Contacts of the helix formed by residues 394 - 406 (chain A) in PDB entry 4PED
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 394 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A LEU* 4.5 11.8 - - + +
280A MSE 6.4 0.4 - - + -
281A LEU* 4.3 26.2 - - + -
376A MSE 3.9 27.4 - - + -
385A LEU* 4.6 13.5 - - + -
389A LEU* 4.3 15.9 - - + -
390A PHE 3.7 17.3 - - - +
391A PRO* 3.0 10.2 + - + +
393A HIS* 1.3 80.7 - - - +
395A ILE* 1.3 65.7 + - - +
396A ASP 3.4 1.3 - - - -
397A VAL* 3.2 9.9 - - + +
398A LEU* 3.0 26.1 + - - +
595A LEU* 3.5 32.1 - - + -
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Residues in contact with ILE 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ASN 6.1 0.2 - - - +
372A VAL* 3.8 23.6 - - + +
373A ASN* 4.4 12.8 - - - +
376A MSE 3.6 25.8 - - + -
391A PRO 3.3 14.8 - - - +
392A GLU* 4.1 14.8 - - - +
393A HIS 3.6 0.8 - - - -
394A LEU* 1.3 79.4 - - - +
396A ASP* 1.3 70.9 + - - +
399A ARG* 2.9 52.4 + - - +
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Residues in contact with ASP 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A GLU 5.0 4.7 + - - +
393A HIS 5.1 2.1 - - - +
394A LEU 3.4 0.4 - - - -
395A ILE* 1.3 85.7 - - - +
397A VAL* 1.3 67.1 + - + +
399A ARG* 2.9 35.1 + - - +
400A ARG* 3.1 34.3 + - - +
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Residues in contact with VAL 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LEU* 6.1 0.2 - - + -
280A MSE 3.9 21.3 - - + -
393A HIS 4.2 6.7 + - - +
394A LEU* 3.2 25.1 - - + +
396A ASP* 1.3 80.0 - - + +
398A LEU* 1.3 64.6 + - - +
400A ARG* 3.4 2.1 + - - +
401A GLU* 3.0 29.5 + - + +
595A LEU* 4.3 14.1 - - + -
604A GLU* 4.0 13.2 - - - +
607A TYR* 3.9 46.7 - - + -
611A ARG* 5.3 3.8 - - - +
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Residues in contact with LEU 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ALA* 3.9 7.4 - - + +
276A LYS* 3.9 11.7 - - + -
277A LEU* 3.9 27.4 - - + +
280A MSE 3.7 26.2 - - - -
372A VAL* 3.8 20.2 - - + -
375A LEU* 3.6 17.5 - - + -
376A MSE 3.6 28.3 - - + -
394A LEU 3.0 19.6 + - - +
395A ILE 3.8 2.7 - - - +
397A VAL* 1.3 75.3 - - - +
399A ARG* 1.3 66.0 + - - +
401A GLU 3.3 0.5 + - - -
402A LEU* 2.8 31.4 + - + +
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Residues in contact with ARG 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A ILE* 3.8 18.6 - - + +
369A ASN* 3.2 42.4 + - - +
372A VAL* 3.9 21.1 - - + -
395A ILE* 2.9 37.6 + - - +
396A ASP* 2.9 32.4 + - - +
398A LEU* 1.3 72.4 - - - +
400A ARG* 1.3 65.3 + - + +
403A ALA* 3.2 22.2 + - - +
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Residues in contact with ARG 400 (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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396A ASP* 3.1 21.7 + - - +
397A VAL 3.9 3.4 - - - +
398A LEU 3.2 0.2 - - - -
399A ARG* 1.3 79.3 - - + +
401A GLU* 1.3 63.4 + - - +
403A ALA* 3.4 7.4 + - - +
404A LEU* 3.3 25.9 + - + +
602A PRO 5.6 1.8 + - - -
604A GLU* 2.5 58.6 + - + +
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Residues in contact with GLU 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A LYS* 3.9 19.7 + - - -
280A MSE 4.0 17.9 - - + -
397A VAL* 3.0 22.4 + - + +
398A LEU 4.0 1.8 - - - +
400A ARG* 1.3 73.2 - - - +
402A LEU* 1.3 67.1 + - - +
404A LEU* 3.2 13.2 + - - +
405A GLU* 3.0 21.3 + - - +
487A THR* 5.0 4.3 + - - -
488A ASP* 4.6 6.8 - - - +
510A ALA* 3.9 22.7 - - - +
512A ARG* 3.5 25.0 + - - -
604A GLU* 4.3 12.5 - - - +
608A SER* 3.8 14.4 + - - -
611A ARG* 4.4 11.7 - - - +
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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
----------------------------------------------------------
272A GLY 3.7 16.4 - - - +
273A ALA* 3.7 26.7 - - + +
276A LYS* 3.8 17.9 - - + +
341A ILE* 3.6 30.6 - - + +
368A ILE* 4.1 25.6 - - + -
371A ASP* 5.4 1.3 - - + -
372A VAL* 3.8 19.3 - - + -
398A LEU* 2.8 19.6 + - + +
399A ARG 3.9 3.8 - - - +
401A GLU* 1.3 77.8 - - - +
403A ALA* 1.3 61.5 + - - +
405A GLU* 3.2 20.7 + - + +
406A CYS* 3.4 11.3 + - - -
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Residues in contact with ALA 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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368A ILE* 3.6 19.0 - - + +
399A ARG 3.2 11.6 + - - +
400A ARG* 3.7 9.0 - - - +
401A GLU 3.3 0.2 - - - -
402A LEU* 1.3 79.4 - - - +
404A LEU* 1.3 65.2 + - + +
406A CYS* 3.2 19.3 + - - +
407A ASP* 4.2 2.9 + - - +
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Residues in contact with LEU 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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400A ARG* 3.3 14.1 + - + +
401A GLU* 3.2 27.4 + - - +
403A ALA* 1.3 78.2 - - + +
405A GLU* 1.3 63.8 + - - +
406A CYS 3.2 0.7 + - - -
407A ASP* 3.2 20.6 + - - +
510A ALA* 4.4 23.2 + - + -
512A ARG* 3.7 29.2 - - + +
604A GLU* 5.9 0.4 - - + -
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Residues in contact with GLU 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A LYS* 2.9 32.6 + - + -
279A GLN* 5.0 3.5 - - - +
339A ALA* 5.0 1.9 - - - +
340A SER* 3.5 26.1 + - - +
341A ILE* 3.6 16.8 - - + -
358A LYS* 5.1 2.3 + - - -
401A GLU 3.0 11.0 + - - +
402A LEU* 3.2 13.6 + - + +
404A LEU* 1.3 76.2 - - - +
406A CYS* 1.3 61.1 + - - +
407A ASP* 3.2 1.6 + - - -
408A TYR* 3.5 21.6 - - + -
411A GLU* 4.7 6.1 - - - +
507A ASP* 4.0 15.4 - - - +
509A GLY* 3.8 27.7 - - - -
510A ALA* 4.2 4.2 + - - +
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Residues in contact with CYS 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ILE* 3.5 19.7 - - - -
360A GLN* 2.9 24.2 + - - +
364A VAL* 4.2 9.4 - - - -
365A ALA* 4.0 34.3 - - + -
368A ILE* 4.2 8.3 - - - -
402A LEU* 3.6 14.4 - - - -
403A ALA* 3.2 12.2 + - - +
404A LEU 3.1 1.2 - - - -
405A GLU* 1.3 76.7 - - - +
407A ASP* 1.3 56.4 + - - +
408A TYR 3.0 4.6 + - - -
440A PRO 3.7 5.2 - - - +
441A HIS* 4.9 2.1 - - + -
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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