Contacts of the helix formed by residues 401 - 413 (chain A) in PDB entry 5E97
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 401 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357A ASP* 3.7 28.5 - - + +
392A HIS* 3.3 47.8 - - + +
393A LEU* 2.9 16.4 + - - +
395A ASP* 4.2 23.3 - - + +
399A ASP 4.3 4.7 - - - +
400A PRO* 1.3 76.8 - - - +
402A PRO* 1.4 74.9 - - + +
403A ASP* 3.2 4.7 - - + +
404A TYR* 2.9 16.0 + - - +
405A TRP* 3.4 8.1 + - - -
491A LYS* 3.8 32.5 - - + +
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Residues in contact with PRO 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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357A ASP 3.7 12.3 - - - +
358A THR 4.0 1.6 - - - -
359A PHE* 3.7 36.8 - - + +
401A LEU* 1.4 89.6 - - + +
403A ASP* 1.3 58.9 + - - +
405A TRP* 3.1 6.3 + - + +
406A LEU* 2.9 27.6 + - - +
480A LEU* 5.8 0.3 - - - +
490A SER 3.7 1.1 - - - +
491A LYS 3.3 32.1 - - - +
492A SER 4.0 8.7 - - - +
493A VAL* 4.3 23.5 - - + +
529A TYR* 5.1 3.4 - - - +
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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
----------------------------------------------------------
356A SER 5.1 1.3 - - - +
357A ASP 6.2 0.4 - - - -
358A THR 4.4 2.9 + - - +
361A ALA* 3.7 20.0 - - - +
362A GLY* 3.2 29.8 + - - -
365A TRP* 3.8 10.8 - - + +
382A ARG* 2.8 33.8 + - - +
392A HIS 5.4 1.6 - - - +
393A LEU* 3.6 19.7 - - + -
401A LEU* 3.2 3.0 + - + +
402A PRO* 1.3 75.6 - - - +
404A TYR* 1.4 56.4 + - - +
406A LEU* 3.8 8.2 - - - +
407A SER* 2.7 37.2 + - - -
529A TYR* 4.9 0.7 + - - -
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Residues in contact with TYR 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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385A PHE* 4.1 6.7 - + - -
393A LEU* 3.3 28.7 + - + +
394A VAL* 4.2 15.3 - - + -
400A PRO* 3.5 20.6 - - + -
401A LEU 2.9 12.2 + - - +
403A ASP* 1.4 77.9 - - - +
405A TRP* 1.3 67.1 + + - +
407A SER* 3.1 4.9 + - - -
408A LEU* 2.8 38.9 + - + +
508A LEU* 3.8 20.9 - - + +
83B LEU* 2.7 55.7 + - + -
86B GLY* 3.8 11.4 - - - -
87B LEU* 4.0 24.7 - - + -
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Residues in contact with TRP 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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400A PRO* 3.4 38.5 + - + +
401A LEU 3.5 22.4 - - - -
402A PRO 3.1 6.1 + - - +
404A TYR* 1.3 80.5 - + - +
406A LEU* 1.3 63.0 + - - +
408A LEU* 3.3 27.9 + - + +
409A LEU* 3.0 30.7 + - + +
480A LEU* 5.3 0.9 - - + -
491A LYS 6.2 0.2 - - - -
492A SER* 6.4 0.2 - - - -
493A VAL* 3.7 23.6 - - + -
500A LEU* 3.6 42.2 + - + +
501A LYS* 3.8 21.3 - - - -
502A MET* 3.9 13.2 - - - -
508A LEU* 4.1 4.3 - - + -
509A PRO* 3.5 40.6 - - + -
511A LEU* 4.7 2.7 - - + -
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Residues in contact with LEU 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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362A GLY* 3.7 37.9 - - - +
365A TRP* 3.9 16.4 - - + -
366A LEU* 4.2 17.3 - - + -
369A LEU* 6.0 1.1 - - + -
402A PRO 2.9 16.1 + - - +
403A ASP* 3.8 11.0 - - - +
405A TRP* 1.3 78.1 - - - +
407A SER* 1.3 56.2 + - - +
409A LEU* 3.4 2.1 + - - +
410A PHE* 2.9 30.0 + - + +
480A LEU* 3.9 22.7 - - + +
529A TYR* 4.1 16.8 - - + +
531A PHE* 3.9 26.0 - - + -
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Residues in contact with SER 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A TRP* 2.8 24.5 + - - +
369A LEU* 5.9 0.2 - - - -
393A LEU* 4.1 11.5 - - - +
403A ASP 2.7 24.8 + - - -
404A TYR* 3.4 6.5 - - - -
406A LEU* 1.3 76.2 - - - +
408A LEU* 1.3 57.9 + - - +
410A PHE* 3.3 2.5 + - - +
411A LYS* 2.9 29.5 + - - +
57B LEU* 3.7 26.3 - - - +
87B LEU* 4.0 14.3 - - - +
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Residues in contact with LEU 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A TYR* 2.8 26.2 + - + +
405A TRP* 3.3 34.7 + - + +
407A SER* 1.3 73.9 - - - +
409A LEU* 1.3 65.2 + - - +
411A LYS* 3.3 3.2 + - - +
412A LYS* 2.9 45.2 + - - +
508A LEU* 4.1 20.4 - - + -
509A PRO 5.4 0.9 - - - +
511A LEU* 4.0 22.7 - - + -
86B GLY* 3.2 40.2 - - - +
87B LEU* 3.9 5.8 - - + +
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Residues in contact with LEU 409 (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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405A TRP 3.0 21.6 + - - +
406A LEU 3.8 3.6 - - - +
408A LEU* 1.3 76.7 - - - +
410A PHE* 1.3 62.7 + - - +
412A LYS* 3.2 1.3 + - - -
413A LEU* 3.0 38.5 + - + +
478A TYR* 3.8 31.6 - - + -
480A LEU* 3.6 39.5 - - + -
495A LEU* 4.0 16.2 - - + -
500A LEU* 4.4 4.7 - - + -
511A LEU* 3.8 27.4 - - + -
531A PHE* 3.9 16.4 - - + -
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Residues in contact with PHE 410 (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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366A LEU* 3.6 19.3 - - + -
369A LEU* 3.8 29.8 - - + -
406A LEU* 2.9 18.8 + - + +
407A SER* 3.5 5.4 - - - +
408A LEU 3.2 0.2 - - - -
409A LEU* 1.3 74.7 - - - +
411A LYS* 1.3 65.3 + - - +
414A VAL* 2.9 52.8 + - + +
436A HIS* 4.6 0.7 - + - -
453A TYR* 3.5 41.5 - + - -
531A PHE* 3.8 17.2 - + + -
56B PHE* 3.8 28.9 - + - -
57B LEU* 4.0 19.3 - - + -
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Residues in contact with LYS 411 (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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407A SER 2.9 16.7 + - - +
408A LEU* 3.4 9.0 - - - +
410A PHE* 1.3 81.1 - - - +
412A LYS* 1.3 68.0 - - + +
414A VAL 4.4 3.3 - - - +
439A ASN* 2.9 23.7 + - - +
54B PRO 4.0 10.6 + - - +
55B SER* 4.5 0.4 - - - +
57B LEU* 2.8 42.7 + - - +
86B GLY 3.9 18.6 - - - +
87B LEU* 3.0 22.4 + - + +
88B SER 4.0 9.2 - - - +
89B PRO* 2.7 31.2 + - + +
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Residues in contact with LYS 412 (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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408A LEU* 2.9 30.9 + - - +
409A LEU 3.2 3.6 + - - +
411A LYS* 1.3 87.6 - - + +
413A LEU* 1.3 59.9 + - + +
439A ASN* 3.5 11.8 + - - +
442A ASN* 3.0 37.7 + - - +
508A LEU* 5.9 1.6 - - - -
511A LEU* 4.1 20.2 - - + -
85B ARG 5.1 0.8 + - - -
86B GLY* 2.9 32.1 + - - -
88B SER 4.3 6.9 + - - -
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Residues in contact with LEU 413 (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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409A LEU* 3.0 25.6 + - + +
412A LYS* 1.3 83.0 - - + +
414A VAL* 1.3 62.2 - - + +
438A THR* 3.5 3.3 - - - +
439A ASN* 3.1 16.8 + - - +
442A ASN* 3.6 22.0 - - - +
445A TYR* 3.9 10.8 - - + -
451A THR* 2.8 33.7 + - + +
478A TYR* 3.6 54.5 - - + +
531A PHE* 3.7 23.3 - - + -
533A VAL* 4.0 4.5 - - + -
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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