Contacts of the helix formed by residues 399 - 420 (chain A) in PDB entry 4MXP
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 399 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357A ASN* 5.0 0.8 + - - -
361A GLU* 2.6 36.9 + - - -
397A THR* 3.6 12.4 + - - -
398A ILE* 1.3 76.4 - - - +
400A PRO* 1.3 71.5 - - - +
401A LYS* 3.4 5.7 + - - +
402A GLY* 2.9 16.9 + - - -
403A TYR* 2.9 29.1 + - - -
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Residues in contact with PRO 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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397A THR* 5.7 0.4 - - - +
398A ILE 4.5 1.1 - - - +
399A SER* 1.3 88.0 - - - +
401A LYS* 1.3 56.3 + - - +
404A ALA* 3.0 19.1 + - - +
455A THR* 3.4 22.2 - - - +
456A PRO* 3.4 1.4 - - + +
457A ASP* 2.9 41.7 + - + +
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Residues in contact with LYS 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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361A GLU* 2.7 42.4 + - - +
362A LYS* 4.3 8.5 - - - +
363A GLY* 4.8 2.6 - - - +
399A SER* 3.2 8.0 + - - +
400A PRO* 1.3 76.0 - - - +
402A GLY* 1.3 66.3 + - - +
404A ALA* 3.1 9.3 + - - +
405A ILE* 3.0 37.3 + - + +
457A ASP* 4.1 8.4 + - + +
460A PHE* 3.6 43.7 - - + -
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Residues in contact with GLY 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A ASN* 5.9 0.4 - - - -
360A LEU* 3.9 24.3 - - - +
361A GLU* 4.4 4.4 + - - -
398A ILE* 4.0 9.4 - - - -
399A SER* 2.9 18.5 + - - -
401A LYS* 1.3 77.0 - - - +
403A TYR* 1.3 56.4 + - - +
405A ILE* 3.2 6.6 + - - +
406A LEU* 2.9 31.1 + - - +
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Residues in contact with TYR 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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398A ILE* 3.3 45.1 - - + +
399A SER 2.9 24.8 + - - +
402A GLY* 1.3 71.9 - - - +
404A ALA* 1.3 62.2 + - - +
406A LEU* 3.3 4.7 + - + +
407A GLN* 3.0 24.6 + - - +
444A MET* 3.8 29.2 - - + -
447A LYS* 4.2 6.8 - - - +
448A LEU* 3.3 30.2 - - + +
454A ALA* 3.5 23.4 - - + +
455A THR* 3.5 31.6 - - - +
456A PRO* 3.6 25.7 - - + +
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Residues in contact with ALA 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 PRO 3.0 14.4 + - - +
401A LYS 3.4 8.3 - - - +
403A TYR* 1.3 76.9 - - - +
405A ILE* 1.3 62.5 + - - +
407A GLN* 3.4 4.7 + - - +
408A SER* 3.0 27.0 + - - -
456A PRO* 3.7 10.6 - - + +
457A ASP 4.0 9.6 - - - +
460A PHE* 4.0 36.1 - - + +
462A VAL* 3.9 3.8 - - + -
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Residues in contact with ILE 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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360A LEU* 3.5 43.3 - - + +
363A GLY* 4.2 10.8 - - - -
365A ILE* 3.7 25.1 - - + -
401A LYS* 3.0 41.4 + - + +
402A GLY* 3.7 6.1 - - - +
404A ALA* 1.3 76.2 - - - +
406A LEU* 1.3 56.0 + - - +
408A SER* 3.2 2.8 + - - -
409A LEU* 2.8 31.7 + - + +
460A PHE* 4.0 15.3 - - + -
462A VAL* 4.1 12.6 - - + -
467A ILE* 4.3 6.7 - - + -
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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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360A LEU* 3.8 21.5 - - + -
368A TYR* 3.2 36.8 - - + +
398A ILE* 4.1 6.5 - - + -
402A GLY 2.9 21.6 + - - +
403A TYR* 3.8 15.3 - - + +
404A ALA 3.3 0.2 - - - -
405A ILE* 1.3 75.6 - - - +
407A GLN* 1.3 57.3 + - - +
409A LEU* 3.5 5.3 + - + +
410A TRP* 3.0 28.9 + - - +
440A SER* 3.4 16.4 + - - +
443A PHE* 4.2 7.6 - - + -
444A MET* 3.9 38.6 - - + -
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Residues in contact with GLN 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 TYR 3.0 17.2 + - - +
404A ALA* 3.7 6.3 - - - +
406A LEU* 1.3 77.3 - - - +
408A SER* 1.3 63.0 + - - +
410A TRP* 3.3 16.9 + - - +
411A GLY* 3.2 19.8 + - - +
456A PRO* 5.3 9.2 - - + -
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Residues in contact with SER 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 ALA 3.0 15.7 + - - -
405A ILE 3.7 6.3 - - - -
407A GLN* 1.3 73.1 - - - +
409A LEU* 1.3 60.3 + - - +
411A GLY* 3.4 1.5 + - - -
412A ALA* 2.9 32.4 + - - +
462A VAL* 3.1 37.8 + - - +
464A LYS* 5.5 3.5 - - - +
467A ILE* 4.3 6.5 - - - -
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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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365A ILE* 4.3 13.7 - - + -
368A TYR* 3.6 22.9 - - + -
369A LEU* 4.1 10.5 - - + -
405A ILE* 2.8 23.1 + - + +
406A LEU* 3.7 6.5 - - + +
408A SER* 1.3 78.0 - - - +
410A TRP* 1.3 56.5 + - - +
413A ALA* 2.9 33.6 + - - +
436A VAL* 4.3 10.1 - - + -
437A ASN* 5.8 0.7 - - - +
440A SER* 3.5 26.9 - - - +
467A ILE* 3.7 29.7 - - + +
471A ILE* 3.9 22.4 - - + -
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Residues in contact with TRP 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 LEU 3.0 18.7 + - - +
407A GLN* 3.6 18.6 - - - +
408A SER 3.3 0.2 - - - -
409A LEU* 1.3 76.9 - - - +
411A GLY* 1.3 59.2 + - - +
414A SER* 2.7 53.9 + - - -
437A ASN* 2.9 60.5 - - + +
440A SER* 5.7 4.0 - - - -
441A ALA* 4.0 19.1 - - + -
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Residues in contact with GLY 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 GLN* 3.2 12.8 + - - -
408A SER* 3.9 1.6 - - - -
410A TRP* 1.3 85.2 - - - +
412A ALA* 1.3 57.4 + - - +
414A SER* 3.4 4.6 + - - -
415A ASP* 3.0 38.7 + - - +
464A LYS* 5.7 0.9 - - - -
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Residues in contact with ALA 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 SER 2.9 19.2 + - - +
409A LEU 3.9 0.2 - - - +
411A GLY* 1.3 76.4 - - - +
413A ALA* 1.3 56.7 + - - +
415A ASP* 3.4 7.0 + - - +
416A TYR* 2.9 31.9 + - - +
464A LYS* 4.3 22.0 - - + +
467A ILE* 3.6 25.1 - - + -
468A LEU* 3.9 19.4 - - + +
471A ILE* 4.5 0.9 - - + -
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Residues in contact with ALA 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 2.9 18.7 + - - +
412A ALA* 1.3 74.7 - - - +
414A SER* 1.3 60.8 + - - +
417A SER* 2.9 29.3 + - - -
433A VAL* 3.3 24.7 - - + +
436A VAL* 4.1 13.5 - - + -
437A ASN* 3.6 22.4 - - - +
471A ILE* 4.1 14.7 - - + +
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Residues in contact with SER 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 TRP* 2.7 40.3 + - - -
411A GLY* 3.6 7.6 - - - -
413A ALA* 1.3 77.0 - - - +
415A ASP* 1.3 64.7 + - - +
417A SER* 3.1 18.0 + - - -
418A ARG* 3.2 12.9 + - - +
437A ASN* 3.2 14.8 + - - +
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Residues in contact with ASP 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 GLY* 3.0 23.9 + - - +
412A ALA* 3.6 5.2 - - - +
414A SER* 1.3 79.2 - - - +
416A TYR* 1.3 58.5 + - - +
418A ARG* 3.0 32.3 + - - +
419A ALA* 2.9 29.6 + - - +
464A LYS* 3.7 25.1 + - - +
516A GLU* 5.1 1.5 - - - +
519A LEU* 4.9 5.8 - - + -
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Residues in contact with TYR 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 ALA 2.9 18.9 + - - +
413A ALA 3.9 2.5 - - - +
415A ASP* 1.3 74.5 - - - +
417A SER* 1.3 60.8 + - - +
419A ALA* 4.4 0.4 - - - -
420A ALA* 2.9 33.5 + - + +
429A GLU* 2.7 34.2 + - - +
433A VAL* 3.6 26.2 - - + -
468A LEU* 4.0 15.0 - - + -
471A ILE* 3.9 22.9 - - + -
472A MET* 3.8 30.0 - - + +
475A ILE* 4.2 2.3 - - + +
494A MET* 3.7 15.6 - - - +
497A LYS* 4.3 0.4 - - - +
519A LEU* 3.8 42.1 - - + +
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Residues in contact with SER 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 ALA 2.9 15.3 + - - -
414A SER* 3.1 16.6 + - - -
416A TYR* 1.3 77.0 - - - +
418A ARG* 1.3 60.7 + - - +
420A ALA* 3.8 0.4 + - - -
421A ALA* 3.6 8.5 + - - +
430A PRO* 3.6 27.3 - - - +
433A VAL* 3.7 18.3 - - - +
434A SER* 3.5 26.2 + - - -
437A ASN* 5.2 1.3 + - - -
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Residues in contact with ARG 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 SER 3.2 8.8 + - - +
415A ASP* 3.0 47.9 + - - +
416A TYR 3.2 0.2 - - - -
417A SER* 1.3 80.1 + - - +
419A ALA* 1.3 65.8 + - - +
421A ALA* 3.2 22.1 + - - +
516A GLU* 3.5 31.9 + - - -
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Residues in contact with ALA 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 ASP 2.9 18.5 + - - +
416A TYR* 3.8 1.3 - - - +
418A ARG* 1.3 78.7 - - - +
420A ALA* 1.3 56.7 + - - +
421A ALA 3.2 0.6 - - - +
422A THR* 3.2 12.5 - - - +
516A GLU* 3.5 32.5 - - - +
519A LEU* 3.8 26.5 - - + -
520A SER* 3.2 26.1 - - - +
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Residues in contact with ALA 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 TYR* 2.9 21.5 + - + +
417A SER 4.3 1.8 - - - +
418A ARG 3.2 0.2 - - - -
419A ALA* 1.3 74.9 - - - +
421A ALA* 1.3 59.5 + - - +
422A THR* 3.6 3.6 - - - -
425A GLU 3.4 4.2 - - - +
429A GLU* 3.8 31.2 - - + +
430A PRO* 3.5 13.4 - - + +
519A LEU 3.7 17.0 - - - +
520A SER* 4.5 0.2 - - - +
522A LYS* 2.8 29.5 + - - +
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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