
362A ILE* 4.5 4.9 - - + -
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Residues in contact with ALA 340 (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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336A GLY 3.2 10.7 + - - +
337A GLN* 2.8 12.7 + - - +
339A TRP* 1.3 78.7 - - + +
341A LEU* 1.3 59.6 + - + +
342A ALA 3.1 11.1 + - - -
345A THR 5.2 0.2 + - - -
346A THR* 2.9 58.2 + - + +
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Residues in contact with LEU 341 (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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337A GLN* 2.8 64.6 + - + +
338A ILE* 3.6 15.9 + - + -
339A TRP 3.4 1.2 - - - -
340A ALA* 1.3 79.8 - - + +
342A ALA* 1.3 57.3 - - - +
343A ASN* 2.9 15.1 + - - +
344A ARG* 6.0 4.0 - - - +
346A THR* 5.8 0.9 - - - +
357A THR* 3.7 13.4 - - - +
361A MET* 3.8 21.8 - - + +
371A ALA* 5.0 3.8 - - + -
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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