Contacts of the helix formed by residues 440 - 457 (chain H) in PDB entry 5YWB
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 ALA 440 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303H SER* 5.2 0.4 - - - +
306H ARG* 3.4 43.1 - - + +
307H ILE* 4.3 14.1 - - + -
310H ASP* 5.3 1.4 - - + +
436H PRO 3.8 1.5 + - - +
437H ASN 3.6 7.1 + - - +
438H LEU 2.9 0.8 - - - -
439H TRP* 1.3 80.5 - - - +
441H MET* 1.3 63.9 + - - +
442H PRO 3.4 2.0 - - - -
443H VAL* 3.2 9.6 - - + +
444H GLN* 3.1 26.6 + - - +
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Residues in contact with MET 441 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437H ASN 3.8 5.5 + - - +
438H LEU* 3.3 23.9 + - + +
440H ALA* 1.3 76.7 - - - +
442H PRO* 1.3 76.4 - - + +
444H GLN* 3.3 7.8 + - - +
445H ILE* 3.0 40.6 + - + +
589H PRO* 4.4 19.3 - - + +
590H LEU* 5.7 3.6 - - + -
593H LEU* 4.2 33.2 - - + -
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Residues in contact with PRO 442 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438H LEU 3.4 14.6 - - - +
439H TRP* 4.3 8.1 - - + +
440H ALA* 3.6 4.7 - - - +
441H MET* 1.3 99.9 - - + +
443H VAL* 1.3 62.5 + - - +
445H ILE* 3.0 14.6 - - + +
446H ILE* 3.0 33.7 + - + +
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Residues in contact with VAL 443 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307H ILE* 3.7 46.7 - - + +
310H ASP* 5.6 3.6 - - + -
314H PHE* 5.9 0.2 - - + -
439H TRP 4.3 2.9 - - - +
440H ALA* 3.2 32.8 - - + +
442H PRO* 1.3 75.3 - - + +
444H GLN* 1.3 61.2 + - - +
446H ILE* 3.4 8.5 + - - +
447H VAL* 2.9 42.6 + - + +
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Residues in contact with GLN 444 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306H ARG* 3.4 27.7 + - - -
310H ASP* 4.6 5.4 - - + +
314H PHE* 3.3 34.1 - - + -
440H ALA 3.1 20.7 + - - +
441H MET* 3.5 7.0 - - - +
443H VAL* 1.3 79.5 - - - +
445H ILE* 1.3 64.2 + - + +
447H VAL 3.4 0.3 + - - -
448H GLY* 2.9 24.3 + - - -
585H ILE* 2.9 44.7 + - - +
586H LEU* 4.6 3.0 - - + +
589H PRO* 3.4 24.7 - - + +
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Residues in contact with ILE 445 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441H MET* 3.0 26.3 + - + +
442H PRO* 3.0 20.6 - - + +
444H GLN* 1.3 80.9 - - + +
446H ILE* 1.3 85.9 + - + +
448H GLY* 3.2 2.4 + - - +
449H VAL* 3.0 23.7 + - + +
586H LEU* 3.5 32.4 - - + +
589H PRO* 5.5 4.0 - - + -
590H LEU* 5.8 6.1 - - + -
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Residues in contact with ILE 446 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442H PRO* 3.0 29.1 + - + +
443H VAL* 3.8 7.6 - - - +
445H ILE* 1.3 87.6 - - + +
447H VAL* 1.3 65.7 + - + +
449H VAL* 3.2 13.6 - - + +
450H ILE* 3.0 27.5 + - + +
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Residues in contact with VAL 447 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311H LEU* 5.4 9.9 - - + -
314H PHE* 3.4 33.0 - - + -
443H VAL* 2.9 31.0 + - + +
446H ILE* 1.3 79.4 - - + +
448H GLY* 1.3 63.7 + - - +
450H ILE* 3.2 14.0 - - + +
451H LEU* 2.9 28.6 + - + +
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Residues in contact with GLY 448 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314H PHE* 4.4 8.2 - - - -
444H GLN 2.9 14.7 + - - -
445H ILE* 3.2 5.5 + - - -
447H VAL* 1.3 76.7 - - - +
449H VAL* 1.3 56.9 + - - +
451H LEU* 3.3 5.9 + - - +
452H LEU* 3.0 33.8 + - - +
582H LEU* 4.7 13.5 - - - +
586H LEU* 6.0 7.9 - - - -
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Residues in contact with VAL 449 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445H ILE* 3.0 14.8 + - + +
446H ILE* 3.2 16.8 - - + +
448H GLY* 1.3 76.0 - - - +
450H ILE* 1.3 67.8 + - + +
452H LEU* 3.2 22.5 + - + +
453H TYR* 3.0 25.3 + - + +
464H ALA* 5.4 9.6 - - + -
467H ILE* 4.3 20.9 - - + -
586H LEU* 6.3 0.2 - - - +
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Residues in contact with ILE 450 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446H ILE* 3.0 16.0 + - + +
447H VAL* 3.2 33.0 - - + +
449H VAL* 1.3 79.3 - - + +
451H LEU* 1.3 59.9 + - + +
453H TYR* 4.2 9.4 + - + +
454H TYR* 3.7 34.4 - - + +
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Residues in contact with LEU 451 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314H PHE* 3.9 28.9 - - + +
315H ALA* 5.5 1.1 - - - -
318H LEU* 5.2 20.9 - - + +
447H VAL* 2.9 20.9 + - + +
448H GLY 3.7 3.6 - - - +
450H ILE* 1.3 79.1 - - + +
452H LEU* 1.3 63.5 + - - +
453H TYR 3.3 1.0 + - - -
454H TYR* 3.4 16.1 + - + +
455H ILE* 3.4 32.6 - - + +
582H LEU* 3.8 27.6 - - + -
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Residues in contact with LEU 452 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448H GLY 3.0 20.4 + - - +
449H VAL* 3.2 31.6 + - + +
451H LEU* 1.3 74.4 - - - +
453H TYR* 1.3 62.8 + - - +
454H TYR 3.4 0.2 - - - -
455H ILE* 3.7 5.3 - - + +
456H LEU* 2.9 35.8 + - + +
460H ALA* 4.6 22.2 - - + +
463H GLY* 5.7 4.7 - - - -
464H ALA* 5.6 4.9 - - + +
467H ILE* 4.8 10.8 - - + -
579H SER* 6.5 0.7 - - - -
582H LEU* 4.3 17.9 - - + -
586H LEU* 5.3 9.2 - - + -
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Residues in contact with TYR 453 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449H VAL* 3.0 16.4 + - + +
450H ILE* 4.3 8.5 - - + +
451H LEU 3.3 0.4 - - - -
452H LEU* 1.3 80.3 - - + +
454H TYR* 1.3 92.9 + + - +
455H ILE 2.9 1.6 + - - -
457H GLY* 2.9 49.5 + - - -
460H ALA* 4.5 14.1 - - + -
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Residues in contact with TYR 454 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450H ILE* 3.7 34.4 - - + +
451H LEU* 3.4 12.6 + - + +
452H LEU 3.4 0.6 - - - -
453H TYR* 1.3 101.4 - + - +
455H ILE* 1.3 61.4 - - + +
457H GLY* 4.8 0.7 - - - -
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Residues in contact with ILE 455 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318H LEU* 5.7 8.1 - - + -
321H PHE* 5.5 8.5 - - + -
451H LEU* 3.4 24.2 - - + +
452H LEU* 3.3 7.4 + - - +
453H TYR 3.0 0.8 - - - -
454H TYR* 1.3 83.2 - - + +
456H LEU* 1.3 64.8 + - - +
575H VAL* 3.4 50.8 - - + +
578H ALA* 4.4 17.7 - - + -
579H SER* 4.8 8.3 - - - +
582H LEU* 3.7 29.8 - - + -
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Residues in contact with LEU 456 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452H LEU* 2.9 20.0 + - + +
453H TYR 4.4 0.2 - - - +
455H ILE* 1.3 79.7 - - - +
457H GLY* 1.3 61.3 + - - +
458H VAL 3.8 2.3 + - - -
459H SER* 4.0 19.6 + - - +
460H ALA* 3.9 25.1 - - - +
558H THR* 6.5 0.7 - - - -
562H HIS* 4.3 14.4 + - - -
567H LYS* 4.7 3.1 - - - -
575H VAL* 5.3 1.8 - - - -
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Residues in contact with GLY 457 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453H TYR* 2.9 31.3 + - - +
454H TYR 4.8 0.6 - - - -
455H ILE 3.7 0.6 - - - -
456H LEU* 1.3 74.8 - - - +
458H VAL* 1.3 61.6 + - - -
459H SER 3.1 4.5 + - - -
460H ALA* 3.4 17.7 + - - +
567H LYS* 4.9 4.5 - - - -
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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
------------------------------------------------------------
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