Contacts of the helix formed by residues 443 - 455 (chain B) in PDB entry 3Q36
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 HIS 443 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363B THR* 5.7 1.6 - - - +
364B PRO* 2.8 26.5 + - + +
365B PHE 3.1 13.5 + - - -
366B SER* 3.3 24.0 - - - -
367B CYS* 3.5 6.1 - - - -
441B LEU* 3.2 6.4 - - - +
442B ASN* 1.3 91.9 - - - +
444B PRO* 1.3 71.1 - - + +
445B ASN* 2.7 55.6 + - + +
446B GLN* 3.1 23.8 + - + +
447B PHE 3.1 9.0 + - - -
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Residues in contact with PRO 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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285B PRO* 3.9 15.4 - - + +
288B MET* 3.9 10.1 - - + -
312B PHE* 3.6 23.9 - - + -
365B PHE 3.1 27.4 - - - +
366B SER* 3.7 5.8 - - - -
367B CYS* 3.7 4.7 - - - +
370B ILE* 3.7 21.5 - - + -
443B HIS* 1.3 87.1 - - + +
445B ASN* 1.3 57.4 + - - +
447B PHE* 3.0 22.4 - - + +
448B PHE 3.1 4.9 + - - -
458B SF4 4.0 22.9 - - - -
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Residues in contact with ASN 445 (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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312B PHE* 3.1 44.7 + - - -
315B GLY* 3.6 24.3 - - - +
316B ILE* 3.6 6.3 - - - +
364B PRO* 3.3 14.4 - - - +
365B PHE 4.5 0.5 - - - +
443B HIS* 2.7 33.7 + - + +
444B PRO* 1.3 73.4 - - - +
446B GLN* 1.3 66.7 + - - +
448B PHE* 3.1 5.0 + - - +
449B CYS* 3.0 30.5 + - - +
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Residues in contact with GLN 446 (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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439B PHE* 3.4 30.5 - - + +
440B SER 3.1 19.8 + - - +
441B LEU* 3.3 1.5 - - - -
442B ASN* 2.7 43.7 + - - +
443B HIS* 3.1 20.4 + - + +
445B ASN* 1.3 80.5 - - - +
447B PHE* 1.3 52.5 + - - +
449B CYS* 3.3 6.1 + - - +
450B GLU* 2.8 43.7 + - + +
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Residues in contact with PHE 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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283B SER 3.3 23.6 - - - -
284B PHE 4.0 3.4 - - - -
285B PRO* 3.4 27.8 - - + -
424B CYS* 3.5 37.5 - - - -
427B TYR* 3.9 22.2 - + - -
428B PHE* 3.4 36.2 - + + -
431B ILE* 4.4 3.4 - - + -
432B HIS* 4.4 7.2 - + - -
439B PHE* 4.8 4.3 - + - -
441B LEU* 4.0 16.6 - - + -
443B HIS 3.1 6.4 + - - +
444B PRO* 3.0 17.5 - - + +
446B GLN* 1.3 80.4 - - - +
448B PHE* 1.3 53.4 + - - -
450B GLU* 3.3 4.4 + - - -
451B SER* 2.9 25.6 + - - -
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Residues in contact with PHE 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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271B ILE* 3.5 33.7 - - + -
279B LEU* 3.7 14.6 - - + -
283B SER* 3.4 38.4 - - - +
284B PHE* 3.4 31.6 - + - -
312B PHE* 4.2 5.6 - + + -
316B ILE* 3.3 29.4 - - + -
444B PRO 3.1 7.2 + - - +
445B ASN 3.1 9.9 + - - +
447B PHE* 1.3 80.3 - - - +
449B CYS* 1.3 65.0 + - - +
451B SER* 3.3 2.1 + - - -
452B GLN* 2.9 56.1 + - + +
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Residues in contact with CYS 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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315B GLY 5.7 4.0 - - - -
316B ILE* 6.2 1.8 - - - -
445B ASN* 3.0 21.3 + - - +
446B GLN* 3.8 6.1 - - - +
448B PHE* 1.3 84.8 - - - +
450B GLU* 1.3 59.9 + - - +
452B GLN* 3.4 7.0 + - - +
453B ARG* 3.0 43.4 + - - +
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Residues in contact with GLU 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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428B PHE* 3.7 5.1 - - + -
437B CYS 4.6 5.4 - - - +
438B GLY 4.7 2.4 - - - +
439B PHE* 3.0 58.3 - - + +
446B GLN* 2.8 27.8 + - - +
447B PHE 3.7 3.1 - - - +
449B CYS* 1.3 73.7 - - - +
451B SER* 1.3 61.4 + - - +
453B ARG* 2.4 57.1 + - - +
454B ILE* 3.5 18.8 - - + +
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Residues in contact with SER 451 (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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282B LYS 3.3 0.3 + - - -
283B SER* 2.6 38.4 + - - -
428B PHE* 3.6 5.8 - - - -
432B HIS* 2.8 36.3 + - - -
447B PHE* 2.9 18.3 + - - -
448B PHE 3.6 3.8 - - - -
450B GLU* 1.3 76.5 - - - +
452B GLN* 1.3 53.0 + - - +
454B ILE* 3.2 7.8 + - - +
455B LEU* 2.8 32.6 + - - +
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Residues in contact with GLN 452 (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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271B ILE* 5.7 1.6 - - - +
279B LEU* 3.8 16.0 - - - +
283B SER* 2.7 25.3 + - - +
448B PHE* 2.9 48.4 + - + +
449B CYS* 3.7 6.7 - - - +
451B SER* 1.3 71.9 - - - +
453B ARG* 1.3 59.8 + - - +
454B ILE 3.0 2.2 - - - -
455B LEU* 2.7 60.8 + - + +
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Residues in contact with ARG 453 (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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449B CYS* 3.0 32.3 + - - +
450B GLU* 2.4 50.7 + - - +
452B GLN* 1.3 77.4 - - - +
454B ILE* 1.3 60.5 + - + +
455B LEU* 4.9 4.3 - - - +
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Residues in contact with ILE 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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428B PHE* 3.9 30.1 - - + -
432B HIS* 4.2 18.8 - - + +
434B VAL* 4.4 22.0 - - + -
437B CYS 5.4 4.7 - - - +
450B GLU* 3.5 13.5 - - + +
451B SER 3.2 4.7 + - - +
452B GLN 3.0 0.2 - - - -
453B ARG* 1.3 78.6 - - + +
455B LEU* 1.3 74.5 + - - +
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Residues in contact with LEU 455 (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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282B LYS* 5.7 5.2 - - - +
283B SER* 5.3 0.9 + - - -
432B HIS* 4.4 11.1 + - - -
451B SER* 2.8 16.1 + - - +
452B GLN* 2.7 49.8 + - + +
453B ARG 4.9 4.3 - - - +
454B ILE* 1.3 86.4 - - - +
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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