Contacts of the helix formed by residues 388 - 408 (chain A) in PDB entry 4BPW
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 388 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR* 4.4 7.2 - - + -
20A LEU* 3.9 22.4 - - + +
22A PRO* 4.8 2.0 - - + -
321A PHE* 4.2 16.8 - - + -
330A ILE* 3.9 33.7 - - + -
332A VAL* 4.2 11.0 - - + -
348A PRO* 4.7 2.7 - - + -
353A ILE* 4.0 30.0 - - + +
383A TYR* 4.6 7.9 - - + +
386A THR* 3.0 12.9 - - - +
387A SER* 1.3 78.5 - - - +
389A ALA* 1.3 66.3 + - - +
390A PRO* 3.5 0.7 - - - -
391A TYR* 3.3 15.9 + - + +
392A VAL* 3.3 21.8 + - + +
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Residues in contact with ALA 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A TYR* 3.9 8.6 + - + -
384A LYS* 3.6 39.3 - - + +
386A THR 3.4 7.5 + - - +
388A LEU* 1.3 77.5 - - - +
390A PRO* 1.3 66.5 - - + +
392A VAL* 2.8 27.6 + - - +
393A LYS* 3.0 25.6 + - - +
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Residues in contact with PRO 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A THR 4.6 0.7 - - - +
387A SER* 3.4 19.5 - - - +
388A LEU 3.6 0.4 - - - -
389A ALA* 1.3 95.6 - - + +
391A TYR* 1.3 71.5 + - + +
393A LYS* 3.4 32.0 - - + +
394A VAL* 3.3 20.1 - - - +
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Residues in contact with TYR 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A PHE* 4.5 3.4 - - + -
332A VAL* 3.8 30.5 - - + -
333A PRO* 3.6 44.6 - - + +
342A PHE* 5.0 9.2 - + - -
346A THR* 4.1 10.4 + - - -
347A VAL* 4.1 5.4 - - - +
348A PRO* 3.2 39.6 - - + +
387A SER 3.6 16.2 - - - -
388A LEU* 3.3 11.6 + - + +
389A ALA 3.0 1.0 - - - -
390A PRO* 1.3 83.2 - - + +
392A VAL* 1.3 66.2 + - - +
393A LYS 3.1 1.6 - - - -
394A VAL* 3.3 11.0 + - + +
395A PHE 3.1 16.5 + - - -
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Residues in contact with VAL 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PRO* 4.1 14.1 - - + -
25A GLN* 3.6 37.2 - - + +
321A PHE* 4.0 24.0 - - + -
383A TYR* 3.8 27.8 - - + -
388A LEU* 3.4 22.9 - - + +
389A ALA 2.8 7.4 + - - +
391A TYR* 1.3 75.6 - - - +
393A LYS* 1.3 57.9 + - + +
395A PHE* 3.2 3.1 + - + +
396A GLU* 2.8 32.0 + - - +
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Residues in contact with LYS 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A LYS* 6.2 6.1 - - - +
389A ALA* 3.0 22.4 + - - +
390A PRO* 3.4 34.6 - - + +
391A TYR 3.1 0.2 - - - -
392A VAL* 1.3 77.6 - - - +
394A VAL* 1.3 52.6 + - + +
396A GLU* 3.0 17.6 + - - +
397A HIS* 2.8 34.2 + - - +
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Residues in contact with VAL 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LEU* 5.3 4.0 - - + -
333A PRO* 4.1 18.8 - - + +
334A ILE 4.1 16.6 - - - +
335A ASP* 4.1 31.2 - - + +
390A PRO 3.3 15.7 - - - +
391A TYR* 3.5 12.3 - - + +
393A LYS* 1.3 75.3 - - + +
395A PHE* 1.3 60.8 + - - +
397A HIS* 3.3 9.3 + - + +
398A PHE* 2.9 27.3 + - + +
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Residues in contact with PHE 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PRO* 5.4 0.7 - - + -
25A GLN* 3.6 38.1 - - + -
26A TYR* 4.1 8.3 - + - -
29A TRP* 3.5 36.8 - + + -
156A LEU* 3.7 24.2 - - + -
320A PRO* 5.4 1.3 - - + -
321A PHE* 3.4 31.2 - + + -
333A PRO* 4.0 10.7 - - + +
391A TYR 3.1 12.3 + - - +
392A VAL* 3.2 8.5 + - + +
394A VAL* 1.3 77.9 - - - +
396A GLU* 1.3 58.3 + - - +
398A PHE* 3.2 36.8 + + - +
399A LEU* 2.8 34.6 + - + +
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Residues in contact with GLU 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLN* 2.7 44.1 + - + +
28A ARG* 4.2 12.6 + - - +
383A TYR* 3.1 8.9 + - - -
384A LYS* 5.1 8.6 + - - -
392A VAL* 2.8 17.4 + - - +
393A LYS* 3.3 21.5 - - - +
395A PHE* 1.3 74.4 - - - +
397A HIS* 1.3 53.7 + - - +
399A LEU* 2.9 9.4 + - - +
400A GLU* 2.6 49.1 + - - +
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Residues in contact with HIS 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A LYS 2.8 16.2 + - - +
394A VAL* 3.7 13.7 - - + +
396A GLU* 1.3 72.3 - - - +
398A PHE* 1.3 62.4 + - - +
400A GLU* 3.9 19.1 + - - +
401A ASN* 3.3 47.7 + - - -
404A LYS* 6.2 0.2 - - - -
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Residues in contact with PHE 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TRP* 3.5 26.0 - + - -
154A HIS* 3.8 34.7 + - + -
155A ARG 4.0 11.9 - - - +
156A LEU* 4.1 27.4 - - + -
170A CYS* 3.5 25.8 - - - -
394A VAL* 2.9 14.4 + - + +
395A PHE* 3.2 35.9 - + - +
397A HIS* 1.3 81.8 - - - +
399A LEU* 1.3 63.7 + - + +
401A ASN* 3.7 5.3 + - - +
402A LEU* 3.4 31.2 + - + +
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Residues in contact with LEU 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLN* 3.1 44.9 - - + +
28A ARG* 3.5 32.1 - - + +
29A TRP* 3.5 35.9 - - + +
395A PHE* 2.8 23.9 + - + +
396A GLU* 2.9 8.0 + - - +
398A PHE* 1.3 87.3 - - + +
400A GLU* 1.3 64.5 + - - +
402A LEU* 3.2 21.5 + - + +
403A ASP* 3.2 17.3 + - - +
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Residues in contact with GLU 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG* 3.9 13.6 + - - +
396A GLU* 2.6 31.4 + - - +
397A HIS* 3.9 21.1 + - - +
399A LEU* 1.3 72.5 - - - +
401A ASN* 1.3 66.2 + - - +
403A ASP* 3.1 17.9 + - - +
404A LYS* 3.2 30.5 + - - +
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Residues in contact with ASN 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LYS 5.8 1.5 + - - +
154A HIS* 3.4 21.4 - - + +
397A HIS* 3.3 46.3 + - - +
398A PHE* 4.0 5.3 - - - +
399A LEU 3.3 0.6 - - - -
400A GLU* 1.3 80.5 - - - +
402A LEU* 1.3 61.6 + - - +
404A LYS* 3.7 26.9 + - - +
405A SER* 3.3 15.4 + - - -
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Residues in contact with LEU 402 (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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28A ARG 5.9 0.2 - - - +
29A TRP* 4.3 9.0 - - + +
32A TYR* 4.4 15.5 - - + -
154A HIS* 3.1 41.1 - - + +
170A CYS* 4.5 11.7 - - + +
175A ARG* 5.4 0.4 - - - +
398A PHE* 3.4 40.6 + - + +
399A LEU* 3.2 21.0 + - + +
400A GLU 3.1 0.8 - - - -
401A ASN* 1.3 76.6 - - - +
403A ASP* 1.3 64.0 + - - +
405A SER* 2.5 22.2 + - - +
406A ARG* 3.1 25.8 + - - +
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Residues in contact with ASP 403 (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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28A ARG* 2.9 31.5 + - - -
33A GLY* 5.1 0.5 - - - -
399A LEU 3.2 6.4 + - - +
400A GLU* 3.1 9.6 + - - +
402A LEU* 1.3 77.7 - - - +
404A LYS* 1.3 63.5 + - + +
406A ARG* 2.2 45.6 + - - +
407A LYS* 3.0 46.4 + - - +
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Residues in contact with LYS 404 (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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397A HIS* 6.2 0.8 - - - -
400A GLU* 3.2 28.8 + - - +
401A ASN* 3.9 24.8 + - - +
402A LEU 3.3 0.2 - - - -
403A ASP* 1.3 75.2 - - + +
405A SER* 1.3 53.6 + - - +
407A LYS* 3.3 9.4 + - + +
408A GLY 2.7 31.2 + - - -
409A GLU* 3.1 39.0 + - + +
410A LEU 3.8 16.7 + - - +
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Residues in contact with SER 405 (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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153A LYS* 6.3 1.6 - - - -
154A HIS* 3.2 35.1 + - - -
401A ASN 3.3 2.9 + - - -
402A LEU* 2.5 23.4 + - - +
404A LYS* 1.3 79.1 - - - +
406A ARG* 1.3 65.2 + - - +
408A GLY* 3.6 10.2 + - - +
409A GLU 4.0 2.9 + - - -
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Residues in contact with ARG 406 (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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28A ARG 5.0 4.8 + - - -
32A TYR* 3.1 57.9 + - - +
33A GLY* 3.4 18.2 - - - +
35A VAL* 3.8 25.5 - - + +
172A GLU* 5.5 6.1 - - - +
402A LEU* 3.1 21.0 + - - +
403A ASP* 2.2 45.3 + - - +
405A SER* 1.3 83.4 + - - +
407A LYS* 1.3 65.2 + - + +
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Residues in contact with LYS 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A ASP* 3.0 35.1 + - - +
404A LYS* 3.6 9.2 - - + +
406A ARG* 1.3 81.2 - - + +
408A GLY* 1.3 58.6 + - - +
409A GLU* 3.8 20.0 - - + +
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Residues in contact with GLY 408 (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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404A LYS 2.7 9.1 + - - -
405A SER* 3.6 9.0 + - - -
407A LYS* 1.3 75.6 - - - +
409A GLU* 1.3 68.0 + - - +
410A LEU* 3.5 12.3 + - - +
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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