Contacts of the helix formed by residues 434 - 449 (chain B) in PDB entry 4AY6
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 ASN 434 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429B HIS* 3.0 52.5 + - - +
432B SER* 3.1 15.9 - - - +
433B GLY* 1.3 77.2 - - - +
435B ILE* 1.3 61.1 + - - +
436B PRO* 3.7 3.4 - - + -
437B GLU* 3.1 26.4 - - - +
438B ALA* 3.4 15.4 + - - +
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Residues in contact with ILE 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B LYS* 4.2 32.5 - - + +
433B GLY* 3.5 14.5 + - - +
434B ASN* 1.3 72.8 - - - +
436B PRO* 1.4 76.8 - - + +
437B GLU 3.1 2.0 - - - -
438B ALA* 2.8 13.2 + - - +
439B ILE* 2.8 17.0 + - + +
462B CYS* 3.7 28.0 - - + +
465B ILE* 4.6 24.2 - - + -
466B VAL* 3.8 26.9 - - + -
869B PRO* 5.6 5.6 - - + -
871B VAL* 5.5 2.2 - - + -
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Residues in contact with PRO 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B ASN* 4.5 1.1 - - - -
435B ILE* 1.4 91.6 - - + +
437B GLU* 1.3 69.7 + - - +
439B ILE* 3.5 10.1 + - + +
440B ALA* 3.0 26.9 + - - +
466B VAL* 6.0 1.6 - - + -
871B VAL* 4.3 27.4 - - + -
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Residues in contact with GLU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B HIS* 3.6 27.8 - - + +
434B ASN* 3.1 41.9 - - + +
436B PRO* 1.3 85.2 - - - +
438B ALA* 1.3 62.9 + - - +
440B ALA* 3.4 8.8 - - - +
441B SER* 3.2 25.3 + - - -
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Residues in contact with ALA 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B ALA* 3.2 26.3 - - - +
429B HIS* 3.8 6.9 - - - +
430B LYS* 3.7 17.5 - - + +
434B ASN 3.4 14.6 + - - +
435B ILE* 2.8 11.3 + - - +
437B GLU* 1.3 81.0 - - - +
439B ILE* 1.3 60.6 + - - +
442B TYR* 3.0 34.7 + - + -
462B CYS* 4.6 5.6 - - - -
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Residues in contact with ILE 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B ILE* 2.8 23.8 + - + +
436B PRO* 3.6 11.2 - - + +
438B ALA* 1.3 73.4 - - - +
440B ALA* 1.3 71.7 + - - +
442B TYR* 3.0 3.3 + - - +
443B ARG* 2.9 49.5 + - - +
459B LEU* 3.9 18.4 - - + -
462B CYS* 3.8 28.0 - - + -
463B LEU* 4.1 19.1 - - + -
466B VAL* 4.4 13.2 - - + -
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Residues in contact with ALA 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B PRO 3.0 14.1 + - - +
437B GLU* 3.4 13.2 - - - +
439B ILE* 1.3 81.5 - - - +
441B SER* 1.3 58.2 + - - +
443B ARG* 2.9 21.3 + - - +
444B THR* 3.1 17.7 + - - -
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Residues in contact with SER 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B HIS* 3.4 25.0 + - - +
425B LEU* 3.6 20.5 - - - +
426B ALA* 3.4 25.1 - - - -
429B HIS* 4.9 2.4 - - - -
437B GLU 3.2 11.8 + - - -
439B ILE 3.2 0.2 - - - -
440B ALA* 1.3 79.9 - - - +
442B TYR* 1.3 61.4 + - - +
444B THR* 3.6 9.3 + - - -
445B ALA* 3.1 17.2 + - - +
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Residues in contact with TYR 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423B SER* 3.6 24.7 - - - -
426B ALA* 3.6 24.5 - - + -
427B SER* 2.9 26.0 + - - -
430B LYS* 4.2 7.3 - - + +
438B ALA* 3.0 25.4 + - + -
439B ILE* 3.0 7.6 + - - +
441B SER* 1.3 73.0 - - - +
443B ARG* 1.3 66.5 + - - +
445B ALA* 3.1 4.7 + - - +
446B LEU* 3.0 27.1 + - - +
455B ALA* 3.9 26.0 - - + +
458B ASN* 3.3 34.8 + - + +
459B LEU* 4.1 29.2 - - + -
462B CYS* 4.2 15.7 - - - -
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Residues in contact with ARG 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B ILE* 2.9 36.8 + - + +
440B ALA* 3.2 10.1 - - - +
442B TYR* 1.3 75.7 - - - +
444B THR* 1.3 58.2 + - - +
446B LEU* 3.1 7.6 + - - +
447B LYS* 2.9 29.6 + - - +
459B LEU* 4.4 18.5 - - + +
463B LEU* 3.9 26.7 - - - +
468B ASP* 4.2 8.3 + - - -
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Residues in contact with THR 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422B HIS* 4.0 28.3 - - + +
440B ALA 3.1 14.1 + - - -
441B SER* 3.8 10.5 - - - -
443B ARG* 1.3 76.5 - - - +
445B ALA* 1.3 62.9 + - - +
447B LYS* 3.2 11.1 + - + +
448B LEU* 3.1 31.8 + - + +
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Residues in contact with ALA 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ALA* 3.6 34.8 - - - +
422B HIS* 3.7 11.8 - - + +
423B SER* 3.8 15.7 - - - +
441B SER 3.1 11.8 + - - +
442B TYR* 3.1 10.8 + - - +
444B THR* 1.3 79.1 - - - +
446B LEU* 1.3 57.4 + - - +
448B LEU* 3.5 1.7 + - - -
449B LYS* 3.1 23.6 + - - +
452B PHE* 4.7 3.9 - - + -
455B ALA* 4.6 7.0 - - + -
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Residues in contact with LEU 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B TYR 3.0 12.0 + - - +
443B ARG* 3.1 8.0 + - - +
445B ALA* 1.3 75.4 - - - +
447B LYS* 1.3 67.7 + - - +
449B LYS 3.7 4.7 - - - +
450B PRO* 3.0 35.7 - - + +
452B PHE* 3.6 35.0 - - + +
455B ALA* 3.8 16.2 - - + -
456B TYR* 3.9 28.0 - - + +
459B LEU* 3.6 30.7 - - + -
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Residues in contact with LYS 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443B ARG 2.9 13.0 + - - +
444B THR* 3.4 15.3 - - + +
446B LEU* 1.3 78.0 - - - +
448B LEU* 1.3 63.8 + - + +
450B PRO* 3.7 12.6 - - - +
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Residues in contact with LEU 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B PRO 4.1 3.4 - - - +
417B ALA* 3.3 42.8 - - + +
419B ALA* 4.0 8.7 - - + -
422B HIS* 3.5 35.4 - - + +
444B THR* 3.1 22.3 + - + +
445B ALA 3.7 5.8 - - - +
447B LYS* 1.3 83.6 - - + +
449B LYS* 1.3 58.8 + - - +
450B PRO* 3.7 4.9 - - - +
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Residues in contact with LYS 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B ALA* 3.7 17.5 - - + +
420B ASP* 3.3 23.1 + - - -
445B ALA 3.1 6.9 + - - +
446B LEU* 3.2 9.8 - - - +
448B LEU* 1.3 78.5 - - - +
450B PRO* 1.4 63.9 - - + +
451B ASP* 3.0 25.7 + - + +
452B PHE* 3.6 38.8 - - + +
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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