Contacts of the helix formed by residues 424 - 444 (chain A) in PDB entry 4BHT
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 ASN 424 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A GLN* 3.5 19.0 + - - +
417A GLY* 2.8 25.3 + - - +
422A GLN 3.4 3.0 + - - +
423A THR* 1.3 73.2 - - - +
425A TYR* 1.3 56.3 + - - +
426A VAL* 3.1 12.4 + - - +
427A GLN* 2.9 40.1 + - + +
428A GLY 2.9 23.9 + - - -
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Residues in contact with TYR 425 (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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218A PHE* 3.9 12.8 - + + -
222A MET* 3.4 33.1 - - + +
225A ARG* 3.9 2.8 - - - -
226A HIS* 3.4 19.3 - + - -
360A GLN* 5.3 1.2 - - - +
365A LEU* 5.2 3.4 - - + -
366A PHE 3.4 27.2 + - - +
367A ALA* 4.3 1.3 - - - -
368A PRO* 3.5 13.6 - - + +
410A HIS* 3.2 36.5 + + - -
413A CYS* 3.7 22.2 - - + -
414A VAL* 4.4 2.2 - - + -
423A THR* 3.5 37.7 + - + -
424A ASN* 1.3 69.9 + - - +
426A VAL* 1.3 61.3 + - - +
428A GLY* 3.8 2.7 - - - +
429A ALA* 2.9 33.3 + - - +
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Residues in contact with VAL 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 4.7 11.9 - - + +
34A THR* 4.3 13.9 - - - +
356A THR* 4.8 5.6 - - + -
360A GLN* 3.8 19.3 - - - +
366A PHE* 4.0 18.6 - - + -
368A PRO* 3.9 22.7 - - + -
370A LYS* 6.2 4.7 - - + -
424A ASN* 3.1 7.5 + - - +
425A TYR* 1.3 77.5 - - - +
427A GLN* 1.3 68.2 + - - +
429A ALA* 4.3 0.7 - - - +
430A ASN* 3.2 29.8 + - - +
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Residues in contact with GLN 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 3.4 22.0 - - + +
416A HIS 3.0 21.1 + - - +
417A GLY 3.9 1.2 - - - -
418A GLY* 3.8 17.6 - - - +
424A ASN* 2.9 32.9 + - - +
426A VAL* 1.3 80.1 - - - +
428A GLY* 1.3 61.3 - - - +
431A ILE* 3.1 40.1 + - + +
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Residues in contact with GLY 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A CYS* 3.3 30.4 - - - -
416A HIS* 3.6 16.0 + - - +
424A ASN 2.9 13.7 + - - -
425A TYR 4.0 0.9 - - - -
427A GLN* 1.3 77.5 - - - +
429A ALA* 1.3 55.0 + - - +
431A ILE* 4.0 1.0 - - - +
432A ALA* 2.9 33.1 + - - +
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Residues in contact with ALA 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A PHE* 5.6 2.3 - - - +
119A LEU* 4.0 15.8 - - + +
368A PRO* 4.6 5.4 - - + -
370A LYS* 4.9 7.9 - - + -
371A ALA* 4.0 19.5 - - + +
413A CYS* 3.7 22.6 - - - -
425A TYR 2.9 19.9 + - - +
426A VAL 4.3 1.1 - - - +
428A GLY* 1.3 75.3 - - - +
430A ASN* 1.3 64.5 + - - +
432A ALA* 4.7 1.6 - - - -
433A GLY* 3.2 19.8 + - - -
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Residues in contact with ASN 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 4.0 10.1 + - - +
31A VAL* 4.1 18.1 - - + +
34A THR* 3.3 38.0 + - + +
35A LEU* 4.1 7.7 - - + +
115A PHE* 5.2 6.2 - - - +
370A LYS* 3.6 34.9 + - - +
426A VAL* 3.2 23.6 + - - +
427A GLN 3.3 0.2 + - - -
429A ALA* 1.3 78.2 - - - +
431A ILE* 1.3 59.4 + - - +
433A GLY* 3.9 0.5 - - - -
434A PHE* 2.9 30.0 + - - +
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Residues in contact with ILE 431 (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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34A THR* 4.4 9.6 - - + +
35A LEU* 3.8 20.9 - - + -
38A PHE* 3.6 51.4 - - + +
416A HIS* 3.6 34.8 - - + +
427A GLN* 3.1 39.2 + - + +
430A ASN* 1.3 76.3 - - - +
432A ALA* 1.3 58.2 + - - +
434A PHE* 3.3 1.2 + - - +
435A VAL* 2.9 29.9 + - + +
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Residues in contact with ALA 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 3.8 21.9 - - + +
412A ALA* 3.8 28.9 - - + +
413A CYS 4.5 0.2 - - - +
416A HIS* 4.0 14.1 - - + -
428A GLY 2.9 19.1 + - - +
429A ALA 4.3 0.2 - - - +
431A ILE* 1.3 79.2 - - - +
433A GLY* 1.3 61.2 + - - +
435A VAL* 3.5 3.4 + - - +
436A LYS* 3.4 19.6 + - - +
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Residues in contact with GLY 433 (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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115A PHE* 3.7 27.8 - - - -
118A ALA* 3.7 7.1 - - - +
119A LEU* 4.1 7.5 - - - +
429A ALA 3.2 18.3 + - - -
430A ASN 3.9 0.4 - - - -
432A ALA* 1.3 73.5 - - - +
434A PHE* 1.3 64.7 + - - +
436A LYS 3.6 1.2 + - - -
437A VAL* 3.4 26.9 + - - +
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Residues in contact with PHE 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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31A VAL* 5.9 1.3 - - + -
35A LEU* 3.7 31.9 - - + -
38A PHE* 4.1 11.2 - + - -
39A LEU* 3.9 17.9 - - + -
45A TYR* 3.8 38.4 - + + -
50A LEU* 4.5 2.9 - - + -
51A LEU* 3.8 17.5 - - + -
54A LEU* 3.7 30.5 - - + -
115A PHE* 3.9 14.6 - + + -
430A ASN 2.9 18.8 + - - +
431A ILE 3.6 2.7 - - - +
433A GLY* 1.3 73.9 - - - +
435A VAL* 1.3 70.7 + - + +
437A VAL* 3.4 1.7 + - - +
438A ALA* 2.9 41.7 + - + +
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Residues in contact with VAL 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PHE* 3.5 36.1 - - + -
45A TYR* 3.6 14.6 - - + +
416A HIS* 4.7 10.5 - - + +
431A ILE* 2.9 24.4 + - + +
432A ALA* 4.0 6.3 - - - +
433A GLY 3.3 0.2 - - - -
434A PHE* 1.3 79.4 - - + +
436A LYS* 1.3 59.7 + - - +
438A ALA* 3.8 3.0 - - - +
439A ASP* 3.0 46.9 + - - +
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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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88A ILE* 3.4 37.5 - - + +
118A ALA* 4.1 16.6 + - + +
121A THR* 4.3 26.3 + - - +
122A LEU 4.8 1.0 + - - -
432A ALA 3.4 10.1 + - - +
433A GLY 4.0 7.0 - - - +
434A PHE 3.2 0.2 - - - -
435A VAL* 1.3 82.4 - - - +
437A VAL* 1.3 63.1 + - - +
439A ASP* 3.5 6.4 + - + +
440A ALA* 3.3 20.0 + - - +
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Residues in contact with VAL 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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54A LEU* 3.7 28.9 - - + -
85A SER* 4.2 17.3 - - - +
87A ALA* 4.2 2.4 - - + +
88A ILE* 3.8 13.0 - - + -
114A THR* 3.9 21.8 - - + +
115A PHE* 4.1 7.6 - - + -
118A ALA* 3.5 20.6 - - + -
433A GLY 3.4 13.4 + - - +
434A PHE 3.4 6.1 + - - +
436A LYS* 1.3 75.2 - - - +
438A ALA* 1.3 57.3 + - - +
440A ALA* 3.3 3.8 + - - +
441A MET* 3.0 40.0 + - + +
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Residues in contact with ALA 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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45A TYR* 3.6 26.5 - - + -
50A LEU* 3.8 12.0 - - + +
54A LEU* 5.9 0.4 - - - +
434A PHE* 2.9 38.0 + - + +
435A VAL 3.8 2.2 - - - +
437A VAL* 1.3 75.3 - - - +
439A ASP* 1.3 64.1 + - - +
441A MET* 3.2 9.6 + - - +
442A LEU* 3.0 29.6 + - - +
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Residues in contact with ASP 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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44A LYS* 4.6 4.9 + - - -
45A TYR* 2.7 29.2 + - - -
435A VAL* 3.0 35.8 + - - +
436A LYS* 3.9 8.2 - - + +
438A ALA* 1.3 74.5 - - - +
440A ALA* 1.3 62.8 + - - +
442A LEU* 3.3 8.2 + - - +
443A ALA* 3.1 25.2 + - - +
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Residues in contact with ALA 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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87A ALA* 3.7 30.3 - - + +
88A ILE* 4.0 8.3 - - + -
436A LYS* 3.3 11.4 + - - +
437A VAL 3.3 9.1 + - - +
438A ALA 3.2 0.6 - - - -
439A ASP* 1.3 79.2 - - - +
441A MET* 1.3 64.5 + - - +
443A ALA* 3.5 4.0 + - - +
444A GLN* 3.0 35.8 + - - +
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Residues in contact with MET 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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50A LEU* 3.8 24.7 - - + +
53A ARG* 3.7 43.8 + - + +
54A LEU* 3.8 39.0 - - - +
85A SER* 5.5 1.3 - - - +
87A ALA* 3.9 17.5 - - + -
437A VAL* 3.0 25.0 + - - +
438A ALA* 3.2 8.5 + - - +
440A ALA* 1.3 78.9 - - - +
442A LEU* 1.3 62.1 + - - +
444A GLN* 3.5 10.0 + - - +
445A GLY* 3.6 15.4 + - - +
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Residues in contact with LEU 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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44A LYS* 4.0 39.3 - - + +
45A TYR* 4.3 15.0 - - + -
47A GLN* 4.7 2.0 - - + +
48A MET* 4.2 24.7 - - + -
50A LEU* 4.1 21.3 - - + -
53A ARG* 4.9 2.5 - - - +
438A ALA 3.0 19.7 + - - +
439A ASP* 3.8 8.1 - - - +
441A MET* 1.3 78.4 - - - +
443A ALA* 1.3 62.7 + - - +
444A GLN 3.3 0.7 + - - -
445A GLY* 3.5 9.0 + - - -
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Residues in contact with ALA 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A ASP 3.1 14.4 + - - +
440A ALA* 4.0 5.4 - - - +
442A LEU* 1.3 79.0 - - - +
444A GLN* 1.3 64.2 + - + +
445A GLY 3.5 0.9 + - - -
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Residues in contact with GLN 444 (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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86A SER 5.0 2.1 - - - +
87A ALA* 2.8 35.0 + - - +
440A ALA* 3.0 31.2 + - - +
441A MET* 3.5 3.8 + - - +
442A LEU 3.2 0.6 - - - -
443A ALA* 1.3 81.8 - - + +
445A GLY* 1.3 62.8 + - - +
447A ILE* 3.9 32.5 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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