Contacts of the helix formed by residues 398 - 420 (chain A) in PDB entry 1MN3
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 SER 398 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399A SER* 1.3 64.3 + - - +
400A LEU* 3.2 6.3 - - - +
401A ILE* 3.8 25.7 - - - +
402A LYS* 2.9 52.3 + - - +
440A GLU* 4.9 9.4 + - - -
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Residues in contact with SER 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A SER* 1.3 80.5 - - - +
400A LEU* 1.3 61.6 + - - +
402A LYS* 3.6 16.6 + - - +
403A LYS* 3.1 22.5 + - - +
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Residues in contact with LEU 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A SER 3.2 3.2 - - - +
399A SER* 1.3 78.0 - - - +
401A ILE* 1.3 62.2 + - + +
403A LYS* 3.2 11.5 + - + +
404A ILE* 2.9 49.6 + - + +
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Residues in contact with ILE 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A SER* 3.4 25.1 + - - +
399A SER 3.4 0.2 - - - -
400A LEU* 1.3 78.1 - - + +
402A LYS* 1.3 59.1 + - + +
404A ILE* 3.2 12.2 + - + +
405A GLU* 2.8 32.2 + - + +
439A ILE* 4.1 12.8 - - + +
440A GLU* 3.8 43.3 - - + +
443A VAL* 4.5 24.5 - - + -
444A ASP* 4.7 11.7 - - - +
447A LEU* 5.9 2.7 - - + -
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Residues in contact with LYS 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A SER* 2.9 44.3 + - - +
399A SER* 4.0 15.4 + - - +
401A ILE* 1.3 74.8 - - + +
403A LYS* 1.3 60.5 + - - +
405A GLU* 3.9 16.8 - - - +
406A GLU* 2.9 30.9 + - - +
440A GLU* 5.9 2.7 - - - +
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Residues in contact with LYS 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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399A SER 3.1 15.1 + - - +
400A LEU* 3.4 20.9 - - + +
401A ILE 3.2 0.2 - - - -
402A LYS* 1.3 76.1 - - - +
404A ILE* 1.3 61.3 + - + +
406A GLU* 3.4 25.0 + - - +
407A ASN* 2.9 62.9 + - - +
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Residues in contact with ILE 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 LEU* 2.9 39.9 + - + +
401A ILE* 3.4 13.5 - - + +
403A LYS* 1.3 74.9 - - + +
405A GLU* 1.3 64.5 + - - +
407A ASN* 3.2 21.3 + - - +
408A GLU* 3.2 13.3 + - - +
439A ILE* 3.8 27.1 - - + -
443A VAL* 5.6 8.1 - - + -
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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
----------------------------------------------------------
401A ILE* 2.8 26.6 + - - +
402A LYS* 3.9 21.9 + - - +
404A ILE* 1.3 75.3 - - - +
406A GLU* 1.3 61.5 + - - +
408A GLU* 2.8 30.2 - - + +
409A ARG* 3.0 10.2 + - - +
437A SER* 3.3 29.5 + - - +
439A ILE* 3.5 20.0 - - + -
440A GLU* 3.7 22.9 + - - +
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Residues in contact with GLU 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 LYS 2.9 19.1 + - - +
403A LYS* 3.5 33.6 + - - +
405A GLU* 1.3 78.5 - - - +
407A ASN* 1.3 57.7 + - - +
409A ARG* 3.9 13.5 + - - +
410A LYS* 2.9 46.2 + - + +
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Residues in contact with ASN 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 LYS* 2.9 62.4 + - - +
404A ILE* 3.4 14.6 - - + +
405A GLU 3.1 0.4 - - - -
406A GLU* 1.3 80.5 - - - +
408A GLU* 1.3 62.1 + - - +
410A LYS* 4.1 6.2 - - - +
411A ASP* 3.1 27.4 + - - +
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Residues in contact with GLU 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 ILE 3.2 4.9 + - - +
405A GLU* 2.8 27.4 - - - +
407A ASN* 1.3 76.7 - - - +
409A ARG* 1.3 66.8 + - + +
411A ASP* 3.9 3.7 - - - +
412A THR* 3.0 29.3 + - - +
433A ILE* 5.8 3.8 - - - +
437A SER* 3.3 17.2 + - - -
438A ARG 5.3 0.3 + - - -
439A ILE* 2.9 37.7 - - - +
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Residues in contact with ARG 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 GLU 3.0 15.3 + - - +
406A GLU* 3.9 13.5 + - - +
408A GLU* 1.3 81.4 - - + +
410A LYS* 1.3 79.1 + - - +
412A THR* 3.1 5.5 + - - -
413A LEU* 3.0 42.8 + - + +
429A GLU* 3.1 36.8 + - - -
433A ILE* 3.8 30.2 - - + +
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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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406A GLU* 2.9 32.1 + - + +
407A ASN* 4.1 6.1 - - - +
409A ARG* 1.3 92.6 - - - +
411A ASP* 1.3 59.2 + - - +
413A LEU* 3.5 4.6 + - - +
414A ASN* 3.0 53.1 + - - +
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Residues in contact with ASP 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 ASN 3.1 19.7 + - - +
408A GLU* 3.9 4.7 - - - +
409A ARG 3.2 0.2 - - - -
410A LYS* 1.3 77.3 - - - +
412A THR* 1.3 66.2 + - - +
414A ASN* 3.5 6.5 + - - +
415A THR* 3.3 29.3 + - - -
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Residues in contact with THR 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 GLU* 3.0 20.3 + - - +
409A ARG* 3.5 4.9 - - - -
411A ASP* 1.3 78.6 - - - +
413A LEU* 1.3 63.6 + - - +
415A THR* 3.4 4.2 + - - -
416A LEU* 3.1 41.8 + - + +
432A CYS* 5.1 5.4 - - + +
433A ILE* 4.3 19.5 - - + -
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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
----------------------------------------------------------
409A ARG* 3.0 57.7 + - - +
410A LYS* 3.8 4.9 - - - +
412A THR* 1.3 77.8 - - - +
414A ASN* 1.3 53.0 + - - +
416A LEU* 3.2 4.2 + - + -
417A GLN* 2.6 55.7 + - - +
425A PRO* 4.7 4.9 - - + +
428A ILE* 4.0 15.9 - - + -
429A GLU* 4.0 28.7 - - + +
433A ILE* 3.4 22.2 - - + -
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Residues in contact with ASN 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* 3.0 44.9 + - - +
411A ASP* 3.7 9.2 - - - +
413A LEU* 1.3 77.5 - - - +
415A THR* 1.3 64.6 + - - +
417A GLN* 3.2 6.4 + - - +
418A ASN* 3.0 37.7 + - - +
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Residues in contact with THR 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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411A ASP* 3.3 20.0 + - - -
412A THR* 3.8 8.5 - - - -
414A ASN* 1.3 78.3 - - - +
416A LEU* 1.3 64.4 + - + +
418A ASN* 3.5 8.3 + - - +
419A MSE 3.2 47.2 + - + +
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Residues in contact with LEU 416 (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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412A THR* 3.1 36.0 + - + +
413A LEU* 3.7 4.5 - - + +
415A THR* 1.3 75.3 - - + +
417A GLN* 1.3 59.6 + - - +
419A MSE 3.1 21.8 + - + -
420A PHE* 2.8 47.5 + - + +
428A ILE* 3.8 21.3 - - + -
432A CYS* 3.5 42.2 - - + -
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Residues in contact with GLN 417 (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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413A LEU* 2.6 54.4 + - - +
414A ASN* 3.5 8.3 - - - +
416A LEU* 1.3 73.1 - - - +
418A ASN* 1.3 64.3 + - - +
420A PHE 3.1 5.9 - - - +
421A PRO* 3.1 28.6 - - + +
423A MSE 5.7 1.3 - - - +
425A PRO* 3.5 33.8 - - + +
428A ILE* 3.7 22.7 - - + +
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Residues in contact with ASN 418 (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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414A ASN* 3.0 31.7 + - - +
415A THR* 3.7 8.6 - - - +
417A GLN* 1.3 81.2 - - - +
419A MSE 1.3 61.8 + - + +
421A PRO* 3.4 16.3 - - - +
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Residues in contact with MSE 419 (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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415A THR* 3.2 42.7 + - + +
416A LEU* 3.1 27.1 + - + +
418A ASN* 1.3 80.5 - - + +
420A PHE* 1.3 85.8 + - + +
421A PRO* 3.3 5.9 - - - +
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Residues in contact with PHE 420 (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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416A LEU* 2.8 34.0 + - + +
417A GLN* 3.1 8.1 - - - +
419A MSE 1.3 100.8 - - + +
421A PRO* 1.3 64.1 - - - +
422A ASP 3.4 2.7 - - - -
423A MSE 3.2 47.9 + - + +
428A ILE* 3.9 11.9 - - + +
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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
------------------------------------------------------------
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