Contacts of the helix formed by residues 329 - 339 (chain A) in PDB entry 1MWT
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 ASP 329 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A ASP* 3.7 3.6 - - - +
157A ARG* 4.1 12.6 - - - -
158A ASN* 4.0 10.8 + - - -
327A THR 3.6 0.4 + - - -
328A ILE* 1.3 73.2 - - - +
330A ALA* 1.3 65.6 + - - +
331A LYS* 2.8 40.6 + - - +
332A VAL* 2.9 14.2 + - + -
333A GLN 3.0 9.9 + - - -
358A LEU* 2.9 17.9 + - + +
664A TYR* 2.7 42.1 + - - +
666A ILE* 3.9 4.8 - - - -
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Residues in contact with ALA 330 (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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156A ASP* 2.8 24.0 + - - +
160A VAL* 3.8 27.8 - - + -
162A LEU* 4.5 4.7 - - + -
245A LEU* 4.2 18.0 - - + +
328A ILE* 3.9 2.8 - - - +
329A ASP* 1.3 69.8 - - - +
331A LYS* 1.3 56.2 + - + +
333A GLN* 3.8 9.1 - - - +
334A LYS* 2.8 40.0 + - - +
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Residues in contact with LYS 331 (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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158A ASN* 3.9 2.0 - - - +
329A ASP* 2.8 36.2 + - - +
330A ALA* 1.3 75.6 - - + +
332A VAL* 1.3 57.0 + - - +
334A LYS* 3.8 4.5 - - - +
335A SER* 3.0 30.0 + - - -
655A GLU* 4.8 0.7 - - - +
656A LEU* 4.0 16.0 - - + +
662A LYS* 5.5 4.5 - - - +
664A TYR* 3.7 18.8 - - - -
665A ASP 3.5 11.5 + - - -
668A GLU* 2.5 44.1 + - + +
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Residues in contact with VAL 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ASP* 2.9 17.0 + - + +
331A LYS* 1.3 69.6 - - - +
333A GLN* 1.3 68.5 + - - +
335A SER* 3.2 1.9 + - - +
336A ILE* 2.8 50.0 + - + +
349A ALA* 4.0 2.9 - - + -
358A LEU* 4.0 4.3 - - + +
359A ALA* 3.6 14.8 - - + -
627A MET* 3.8 25.6 - - - -
629A MET* 4.0 3.6 - - + -
656A LEU* 4.3 11.4 - - + -
664A TYR* 3.3 37.7 - - + +
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Residues in contact with GLN 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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245A LEU* 4.1 4.7 - - + -
248A ALA* 3.0 18.9 - - - +
249A THR* 3.7 28.9 - - + +
252A LEU* 5.0 4.5 - - - +
328A ILE* 3.6 21.0 - - + +
329A ASP 3.0 15.0 + - - +
330A ALA* 3.8 6.5 - - - +
332A VAL* 1.3 76.5 - - - +
334A LYS* 1.3 63.0 + - - +
337A TYR* 3.2 24.1 + - - +
359A ALA* 3.2 15.3 - - - +
360A LEU 2.7 47.3 + - - +
361A VAL* 3.4 11.7 - - - +
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Residues in contact with LYS 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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245A LEU* 4.4 29.8 - - + +
248A ALA* 4.8 5.2 - - + -
330A ALA* 2.8 28.2 + - - +
331A LYS* 3.8 4.7 - - - +
333A GLN* 1.3 75.2 - - - +
335A SER* 1.3 66.8 + - - +
337A TYR* 3.2 6.3 + - + +
338A ASN* 2.9 43.3 + - - +
655A GLU* 5.4 2.7 - - - +
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Residues in contact with SER 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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331A LYS 3.0 18.9 + - - -
332A VAL* 3.8 3.4 - - - -
334A LYS* 1.3 77.2 - - - +
336A ILE* 1.3 63.1 + - - +
338A ASN* 3.3 2.3 + - - -
339A ASN* 3.1 28.3 + - - -
652A VAL* 3.5 30.7 - - - +
655A GLU* 3.0 41.0 + - - +
656A LEU* 4.6 4.7 - - - -
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Residues in contact with ILE 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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332A VAL* 2.8 33.6 + - + +
335A SER* 1.3 73.9 - - - +
337A TYR* 1.3 63.6 + - - +
339A ASN* 3.4 2.1 + - - +
340A MET* 3.2 32.7 + - - +
347A GLY* 3.7 34.5 - - - -
349A ALA* 4.4 3.4 - - + -
359A ALA* 4.2 11.4 - - + -
361A VAL* 3.9 15.9 - - + -
629A MET* 3.1 45.5 - - + -
631A ILE* 4.4 3.6 - - + -
648A ILE* 6.1 0.2 - - - -
652A VAL* 4.0 13.0 - - + -
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Residues in contact with TYR 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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247A LYS* 3.5 33.2 - - + +
248A ALA* 3.6 33.0 - - + -
333A GLN 3.2 17.6 + - - +
334A LYS* 3.2 4.1 + - - +
335A SER 3.2 0.4 - - - -
336A ILE* 1.3 79.3 - - - +
338A ASN* 1.3 74.5 - - - +
340A MET* 2.9 2.8 + - - -
341A LYS* 2.8 62.9 + - + +
361A VAL* 4.0 13.7 - - + -
362A SER 5.1 0.4 - - - -
363A THR* 3.9 17.5 - - + -
365A SER* 3.8 25.9 + - - -
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Residues in contact with ASN 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 LYS* 2.9 37.1 + - - +
335A SER* 3.9 4.5 - - - +
337A TYR* 1.3 94.0 - - - +
339A ASN* 1.3 64.3 + - - +
340A MET 3.7 0.2 + - - -
341A LYS* 4.1 25.6 + - + +
655A GLU* 4.9 9.3 + - - +
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Residues in contact with ASN 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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335A SER* 3.1 26.6 + - - +
336A ILE 3.4 3.6 + - - +
337A TYR 3.0 1.4 - - - -
338A ASN* 1.3 81.1 - - - +
340A MET* 1.3 59.1 + - - +
343A ASP* 4.4 2.4 - - - +
644A TYR* 4.9 1.2 + - - -
648A ILE* 3.6 36.2 - - + +
651A LYS* 3.7 38.8 + - - +
652A VAL* 4.2 6.5 - - + +
655A GLU* 3.7 19.4 + - - -
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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
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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