Contacts of the helix formed by residues 382 - 395 (chain A) in PDB entry 4LT6
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 THR 382 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A ALA* 4.1 0.5 - - - +
381A SER* 1.3 88.4 + - - +
383A GLU* 1.3 53.0 + - - +
384A GLU* 3.1 29.5 + - - +
385A ASN* 3.1 22.1 + - - +
386A HIS* 2.7 30.7 + - - +
432A TYR* 3.2 13.3 - - - -
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Residues in contact with GLU 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A THR* 1.3 71.0 - - - +
384A GLU* 1.3 69.9 + - + +
386A HIS* 2.8 18.8 + - - +
387A LEU* 3.0 20.2 + - - +
432A TYR* 3.1 38.8 + - + +
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Residues in contact with GLU 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A THR* 3.1 26.1 + - - +
383A GLU* 1.3 80.3 + - + +
385A ASN* 1.3 65.9 + - - +
386A HIS 3.5 0.2 + - - -
387A LEU* 4.0 6.1 + - - +
388A GLU* 3.5 23.0 + - - +
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Residues in contact with ASN 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ALA* 3.6 8.1 - - + +
381A SER* 3.0 22.6 + - - -
382A THR* 3.1 35.6 + - - +
383A GLU 3.0 0.8 - - - -
384A GLU* 1.3 82.9 - - - +
386A HIS* 1.3 63.8 + - - +
388A GLU* 3.8 4.3 + - - +
389A TRP* 3.3 21.5 + - - +
477A LYS* 3.9 27.2 - - - +
478A GLU 3.9 11.7 + - - -
480A MET* 3.8 15.5 - - - +
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Residues in contact with HIS 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ALA 3.7 7.2 - - - -
379A SER 4.4 0.4 - - - -
380A ALA* 3.4 14.1 + - + +
382A THR 2.7 16.2 + - - +
383A GLU* 2.8 10.6 + - - +
385A ASN* 1.3 72.5 - - - +
387A LEU* 1.3 70.2 + - - +
388A GLU 2.8 1.7 + - - -
389A TRP* 2.9 14.5 + - - +
390A VAL* 2.9 37.8 + - + +
432A TYR* 3.6 27.9 + + + -
433A VAL* 3.3 28.2 + - - -
434A SER* 2.8 26.1 + - - -
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Residues in contact with LEU 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ARG* 6.2 2.0 - - - +
383A GLU* 3.0 15.4 + - - +
384A GLU* 4.4 5.6 - - - +
386A HIS* 1.3 81.1 - - - +
388A GLU* 1.3 64.0 + - - +
390A VAL* 4.0 9.1 - - - +
391A GLY* 3.2 17.5 + - - -
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Residues in contact with GLU 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A GLU 3.5 18.4 + - - +
385A ASN* 4.1 5.1 - - - +
386A HIS 2.8 4.8 + - - -
387A LEU* 1.3 75.5 - - - +
389A TRP* 1.3 59.7 + - - +
391A GLY* 3.0 16.3 + - - -
392A LEU* 3.0 12.0 + - - +
475A MET* 3.4 25.1 - - + +
477A LYS* 2.6 36.2 + - - +
480A MET* 5.2 0.7 - - - +
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Residues in contact with TRP 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ALA* 4.4 6.1 - - + -
379A SER 3.1 30.3 + - - +
380A ALA* 4.4 1.6 - - + -
385A ASN 3.3 16.1 + - - +
386A HIS* 2.9 4.5 + - - +
388A GLU* 1.3 75.3 - - - +
390A VAL* 1.3 58.9 + - - +
391A GLY 3.0 1.6 - - - -
392A LEU* 2.8 52.1 + - + +
393A VAL* 2.9 26.1 + - + +
466A VAL* 3.9 20.0 - - + -
467A TYR* 4.0 18.8 - + - -
470A ALA* 4.1 10.8 - - + -
475A MET* 3.8 5.8 - - + +
476A LEU* 4.8 1.6 - - + -
480A MET* 3.6 40.6 - - + -
481A LYS 2.8 24.9 + - - -
482A ILE* 3.5 24.7 - - + -
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Residues in contact with VAL 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ALA* 4.7 5.8 - - + -
386A HIS* 2.9 51.4 + - + +
387A LEU* 4.0 8.1 - - - +
389A TRP* 1.3 75.7 - - + +
391A GLY* 1.3 63.9 + - - +
393A VAL* 3.9 6.9 - - - +
394A GLU* 3.0 27.5 + - + +
434A SER* 3.5 16.8 - - - +
436A TRP* 4.2 17.9 - - + -
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Residues in contact with GLY 391 (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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239A MET* 5.5 0.5 - - - +
387A LEU 3.2 11.9 + - - -
388A GLU 3.0 10.9 + - - -
390A VAL* 1.3 82.2 - - - +
392A LEU* 1.3 61.6 + - - +
394A GLU* 3.7 4.9 - - - +
395A SER* 3.1 21.8 + - - -
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Residues in contact with LEU 392 (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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388A GLU 3.0 9.3 + - - +
389A TRP* 2.8 41.8 + - + +
391A GLY* 1.3 70.5 - - - +
393A VAL* 1.3 64.2 + - - +
395A SER* 2.7 24.1 + - - +
396A LYS* 3.2 36.5 - - + +
466A VAL* 4.5 9.2 - - + +
469A GLN 5.6 0.9 - - - -
470A ALA* 3.6 27.6 - - + +
473A ILE* 4.7 14.6 - - + -
475A MET* 3.6 18.8 - - + -
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Residues in contact with VAL 393 (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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376A LEU* 4.3 12.1 - - + -
378A ALA* 4.1 13.0 - - + -
389A TRP* 2.9 54.6 + - + +
390A VAL* 3.9 3.6 - - - +
392A LEU* 1.3 71.6 - - - +
394A GLU* 1.3 55.9 + - - +
396A LYS* 2.6 31.9 + - - +
397A ILE* 3.2 9.1 + - + -
436A TRP* 3.7 26.0 - - + -
462A PHE* 5.1 1.5 - - + -
466A VAL* 4.6 5.2 - - + -
482A ILE* 3.7 25.6 - - + -
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Residues in contact with GLU 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A MET* 3.1 35.4 - - - +
240A LEU* 3.9 23.2 - - + +
390A VAL* 3.0 19.1 + - + +
391A GLY* 3.7 4.5 - - - +
393A VAL* 1.3 79.9 - - - +
395A SER* 1.3 57.6 + - - +
396A LYS 3.2 4.3 + - - -
397A ILE* 3.5 25.8 + - + +
398A ARG 4.8 0.7 + - - -
417A PRO 5.3 1.9 - - - +
419A SER* 6.1 0.2 - - - -
436A TRP* 4.0 28.2 + - + +
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Residues in contact with SER 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A MET* 3.9 25.9 - - - +
391A GLY 3.1 12.1 + - - -
392A LEU* 2.7 23.4 + - - +
393A VAL 3.0 1.4 + - - -
394A GLU* 1.3 75.0 - - - +
396A LYS* 1.3 77.1 + - - +
397A ILE 3.7 0.2 - - - -
398A ARG* 4.3 17.0 + - - +
399A VAL* 5.7 0.9 - - - +
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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