Contacts of the helix formed by residues 400 - 415 (chain A) in PDB entry 4E2I
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 LYS 400 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131 GLN* 5.1 22.9 + - + +
141 ILE* 5.8 1.2 - - - +
395A HIS* 4.6 11.0 - - - -
398A LEU 3.2 1.8 + - - -
399A PRO* 1.3 76.8 - - + +
401A MET* 1.3 65.7 + - - +
402A ASP* 3.4 7.9 - - - -
403A SER* 3.1 28.8 + - - +
404A VAL* 3.0 23.0 + - + +
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Residues in contact with MET 401 (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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394A LEU* 3.2 34.5 - - + +
395A HIS* 3.8 12.7 + - - -
397A LEU* 3.5 32.3 - - + -
398A LEU* 3.1 39.8 + - + +
399A PRO 4.3 0.9 - - - -
400A LYS* 1.3 73.8 - - - +
402A ASP* 1.3 65.8 + - - +
404A VAL* 3.0 22.3 + - - +
405A VAL* 3.0 19.4 + - - +
435A LEU* 3.8 27.6 - - + -
575A LEU* 5.5 0.2 - - + -
578A MET* 3.5 19.3 - - + -
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Residues in contact with ASP 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A HIS* 2.9 23.9 + - + -
400A LYS* 3.9 4.5 - - - -
401A MET* 1.3 75.1 - - - +
403A SER* 1.3 72.4 + - - +
405A VAL* 3.3 11.7 + - - +
406A TYR* 3.3 13.5 + - - +
578A MET* 3.7 36.3 - - + +
579A LEU* 4.5 4.8 - - + +
582A TYR* 3.2 40.5 - - + +
583A ARG* 3.7 19.4 + - + +
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Residues in contact with SER 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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400A LYS* 3.1 44.0 + - - +
402A ASP* 1.3 84.1 + - - +
404A VAL* 1.3 57.3 + - - +
406A TYR* 3.4 6.1 + - - +
407A ASP* 2.7 33.5 + - - +
583A ARG* 2.8 32.0 + - - +
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Residues in contact with VAL 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A LEU* 5.7 5.6 - - + -
399A PRO 3.9 11.9 - - - +
400A LYS* 3.0 17.6 + - + +
401A MET* 3.0 13.9 + - - +
403A SER* 1.3 73.7 - - - +
405A VAL* 1.3 61.4 + - + +
407A ASP* 3.1 10.3 + - - +
408A PHE* 2.9 28.1 + - + +
422A TRP* 3.5 30.3 - - + -
543A LYS* 5.1 9.9 - - - -
545A ILE* 4.2 13.7 - - + -
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Residues in contact with VAL 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A MET* 3.0 25.0 + - + +
402A ASP 3.4 6.3 - - - +
403A SER 3.3 0.2 - - - -
404A VAL* 1.3 75.2 - - - +
406A TYR* 1.3 57.7 + - - +
408A PHE* 3.3 6.9 + - - +
409A LEU* 2.9 37.1 + - + +
435A LEU* 5.5 0.4 - - + -
439A LEU* 4.4 14.6 - - + -
442A LEU* 3.7 25.6 - - + -
575A LEU* 4.7 6.7 - - + -
578A MET* 3.5 24.2 - - + -
579A LEU* 3.5 23.8 - - + -
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Residues in contact with TYR 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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402A ASP 3.3 4.5 + - - +
403A SER 3.7 8.7 - - - +
404A VAL 3.3 0.4 - - - -
405A VAL* 1.3 79.3 - - - +
407A ASP* 1.3 70.3 + - - +
409A LEU* 3.5 16.6 + - + +
410A LYS* 3.2 63.2 + - + +
579A LEU* 4.6 2.8 - - + +
583A ARG* 3.9 32.8 - - + +
587A GLU* 3.1 59.3 + - + +
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Residues in contact with ASP 407 (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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403A SER* 2.7 24.7 - - - +
404A VAL* 3.1 10.4 + - - +
406A TYR* 1.3 83.7 - - - +
408A PHE* 1.3 60.1 + - - +
410A LYS* 3.5 3.9 + - - +
411A CYS* 2.8 31.2 + - - +
422A TRP* 4.2 14.6 - - + -
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Residues in contact with PHE 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 VAL* 2.9 16.3 + - + +
405A VAL* 3.7 7.2 - - - +
407A ASP* 1.3 74.6 - - - +
409A LEU* 1.3 69.8 + - + +
411A CYS* 3.1 3.5 + - - +
412A MET* 2.9 62.6 + - + +
422A TRP* 3.9 38.3 - + + -
424A PHE* 6.3 0.4 - + - -
439A LEU* 4.4 26.0 - - + -
443A CYS* 4.0 15.5 - - - -
469A LEU* 3.7 23.3 - - + -
524A GLY 4.3 3.6 - - - -
525A ILE* 3.5 39.0 - - + -
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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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361A LEU* 4.2 9.8 - - + +
365A PHE* 3.9 26.2 - - + -
405A VAL* 2.9 27.3 + - + +
406A TYR* 3.6 20.9 - - + +
408A PHE* 1.3 77.5 - - + +
410A LYS* 1.3 66.0 + - + +
412A MET* 3.0 18.0 + - - +
413A VAL* 3.0 18.7 + - - +
442A LEU* 4.4 7.4 - - + -
443A CYS* 3.5 28.9 - - - -
579A LEU* 3.9 29.6 - - + -
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Residues in contact with LYS 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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358A GLU* 3.3 30.1 + - - +
406A TYR* 3.2 58.0 + - + +
407A ASP* 4.0 3.8 - - - +
409A LEU* 1.3 78.6 - - + +
411A CYS* 1.3 57.7 + - - +
413A VAL* 2.9 12.5 + - + +
414A TYR* 2.7 63.3 + - + +
587A GLU 4.0 11.1 + - - -
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Residues in contact with CYS 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 ASP 2.8 20.5 + - - +
408A PHE 3.2 6.3 - - - +
410A LYS* 1.3 76.6 - - - +
412A MET* 1.3 64.0 + - + +
414A TYR* 4.3 5.3 - - - +
415A ASN* 3.4 16.8 + - - -
416A ILE* 4.7 4.7 + - - +
419A LYS 4.2 14.8 - - - +
420A ARG* 3.9 16.1 - - - +
422A TRP* 3.2 32.1 - - + +
542A VAL* 4.4 10.8 - - - -
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Residues in contact with MET 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A ARG* 2.8 33.3 + - - +
408A PHE* 2.9 56.4 + - + +
409A LEU* 3.2 9.0 - - - +
410A LYS 3.0 0.2 - - - -
411A CYS* 1.3 83.4 - - - +
413A VAL* 1.3 57.2 + - - +
415A ASN* 3.7 5.4 + - - +
420A ARG 3.2 27.4 - - - +
443A CYS* 5.2 0.4 - - - -
468A PHE* 3.7 25.6 - - + -
469A LEU* 4.0 12.1 - - + -
523A PRO* 3.6 32.7 - - + +
524A GLY 4.0 7.6 - - - +
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Residues in contact with VAL 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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357A ARG* 3.7 24.6 - - + +
358A GLU* 3.5 42.2 - - + +
361A LEU* 3.5 24.7 - - + -
409A LEU* 3.1 16.6 - - + +
410A LYS* 2.9 21.0 + - + +
412A MET* 1.3 77.8 - - - +
414A TYR* 1.3 73.7 + - + +
415A ASN* 3.1 1.0 + - - +
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Residues in contact with TYR 414 (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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410A LYS* 2.7 56.7 + - + +
411A CYS* 4.3 5.4 - - - +
413A VAL* 1.3 78.3 - - + +
415A ASN* 1.3 71.2 + - - +
416A ILE* 4.0 25.7 - - + +
561B GLU* 5.7 5.2 - - + -
565B GLU* 3.7 58.2 - - + +
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Residues in contact with ASN 415 (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 ARG* 3.7 36.2 + - - +
411A CYS 3.4 10.7 + - - -
412A MET* 3.7 4.5 + - - +
413A VAL 3.1 1.6 - - - +
414A TYR* 1.3 84.8 - - - +
416A ILE* 1.3 58.2 + - - +
417A PRO* 3.6 7.3 - - - +
420A ARG* 3.0 35.5 + - - +
520A ILE* 5.3 2.3 - - - +
523A PRO* 5.1 3.1 - - + +
564B LEU 4.1 4.2 - - - +
565B GLU 4.8 0.7 - - - +
567B ARG* 2.8 34.7 + - - +
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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