Contacts of the helix formed by residues 441 - 455 (chain B) in PDB entry 3IAD
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 LYS 441 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393B SER* 3.8 21.8 - - - -
435B LEU* 3.6 29.8 - - - +
436B ALA* 4.6 8.7 - - - +
438B ASP* 2.8 17.0 + - + +
440B SER* 1.3 79.7 - - - +
442B HIS* 1.3 63.3 + - - +
443B MET 3.4 2.6 + - - -
444B ASN* 3.4 18.7 + - + +
445B LEU* 3.1 28.6 + - + +
606B ASP* 4.9 10.5 + - - +
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Residues in contact with HIS 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B ALA 6.0 0.2 - - - -
438B ASP 4.0 0.8 + - - -
439B MET 3.2 18.6 + - - +
440B SER 3.2 2.2 - - - -
441B LYS* 1.3 77.1 - - - +
443B MET* 1.3 79.7 + - + +
445B LEU* 3.3 7.1 + - - +
446B LEU* 3.0 39.8 + - + +
481B HIS* 2.8 37.8 + + + +
485B LEU* 4.1 1.6 - - - +
541B TYR 5.1 0.6 + - - -
542B ILE* 3.7 38.0 + - + +
546B LEU* 4.0 21.8 - - + -
604B PHE* 3.6 24.9 - + + +
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Residues in contact with MET 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B SER 4.9 0.9 + - - +
441B LYS 3.4 1.0 - - - -
442B HIS* 1.3 92.6 - - + +
444B ASN* 1.3 61.6 + - - +
446B LEU* 3.3 13.7 + - + +
447B ALA* 2.8 31.3 + - - +
541B TYR 4.8 12.3 - - - +
542B ILE* 5.4 3.1 - - + -
600B ILE* 5.9 3.8 - - + -
604B PHE* 3.6 10.6 + - + +
605B LEU* 3.5 38.4 - - + -
606B ASP 5.8 1.3 - - - +
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Residues in contact with ASN 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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440B SER 4.8 0.6 + - - -
441B LYS* 3.4 25.7 + - + +
443B MET* 1.3 78.5 - - - +
445B LEU* 1.3 63.4 + - + +
447B ALA* 3.4 6.1 + - - +
448B ASP* 3.0 35.3 + - - +
606B ASP* 4.3 22.2 + - - +
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Residues in contact with LEU 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B ALA* 3.3 44.6 - - + +
441B LYS* 3.1 17.6 + - + +
442B HIS* 3.4 10.8 - - - +
443B MET 3.3 0.2 - - - -
444B ASN* 1.3 80.6 - - + +
446B LEU* 1.3 58.0 + - - +
448B ASP* 3.5 6.9 + - - +
449B LEU 3.1 19.2 + - - -
474B GLN* 6.3 1.6 - - + -
477B GLN* 4.2 19.5 - - + +
478B ASN* 3.0 33.8 + - - +
481B HIS* 3.7 35.4 - - + +
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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 HIS* 3.0 36.1 + - + +
443B MET* 3.7 13.9 - - - +
445B LEU* 1.3 75.7 - - - +
447B ALA* 1.3 59.9 + - - +
449B LEU* 3.2 3.6 + - + -
450B LYS* 2.9 44.2 + - + +
478B ASN* 4.5 1.8 - - - -
541B TYR 6.0 0.7 - - - +
545B PRO* 3.9 29.2 - - + +
546B LEU* 4.0 18.8 - - + +
549B THR* 3.6 33.9 - - + +
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Residues in contact with ALA 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 MET 2.8 20.4 + - - +
444B ASN* 3.6 8.3 - - - +
446B LEU* 1.3 74.3 - - - +
448B ASP* 1.3 64.1 + - - +
450B LYS* 3.5 10.0 + - - +
451B THR* 3.1 26.5 + - - -
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Residues in contact with ASP 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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444B ASN* 3.0 25.3 + - - +
445B LEU* 3.8 9.7 - - - +
447B ALA* 1.3 77.1 - - - +
449B LEU* 1.3 60.4 + - - +
451B THR* 3.4 7.2 + - - -
452B MET* 3.0 27.7 + - - +
474B GLN* 3.5 43.9 + - + +
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Residues in contact with LEU 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B LEU 3.1 16.8 + - - +
446B LEU* 3.2 6.5 + - + +
448B ASP* 1.3 72.9 - - - +
450B LYS* 1.3 58.8 + - - +
452B MET* 3.2 8.0 + - + +
453B VAL* 2.9 33.5 + - + +
474B GLN* 6.1 0.2 - - - -
475B VAL* 5.5 4.0 - - + -
478B ASN* 3.8 28.0 - - + +
546B LEU* 4.2 15.3 - - + +
549B THR* 3.4 28.7 - - + +
550B TRP* 3.8 30.3 - - + +
553B LEU* 3.6 32.1 - - + -
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Residues in contact with LYS 450 (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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446B LEU* 2.9 36.1 + - + +
447B ALA* 3.8 8.1 - - - +
449B LEU* 1.3 75.7 - - - +
451B THR* 1.3 57.1 + - - +
453B VAL* 3.3 5.2 + - - +
454B GLU* 2.9 42.6 + - - +
545B PRO* 5.2 5.6 - - - +
549B THR* 3.6 31.4 - - + +
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Residues in contact with THR 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B ALA 3.1 18.0 + - - -
448B ASP* 3.7 7.1 - - - -
450B LYS* 1.3 73.4 - - - +
452B MET* 1.3 69.8 + - + +
454B GLU* 3.4 12.5 + - + +
455B THR* 2.9 41.7 + - + +
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Residues in contact with MET 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B ASP 3.0 11.4 + - - +
449B LEU* 3.2 15.9 + - + +
451B THR* 1.3 83.0 - - + +
453B VAL* 1.3 57.3 + - - +
455B THR* 3.5 7.8 - - - +
456B LYS* 3.0 28.6 + - - +
464B LEU* 6.3 0.7 - - + -
466B LEU* 5.2 6.7 - - + -
471B ASP* 3.1 50.0 - - - +
474B GLN* 3.2 25.8 - - - +
475B VAL* 4.6 15.5 - - + -
553B LEU* 4.3 13.5 - - + +
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Residues in contact with VAL 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B LEU* 2.9 17.3 + - + +
450B LYS* 3.6 8.7 - - - +
451B THR 3.3 0.2 - - - -
452B MET* 1.3 75.0 - - - +
454B GLU* 1.3 66.4 + - + +
456B LYS* 3.3 20.9 + - + +
549B THR* 3.6 28.5 - - + +
552B ASP* 4.0 23.8 - - + +
553B LEU* 3.6 28.9 - - + +
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Residues in contact with GLU 454 (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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450B LYS* 2.9 32.3 + - + +
451B THR* 3.4 11.8 + - - +
453B VAL* 1.3 79.1 - - + +
455B THR* 1.3 64.1 + - + +
456B LYS 3.5 0.8 + - - -
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Residues in contact with THR 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B THR* 2.9 32.1 + - + +
452B MET* 3.5 9.7 + - - +
454B GLU* 1.3 82.7 - - + +
456B LYS* 1.3 66.3 + - - +
457B LYS* 3.4 16.9 + - - +
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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