Contacts of the helix formed by residues 426 - 436 (chain A) in PDB entry 4M0A
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 GLN 426 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422A ALA* 4.6 5.0 - - + +
423A PRO* 2.8 35.3 + - + +
425A SER* 1.3 87.8 + - - +
427A PHE* 1.3 65.0 + - - +
428A PRO* 3.3 4.0 - - - -
429A PHE* 3.0 18.2 + - - +
430A ALA* 3.0 11.9 + - - +
458A SER 4.9 0.9 - - - +
459A HIS* 3.3 55.8 + - - +
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Residues in contact with PHE 427 (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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314A THR* 5.4 0.2 - - - -
316A THR* 3.7 26.7 - - + -
334A LEU* 3.5 32.5 - - + -
336A THR* 3.6 31.4 - - + +
422A ALA* 4.6 2.7 - - + -
423A PRO 3.1 8.6 + - - +
424A VAL* 3.1 22.8 + - + +
426A GLN* 1.3 77.1 - - - +
428A PRO* 1.3 68.9 - - + +
430A ALA* 3.1 5.7 + - - +
431A LEU* 2.7 57.5 + - + +
507A EDO 3.7 28.3 - - - -
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Residues in contact with PRO 428 (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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424A VAL 3.7 8.1 - - - +
425A SER 4.0 6.7 - - - +
426A GLN 3.5 3.6 - - - -
427A PHE* 1.3 102.9 - - + +
429A PHE* 1.3 57.7 + - + +
431A LEU* 3.7 5.0 - - + +
432A LEU* 2.9 29.8 + - - +
472A ALA* 3.4 24.7 - - + +
473A ALA 3.6 6.5 - - - +
474A SER* 3.6 39.3 - - - +
475A GLU* 4.1 5.4 - - + +
478A ILE* 3.6 10.1 - - + +
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Residues in contact with PHE 429 (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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425A SER 4.3 6.3 - - - -
426A GLN* 3.0 17.1 + - - +
428A PRO* 1.3 78.0 - - + +
430A ALA* 1.3 58.6 + - - +
432A LEU* 3.5 3.3 + - + +
433A GLY* 3.0 21.8 + - - -
456A LEU* 4.1 12.3 - - + -
457A ASN 4.0 2.5 - - - +
458A SER* 3.4 21.6 - - - +
459A HIS 3.7 5.8 - - - -
460A GLY* 3.5 36.1 - - - +
461A LEU* 3.6 26.9 - - + -
470A PHE* 3.6 27.1 - - + -
471A GLN* 5.2 0.2 - - - -
472A ALA* 3.6 28.7 - - + -
478A ILE* 3.5 23.8 - - + -
481A HIS* 5.3 0.4 - + - -
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Residues in contact with ALA 430 (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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334A LEU* 3.8 15.0 - - + -
420A VAL* 5.6 2.0 - - + -
422A ALA* 3.9 24.5 - - + -
426A GLN 3.0 11.2 + - - +
427A PHE 3.7 4.9 - - - +
429A PHE* 1.3 74.1 - - - +
431A LEU* 1.3 61.2 + - - +
434A TRP* 2.9 41.8 + - + +
458A SER* 3.2 21.2 + - - +
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Residues in contact with LEU 431 (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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316A THR* 4.0 13.7 - - + -
318A THR* 3.5 28.0 - - + -
322A ARG* 3.4 44.2 - - - +
334A LEU* 3.4 12.2 - - + +
427A PHE* 2.7 42.1 + - + +
428A PRO* 3.7 4.7 - - + +
430A ALA* 1.3 70.7 - - - +
432A LEU* 1.3 65.8 + - - +
434A TRP 3.8 0.3 - - - -
435A THR* 2.8 30.1 + - - -
475A GLU* 3.7 14.1 - - + +
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Residues in contact with LEU 432 (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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428A PRO 2.9 18.9 + - - +
429A PHE* 3.7 4.9 - - - +
431A LEU* 1.3 79.1 - - - +
433A GLY* 1.3 64.0 + - - +
435A THR* 3.3 8.0 + - - -
436A GLY 3.5 1.4 + - - -
440A PHE* 5.0 0.2 - - + -
441A GLN* 3.1 34.0 + - - +
444A LEU* 3.6 22.0 - - + -
456A LEU* 4.8 8.3 - - + -
475A GLU* 3.3 15.4 + - + +
478A ILE* 3.6 38.6 - - + -
479A PHE* 4.0 23.3 - - + -
492A ARG* 3.7 21.5 + - - +
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Residues in contact with GLY 433 (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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429A PHE 3.0 16.0 + - - -
430A ALA 3.9 0.7 - - - -
432A LEU* 1.3 80.2 - - - +
434A TRP* 1.3 60.5 + - - +
435A THR 3.2 1.0 + - - -
436A GLY 3.3 1.7 + - - -
441A GLN* 3.5 17.0 - - - +
445A ARG* 4.3 7.2 - - - -
458A SER* 4.7 1.8 - - - -
5P T 3.3 23.7 + - - +
101P EDO 3.6 19.6 - - - -
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Residues in contact with TRP 434 (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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318A THR* 3.7 18.1 + - + +
319A GLY* 2.8 26.3 + - - -
332A ASP* 4.1 18.2 - - + -
333A PHE 5.9 0.2 - - - -
334A LEU* 5.2 4.0 - - + -
387A ARG* 3.7 31.6 - - - +
389A PHE* 4.5 6.5 - + - -
418A ASP* 4.2 5.4 - - + -
420A VAL* 3.4 47.1 - - + +
430A ALA* 2.9 39.6 + - + +
431A LEU 3.8 0.4 - - - -
433A GLY* 1.3 72.9 - - - +
435A THR* 1.3 56.8 + - - +
436A GLY 3.4 0.4 - - - -
458A SER* 4.8 3.3 + - - -
4P A 3.5 42.2 - - + -
5P T 3.3 29.2 - - - +
101P EDO 3.6 26.8 + - - -
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Residues in contact with THR 435 (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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318A THR* 4.1 2.4 - - - -
319A GLY 3.7 6.4 - - - +
322A ARG* 2.9 44.6 + - + +
323A ARG* 2.8 39.7 + - + +
431A LEU* 2.8 25.1 + - - +
432A LEU 3.9 3.8 - - - -
433A GLY 3.2 0.4 - - - -
434A TRP* 1.3 79.3 - - - +
436A GLY* 1.3 63.9 + - - +
489A PRO* 3.9 15.9 - - + -
492A ARG* 3.9 9.9 - - - +
5P T 3.6 1.6 - - - -
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Residues in contact with GLY 436 (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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323A ARG* 3.8 1.6 - - - -
432A LEU 3.5 3.2 + - - -
433A GLY 3.3 6.9 + - - -
434A TRP 3.4 0.4 - - - -
435A THR* 1.3 82.6 - - - +
437A SER* 1.3 70.0 + - - -
440A PHE* 3.9 1.6 - - - +
441A GLN* 3.3 20.0 + - - -
492A ARG* 3.5 23.4 - - - +
5P T 3.2 15.7 - - - -
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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