Contacts of the strand formed by residues 331 - 336 (chain A) in PDB entry 1MPX
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 ASN 331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295A LEU* 4.2 6.9 - - + +
299A THR* 3.5 3.6 - - - +
301A TRP* 3.0 26.2 + - - -
318A TYR* 3.0 38.8 + - - -
321A MSE 3.7 17.5 - - - +
322A GLU* 3.0 29.4 + - - +
325A ASP* 3.1 15.0 + - + +
329A THR 3.8 0.4 - - - -
330A LEU* 1.3 80.2 - - - +
332A TYR* 1.3 64.3 + - - +
638A CA 2.3 30.8 - - - -
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Residues in contact with TYR 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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298A PRO* 5.3 0.4 - - + -
299A THR 2.8 18.6 + - - +
300A MSE 3.9 21.5 - - + -
301A TRP* 2.9 25.1 + - - +
318A TYR* 3.4 12.3 - - - -
328A ASN 3.8 6.4 + - - -
329A THR* 3.3 49.4 + - - +
330A LEU 4.0 2.0 - - - -
331A ASN* 1.3 78.6 - - - +
333A LEU* 1.3 61.2 + - - +
334A VAL* 5.6 0.2 - - + -
371A PHE* 3.8 22.4 - + - -
375A TYR* 5.1 2.1 + - - -
385A THR* 3.5 34.3 + - + -
386A PRO 3.3 19.3 - - - +
387A PRO* 3.5 21.8 - - + -
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Residues in contact with LEU 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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301A TRP* 3.4 11.4 - - + +
314A ALA* 4.6 1.8 - - + +
315A ILE* 3.9 24.9 - - + +
318A TYR* 3.7 35.9 - - + -
332A TYR* 1.3 76.6 - - - +
334A VAL* 1.3 72.4 + - - +
335A MSE 3.9 25.4 - - + +
386A PRO 5.0 0.7 - - - +
387A PRO 3.2 5.9 + - - +
388A VAL* 3.4 13.8 - - + -
389A PHE 2.9 24.8 + - - -
390A ILE* 5.2 1.3 - - + -
404A TRP* 3.8 41.1 - - + -
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Residues in contact with VAL 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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300A MSE 3.7 31.4 - - + -
301A TRP 2.8 7.6 + - - +
302A LEU* 3.2 29.1 - - + -
303A GLN 3.1 22.9 + - - -
332A TYR* 5.6 0.2 - - + -
333A LEU* 1.3 81.0 - - - +
335A MSE 1.3 69.5 + - - +
338A TRP* 4.2 11.7 - - + -
363A PHE* 3.9 25.1 - - + -
367A VAL* 5.1 0.7 - - + -
386A PRO 6.2 0.2 - - - +
389A PHE* 3.2 26.9 - - + +
398A TRP* 4.5 1.3 - - + -
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Residues in contact with MSE 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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303A GLN* 3.2 43.5 - - + +
304A GLY 4.6 2.2 - - - +
305A LEU* 4.0 19.1 - - + +
311A MSE 5.9 1.1 - - - -
315A ILE* 4.2 24.7 - - + -
333A LEU* 3.9 18.1 - - + -
334A VAL* 1.3 80.1 - - - +
336A GLY* 1.3 61.9 + - - +
389A PHE 3.0 8.9 + - - -
390A ILE* 3.4 23.9 - - + +
391A TYR* 3.1 24.8 + - - +
398A TRP* 3.8 1.1 - - - -
404A TRP* 4.7 0.2 - - - -
573A THR* 3.8 39.7 - - + +
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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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303A GLN 3.3 8.3 + - - -
304A GLY* 3.6 0.7 - - - -
305A LEU* 2.9 32.3 + - - +
335A MSE 1.3 73.8 - - - +
337A PRO* 1.3 68.3 - - - +
338A TRP* 2.9 26.6 + - - -
391A TYR* 4.2 0.4 - - - -
398A TRP* 3.6 12.3 - - - -
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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