Contacts of the helix formed by residues 433 - 442 (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 ASP 433 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A ASN* 5.8 0.3 + - - -
414A MET* 3.6 11.5 - - + +
418A LEU* 6.1 0.4 - - + -
431A PRO 3.3 6.4 + - - +
432A ILE* 1.3 68.4 - - - +
434A GLY* 1.3 59.4 + - - +
435A ARG* 3.5 19.0 + - - +
436A LYS* 3.0 31.1 + - + +
437A LEU* 3.0 23.9 + - - +
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Residues in contact with GLY 434 (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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144A VAL* 5.5 2.0 - - - -
166A ASN* 3.2 27.6 - - - +
168A PRO* 4.0 3.9 - - - +
187A TYR* 3.7 6.8 - - - -
432A ILE* 3.1 10.7 + - - -
433A ASP* 1.3 69.8 + - - +
435A ARG* 1.3 59.1 + - - +
437A LEU* 3.4 10.8 + - - +
438A LEU* 3.1 25.6 + - - +
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Residues in contact with ARG 435 (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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166A ASN* 4.3 10.8 - - - +
187A TYR* 3.5 20.1 + - - +
433A ASP* 3.2 12.5 + - - +
434A GLY* 1.3 76.5 - - - +
436A LYS* 1.3 59.7 + - + +
438A LEU* 3.5 6.8 - - - +
439A GLU* 3.2 22.5 + - - +
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Residues in contact with LYS 436 (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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414A MET* 3.9 16.5 - - + +
418A LEU* 5.3 7.6 - - + -
433A ASP* 3.0 33.6 + - + +
435A ARG* 1.3 78.2 - - + +
437A LEU* 1.3 64.2 + - - +
439A GLU* 3.2 8.6 + - + +
440A SER* 3.1 22.9 + - - -
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Residues in contact with LEU 437 (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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144A VAL* 3.3 45.3 - - + +
168A PRO* 3.9 8.1 - - + -
407A MET* 4.5 11.7 - - - +
410A GLY* 3.8 29.4 - - - +
411A LEU* 3.8 18.8 - - + +
414A MET* 3.8 12.2 - - - -
432A ILE* 4.6 1.8 - - + -
433A ASP 3.0 12.0 + - - +
434A GLY* 3.6 11.4 - - - +
435A ARG 3.4 0.2 - - - -
436A LYS* 1.3 76.5 - - - +
438A LEU* 1.3 56.2 + - - +
440A SER* 3.2 1.8 + - - -
441A LEU* 2.9 50.3 + - + +
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Residues in contact with LEU 438 (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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168A PRO* 4.0 6.1 - - + +
186A LYS* 3.6 43.7 - - + +
187A TYR* 3.6 39.3 - - + +
189A MET* 3.5 27.8 - - + -
434A GLY 3.1 14.0 + - - +
435A ARG 3.5 10.3 - - - +
436A LYS 3.3 0.2 - - - -
437A LEU* 1.3 73.4 - - - +
439A GLU* 1.3 66.2 + - - +
441A LEU* 3.4 2.9 + - - -
442A MET* 2.9 42.4 + - + +
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Residues in contact with GLU 439 (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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435A ARG 3.2 11.4 + - - +
436A LYS* 3.2 13.2 + - + +
438A LEU* 1.3 80.5 - - - +
440A SER* 1.3 61.3 + - - +
442A MET* 3.3 13.2 + - - +
443A LYS* 3.6 23.2 + - + +
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Residues in contact with SER 440 (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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410A GLY* 2.7 32.4 + - - -
413A ASN* 3.5 23.7 + - - +
414A MET* 3.7 10.9 + - - -
436A LYS 3.1 13.3 + - - -
437A LEU* 3.6 4.3 - - - -
439A GLU* 1.3 78.1 - - - +
441A LEU* 1.3 59.0 + - - +
443A LYS* 3.2 30.9 + - - +
444A THR* 3.8 1.2 + - - -
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Residues in contact with LEU 441 (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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168A PRO* 3.6 31.6 - - + -
170A ILE* 3.9 12.8 - - + -
189A MET* 3.7 16.6 - - + -
406A SER 3.1 34.3 - - - +
407A MET* 3.8 18.4 - - - +
410A GLY* 3.5 12.6 - - - -
437A LEU* 2.9 32.3 + - + +
438A LEU 4.0 1.8 - - - +
440A SER* 1.3 71.8 - - - +
442A MET* 1.3 58.3 + - - +
443A LYS 3.0 5.4 - - - -
444A THR* 2.5 26.4 + - - +
456A PHE* 3.0 15.0 - - + -
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Residues in contact with MET 442 (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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182A LYS* 4.9 10.1 - - + -
186A LYS 5.4 1.1 - - - +
189A MET* 3.8 25.8 - - - +
438A LEU* 2.9 38.5 + - + +
439A GLU* 3.7 7.4 - - - +
440A SER 3.2 0.6 - - - -
441A LEU* 1.3 76.1 - - - +
443A LYS* 1.3 60.0 + - + +
444A THR 3.4 1.7 + - - -
456A PHE* 4.3 18.6 - - - +
457A ASP 3.9 12.6 - - - +
458A GLU* 3.2 28.7 - - - +
459A ASN 4.7 0.7 - - - -
460A GLY* 3.9 10.5 - - - +
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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