Contacts of the helix formed by residues 424 - 436 (chain A) in PDB entry 4WTM
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 VAL 424 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A LEU* 3.7 26.7 - - + -
392A LEU* 4.4 15.9 - - + -
420A TRP* 3.2 19.2 + - + +
423A MET* 1.3 82.1 - - + +
425A LEU* 1.3 68.5 + - + +
426A MET 3.4 0.4 - - - -
427A THR* 3.4 3.1 + - - -
428A HIS* 3.0 22.7 + - - +
485A VAL* 5.4 0.2 - - + -
489A LEU* 4.1 16.2 - - + -
497A LEU* 4.1 17.5 - - + -
500A TRP* 3.7 36.3 - - + +
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Residues in contact with LEU 425 (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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30A LEU* 4.6 11.0 - - + -
391A PRO* 5.1 6.1 - - + +
392A LEU* 4.4 17.0 - - + -
395A ALA* 4.3 22.9 - - + -
408A TRP* 4.4 20.4 - - + +
411A ASN* 3.7 31.9 - - + +
412A ILE* 4.1 12.3 - - + +
420A TRP* 3.2 28.2 + - + +
421A VAL* 4.0 9.6 - - + +
424A VAL* 1.3 81.3 - - + +
426A MET* 1.3 59.3 + - - +
428A HIS* 3.9 3.5 - - + +
429A PHE* 2.9 32.9 + - - +
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Residues in contact with MET 426 (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 ILE* 3.7 32.0 - - + +
416A ALA* 4.3 12.1 - - + +
421A VAL* 2.8 31.0 + - + +
422A ARG* 3.6 25.4 - - + +
425A LEU* 1.3 72.2 - - - +
427A THR* 1.3 62.7 + - - +
429A PHE* 4.4 0.2 - - - -
430A PHE* 3.0 32.8 + - + +
463A ILE* 3.7 30.5 - - + -
472A PHE* 5.9 0.9 - - + -
525A LEU* 4.1 39.7 - - + +
526A PHE* 3.8 9.6 - - + -
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Residues in contact with THR 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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422A ARG 3.7 1.4 + - - -
423A MET 2.7 27.8 + - - -
424A VAL 3.4 3.7 + - - -
425A LEU 3.3 0.6 - - - -
426A MET* 1.3 75.7 - - - +
428A HIS* 1.3 62.3 + - - +
430A PHE* 4.4 0.2 - - - +
431A SER* 3.1 26.6 + - - -
500A TRP* 3.8 11.2 - - + +
503A ARG* 3.8 17.9 - - + +
504A ALA* 3.6 37.0 - - + +
507A VAL* 3.8 7.6 - - + +
526A PHE* 3.5 19.5 - - - -
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Residues in contact with HIS 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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26A LEU 2.8 26.1 + - - -
27A SER* 4.3 0.2 - - - -
29A SER* 3.3 27.9 + - - -
30A LEU* 3.7 37.8 + - + +
408A TRP* 3.5 34.2 - + + -
424A VAL 3.0 17.0 + - - +
425A LEU* 3.9 5.6 - - + +
427A THR* 1.3 75.8 - - - +
429A PHE* 1.3 58.9 + - - +
431A SER* 3.4 5.8 + - - -
432A ILE* 2.9 45.5 + - + +
500A TRP* 4.1 15.2 - - + -
503A ARG* 5.2 1.4 + - - -
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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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405A ILE* 4.1 6.5 - - + -
408A TRP* 3.8 34.3 - + + -
409A LEU* 4.1 24.2 - - + -
412A ILE* 3.5 19.3 - - + -
425A LEU 2.9 19.6 + - - +
426A MET 3.8 1.3 - - - +
428A HIS* 1.3 75.6 - - - +
430A PHE* 1.3 83.9 + + - +
432A ILE* 3.4 1.4 + - - +
433A LEU* 3.0 54.0 + - + +
443A LEU* 3.9 25.4 - - + -
456A PRO* 4.0 12.3 - - + -
459A LEU* 3.9 18.8 - - + -
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Residues in contact with PHE 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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426A MET* 3.0 29.0 + - + +
429A PHE* 1.3 99.5 - + - +
431A SER* 1.3 57.9 + - - +
433A LEU* 3.8 1.9 - - - +
434A MET* 2.9 37.3 + - - +
439A LEU* 3.6 27.8 - - + -
456A PRO 3.8 20.6 - - - -
457A LEU* 5.0 0.2 - - + -
459A LEU* 4.1 9.6 - - + -
507A VAL* 3.9 18.4 - - + -
511A LEU* 4.0 14.1 - - + -
521A CYS* 4.0 20.6 - - + -
525A LEU* 3.4 31.9 - - + -
526A PHE* 4.2 12.8 - + + -
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Residues in contact with SER 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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427A THR* 3.1 21.7 + - - -
428A HIS* 3.7 6.5 - - - -
430A PHE* 1.3 75.4 - - - +
432A ILE* 1.3 65.3 + - - +
434A MET* 3.5 7.4 + - - +
435A VAL* 3.1 32.2 + - - +
507A VAL* 3.7 20.9 - - - +
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Residues in contact with ILE 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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25A PRO 4.8 3.6 - - - +
26A LEU* 3.5 44.9 - - + +
29A SER* 4.6 5.2 - - - +
405A ILE* 4.6 1.8 - - + -
408A TRP* 3.7 20.9 - - + -
428A HIS* 2.9 46.8 + - + +
429A PHE 3.8 3.1 - - - +
431A SER* 1.3 73.5 - - - +
433A LEU* 1.3 64.3 + - + +
435A VAL* 3.4 3.9 + - - +
436A GLN* 2.9 40.2 + - + +
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Residues in contact with LEU 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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405A ILE* 4.2 27.4 - - + -
408A TRP* 5.6 0.4 - - + -
429A PHE* 3.0 56.2 + - + +
430A PHE 4.1 0.2 - - - +
432A ILE* 1.3 74.8 - - + +
434A MET* 1.3 66.9 + - - +
436A GLN* 3.4 8.6 + - - +
437A ASP 3.0 3.3 + - - -
438A THR* 2.9 49.6 + - - +
439A LEU* 3.8 19.9 + - + +
443A LEU* 4.5 6.5 - - + -
456A PRO* 3.8 21.3 - - + -
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Residues in contact with MET 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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430A PHE 2.9 18.9 + - - +
431A SER* 3.9 8.3 - - - +
433A LEU* 1.3 74.7 - - - +
435A VAL* 1.3 61.9 + - + +
437A ASP* 2.8 21.7 + - - +
439A LEU* 3.7 23.5 - - + +
507A VAL* 3.8 38.1 - - + +
510A SER* 3.3 30.5 - - - +
511A LEU* 3.7 23.3 - - + -
514A ARG* 3.5 29.8 + - - +
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Residues in contact with VAL 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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431A SER* 3.1 23.5 + - - +
432A ILE* 3.9 4.3 - - - +
434A MET* 1.3 78.2 - - + +
436A GLN* 1.3 61.8 + - + +
437A ASP* 3.1 2.0 + - - +
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Residues in contact with GLN 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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26A LEU* 3.6 29.5 - - + +
405A ILE* 4.3 9.9 - - - +
432A ILE* 2.9 29.0 + - + +
433A LEU* 3.7 6.3 - - - +
435A VAL* 1.3 75.6 - - + +
437A ASP* 1.3 68.5 + - - +
438A THR* 2.9 37.2 + - + +
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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