Contacts of the helix formed by residues 334 - 343 (chain A) in PDB entry 3LMK
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 VAL 334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A PRO 4.1 2.2 - - - +
333A ASP* 1.3 73.2 - - - +
335A LYS* 1.3 67.1 + - - +
336A TRP* 3.4 44.2 - - + +
337A PHE* 3.1 12.7 + - + +
338A ASP* 4.9 0.2 - - - -
393A GLN* 3.0 23.7 + - - +
397A MET* 4.0 4.3 - - + -
398A GLY* 3.8 27.6 - - - +
401A ILE* 3.8 21.8 - - + -
449A VAL* 3.7 20.0 - - + -
450A SER* 5.3 0.7 - - - +
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Residues in contact with LYS 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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333A ASP* 3.7 4.8 + - - -
334A VAL* 1.3 73.6 - - - +
336A TRP* 1.3 65.6 + - + +
337A PHE 3.2 0.7 + - - -
338A ASP* 3.5 12.6 + - - +
339A ASP* 3.3 15.7 + - - +
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Residues in contact with TRP 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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71A ALA 5.3 0.9 - - - -
74A HIS* 3.5 29.0 + + + +
75A THR* 3.5 26.0 - - - -
78A ARG* 3.1 58.1 - - - +
334A VAL* 3.4 11.6 - - + +
335A LYS* 1.3 79.3 - - + +
337A PHE* 1.3 94.1 + + + +
339A ASP* 3.2 15.2 + - + +
340A TYR* 3.1 20.6 + - - +
401A ILE* 3.5 32.8 - - + -
405A TYR* 4.9 4.7 - + - -
449A VAL* 3.5 21.6 - - + +
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Residues in contact with PHE 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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67A GLN* 3.2 44.9 - - + -
70A GLU* 4.1 5.6 - - + -
71A ALA* 3.5 30.1 - - + -
334A VAL* 3.1 24.4 + - + +
336A TRP* 1.3 97.8 - + + +
338A ASP* 1.3 66.3 + - - +
340A TYR* 3.3 8.8 + + - +
341A TYR* 2.8 69.0 + + + +
391A HIS* 5.1 0.2 - + - -
393A GLN* 3.8 11.7 - - + +
397A MET* 3.8 19.3 - - + -
401A ILE* 4.7 1.3 - - + -
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Residues in contact with ASP 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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333A ASP* 5.5 2.3 - - - +
334A VAL 3.9 1.3 + - - -
335A LYS* 3.5 9.2 + - - +
336A TRP 3.3 0.2 - - - -
337A PHE* 1.3 80.0 - - - +
339A ASP* 1.3 66.0 + - - +
341A TYR* 4.3 4.7 - - - -
342A LEU* 2.9 41.9 + - + +
391A HIS* 3.0 36.3 + - - -
393A GLN* 2.8 30.4 + - - +
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Residues in contact with ASP 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 LYS* 3.3 17.1 + - - +
336A TRP* 3.2 16.4 + - + +
338A ASP* 1.3 80.9 - - - +
340A TYR* 1.3 61.1 + - - +
342A LEU* 4.9 0.3 - - - +
343A LYS* 3.2 43.1 + - - +
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Residues in contact with TYR 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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70A GLU* 2.6 40.6 + - + -
73A LEU* 4.5 0.2 - - - +
74A HIS* 3.2 63.3 - + + +
77A GLU* 4.0 1.3 - - - -
336A TRP 3.1 4.6 + - - +
337A PHE* 3.8 12.3 - + - +
339A ASP* 1.3 79.5 - - - +
341A TYR* 1.3 71.7 + - + +
343A LYS* 3.4 16.9 + - - +
344A LEU* 3.8 34.7 - - + +
349A ASN* 5.0 0.2 + - - -
351A ARG* 2.8 30.9 + - - -
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Residues in contact with TYR 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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62A GLU* 3.1 23.2 + - - +
66A ILE* 4.0 7.6 - - + +
67A GLN* 3.4 27.3 - - + +
70A GLU* 4.0 27.1 - - + -
337A PHE* 2.8 48.1 + + + +
338A ASP* 4.1 2.5 - - - +
340A TYR* 1.3 80.2 - - - +
342A LEU* 1.3 67.1 + - + +
344A LEU* 3.1 27.6 + - + +
355A PHE* 4.8 1.6 - + - -
358A PHE* 3.5 18.4 - - - -
387A LEU* 3.9 24.0 - - + +
391A HIS* 3.8 29.2 - + - -
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Residues in contact with LEU 342 (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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338A ASP* 2.9 38.6 + - + +
339A ASP 4.9 0.9 - - - +
341A TYR* 1.3 79.3 - - + +
343A LYS* 1.3 62.4 + - + +
344A LEU 3.3 5.1 + - - +
345A ARG* 5.2 3.3 + - - -
386A THR* 4.4 11.4 + - - -
387A LEU* 3.6 23.7 + - + +
388A LYS* 3.6 57.3 - - + +
391A HIS* 3.7 30.1 - - + +
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Residues in contact with LYS 343 (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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339A ASP* 3.2 31.5 + - - +
340A TYR* 3.4 9.8 + - - +
341A TYR 3.2 0.6 - - - -
342A LEU* 1.3 79.8 - - + +
344A LEU* 1.3 63.6 + - - +
345A ARG* 3.7 13.3 + - - +
388A LYS* 6.0 7.4 - - - +
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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