Contacts of the helix formed by residues 343 - 352 (chain A) in PDB entry 3K1L
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 LEU 343 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A ILE* 3.6 12.1 - - + -
327A VAL* 4.1 23.8 - - + -
336A LEU* 5.8 3.4 - - + -
338A CYS* 3.8 25.1 - - + -
339A HIS 3.4 2.8 + - - +
340A ALA 2.8 9.7 + - - +
341A VAL 2.8 1.2 - - - -
342A CYS* 1.3 80.0 - - - +
344A GLU* 1.3 64.5 + - - +
345A GLU* 3.2 4.3 + - - -
346A TRP* 3.2 17.4 + - + +
347A PHE* 3.1 35.0 + - + -
365A PRO* 5.4 5.2 - - + -
371A LEU* 4.8 9.6 - - + -
16B PRO* 3.3 39.0 - - + -
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Residues in contact with GLU 344 (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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340A ALA 3.1 5.9 + - - -
341A VAL* 2.9 30.5 + - - +
342A CYS 3.6 0.2 - - - -
343A LEU* 1.3 77.0 - - - +
345A GLU* 1.3 80.3 + - - +
347A PHE* 3.3 5.7 + - - +
348A LYS* 3.1 46.6 + - + +
379A LEU* 3.8 30.8 - - + +
380A ASN 5.2 2.9 + - - -
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Residues in contact with GLU 345 (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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341A VAL 4.8 2.1 - - - +
342A CYS 5.5 1.2 - - - +
343A LEU* 3.3 1.1 - - - -
344A GLU* 1.3 90.1 + - - +
346A TRP* 1.3 55.6 + - - +
348A LYS* 2.6 13.4 + - - +
349A THR* 2.6 41.2 + - + +
12B CYS* 5.0 2.9 - - - -
387B AU 4.4 10.3 - - - -
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Residues in contact with TRP 346 (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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343A LEU* 3.2 27.4 + - + +
345A GLU* 1.3 76.0 - - - +
347A PHE* 1.3 97.0 + + - +
349A THR* 3.4 12.7 - - + +
350A LEU* 3.0 45.7 + - + +
362A GLY* 3.6 25.6 - - - -
363A GLN 3.3 33.1 + - - -
365A PRO* 4.2 7.5 - - + +
371A LEU* 3.9 24.2 - - + -
12B CYS 3.4 22.0 - - - -
13B GLN* 3.2 19.2 + - - -
16B PRO* 3.8 13.7 - - + -
387B AU 4.1 9.7 - - - -
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Residues in contact with PHE 347 (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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327A VAL* 4.2 20.2 - - + -
340A ALA* 4.2 9.9 - - - -
343A LEU* 3.1 38.9 + - + -
344A GLU 3.5 7.2 - - - +
345A GLU 2.8 2.2 + - - -
346A TRP* 1.3 103.5 - + - +
348A LYS* 1.3 59.3 + - + +
350A LEU* 4.2 1.6 - - - +
351A MET* 3.1 34.2 + - - +
371A LEU* 4.9 2.0 - - + -
372A SER 4.0 17.3 - - - -
373A THR* 4.1 14.8 - - + -
375A PHE* 3.4 30.3 - + + -
376A ALA* 4.2 19.3 - - + -
379A LEU* 4.0 17.7 - - + -
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Residues in contact with LYS 348 (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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344A GLU* 3.1 45.1 + - + +
345A GLU* 2.6 14.3 + - - +
347A PHE* 1.3 75.4 - - + +
349A THR* 1.3 54.3 + - - +
350A LEU 3.0 4.9 - - - -
351A MET* 4.5 3.1 - - + +
352A ASP* 2.9 37.5 + - - +
376A ALA* 6.4 0.7 - - + -
379A LEU* 4.4 13.8 - - + +
380A ASN* 5.6 4.3 - - - +
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Residues in contact with THR 349 (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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345A GLU* 2.6 27.4 + - - +
346A TRP* 3.4 15.0 - - + +
348A LYS* 1.3 72.4 - - - +
350A LEU* 1.3 57.7 + - + +
352A ASP* 4.6 9.0 - - - +
12B CYS* 3.3 34.8 - - - -
13B GLN* 4.7 12.1 + - + +
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Residues in contact with LEU 350 (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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346A TRP* 3.0 38.5 + - + +
347A PHE 4.2 2.7 - - - +
348A LYS 3.0 0.6 - - - -
349A THR* 1.3 82.1 - - + +
351A MET* 1.3 58.5 + - - +
352A ASP* 3.3 9.6 + - - +
354A LYS* 4.4 5.9 + - - -
359A VAL* 3.9 15.0 - - + +
361A PHE 3.6 9.9 - - - +
362A GLY* 3.6 33.7 - - - -
363A GLN 5.4 0.2 - - - +
373A THR* 3.7 20.4 - - + -
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Residues in contact with MET 351 (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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347A PHE* 3.1 21.9 + - - +
348A LYS* 3.8 3.6 - - + -
350A LEU* 1.3 78.7 - - + +
352A ASP* 1.3 63.6 + - - +
353A GLY 3.2 1.6 + - - -
354A LYS* 2.5 30.1 - - - +
355A THR 3.6 5.6 - - - +
356A PHE* 3.5 24.2 - - + +
359A VAL* 3.4 30.1 - - + +
373A THR* 3.2 37.9 - - + +
376A ALA* 4.0 20.2 - - - -
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Residues in contact with ASP 352 (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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348A LYS* 2.9 20.8 + - - +
349A THR* 4.7 7.9 - - - +
350A LEU 3.3 5.3 - - - +
351A MET* 1.3 73.6 - - - +
353A GLY* 1.3 52.1 + - - +
354A LYS* 2.6 43.7 + - - +
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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