Contacts of the helix formed by residues 447 - 461 (chain B) in PDB entry 1U3Q
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 SER 447 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446B ILE* 1.3 77.2 - - - +
448B SER* 1.3 56.9 + - - +
449B GLN* 3.0 20.3 + - - +
450B GLN* 2.9 28.8 + - - -
451B GLN* 2.7 36.7 + - - +
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Residues in contact with SER 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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446B ILE 3.7 1.4 + - - -
447B SER* 1.3 72.5 + - - +
449B GLN* 1.3 62.5 + - - +
451B GLN* 3.2 13.7 + - - +
452B SER* 3.1 25.8 + - - -
448D SER* 5.0 7.3 + - - -
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Residues in contact with GLN 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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447B SER* 3.0 10.4 + - - +
448B SER* 1.3 79.1 - - - +
450B GLN* 1.3 62.9 + - + +
452B SER* 3.2 4.8 + - - -
453B MET* 2.7 44.1 + - + +
435D ASP* 3.2 27.9 - - - +
438D VAL* 4.2 17.8 - - - +
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Residues in contact with GLN 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 ILE* 3.7 26.9 - - + +
447B SER* 2.9 34.3 + - - +
449B GLN* 1.3 84.8 - - + +
451B GLN* 1.3 58.3 + - - +
453B MET* 3.7 8.7 - - + +
454B ARG* 3.0 28.4 + - - +
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Residues in contact with GLN 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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438B VAL* 4.6 1.4 - - - +
441B ILE* 3.7 24.8 - - + +
442B ALA* 2.8 40.3 + - - +
445B GLY 4.1 5.3 + - - -
446B ILE* 2.6 41.7 + - + -
447B SER 2.7 18.3 + - - +
448B SER* 3.6 11.1 - - - +
449B GLN 3.2 0.4 - - - -
450B GLN* 1.3 72.2 - - - +
452B SER* 1.3 65.5 + - - +
455B LEU* 3.0 23.6 + - - +
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Residues in contact with SER 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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448B SER* 3.1 13.0 + - - -
449B GLN* 3.6 8.5 - - - -
451B GLN* 1.3 76.2 - - - +
453B MET* 1.3 63.8 + - - +
455B LEU* 3.2 10.4 + - - +
456B ALA* 3.0 18.9 + - - +
438D VAL* 3.9 33.2 - - - +
451D GLN* 6.0 2.4 - - - +
452D SER* 4.6 12.3 + - - -
455D LEU* 3.6 15.7 - - - +
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Residues in contact with MET 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 GLN* 2.7 46.7 + - + +
450B GLN* 3.7 10.1 - - + +
452B SER* 1.3 77.7 - - - +
454B ARG* 1.3 57.2 + - - +
456B ALA* 3.0 6.8 + - - +
457B ASN* 2.8 44.0 + - - +
431D ASN* 4.1 23.1 - - - +
434D THR* 3.6 26.7 - - + -
435D ASP* 3.2 33.4 - - - +
438D VAL* 4.5 4.7 - - + -
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Residues in contact with ARG 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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390B LEU* 2.8 46.1 + - + +
391B LYS 3.0 14.8 + - - -
392B LEU* 3.8 3.4 - - - +
393B GLN* 4.8 2.0 - - - +
396B GLU* 2.6 43.5 + - - -
441B ILE* 4.3 15.0 - - + +
444B SER* 5.5 5.0 - - - -
446B ILE* 4.7 11.9 - - + -
450B GLN 3.0 18.3 + - - +
451B GLN* 4.0 5.2 - - - +
452B SER 3.4 0.2 - - - -
453B MET* 1.3 73.7 - - - +
455B LEU* 1.3 65.6 + - - +
457B ASN* 3.9 9.5 - - - +
458B LEU* 3.0 37.3 + - + +
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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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434B THR* 5.3 1.6 - - + -
437B LEU* 3.8 29.2 - - + -
438B VAL* 4.5 12.3 - - + -
441B ILE* 3.9 13.6 - - + +
451B GLN 3.0 15.4 + - - +
452B SER* 3.3 11.2 - - - +
453B MET 3.2 0.2 - - - -
454B ARG* 1.3 76.5 - - - +
456B ALA* 1.3 64.3 + - - +
458B LEU* 3.7 2.1 - - - +
459B LEU* 3.1 38.4 + - + +
452D SER* 3.5 44.2 - - - +
455D LEU* 4.4 11.7 - - + -
456D ALA* 4.3 7.4 - - + -
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Residues in contact with ALA 456 (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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452B SER 3.0 12.9 + - - +
453B MET 3.1 9.6 - - - +
455B LEU* 1.3 77.5 - - - +
457B ASN* 1.3 58.0 + - - +
458B LEU 3.2 0.3 + - - -
459B LEU* 3.3 2.8 + - - +
460B MET* 2.9 40.5 + - + +
434D THR* 3.4 33.0 - - + -
455D LEU* 4.4 5.4 - - + -
459D LEU* 3.9 19.6 - - + +
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Residues in contact with ASN 457 (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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390B LEU* 4.0 28.4 - - + +
453B MET* 2.8 40.7 + - - +
454B ARG* 4.0 7.0 - - - +
456B ALA* 1.3 73.5 - - - +
458B LEU* 1.3 64.0 + - - +
460B MET* 4.4 15.9 - - - +
461B LEU* 3.6 24.9 + - - +
430D LEU* 6.0 1.6 - - - +
431D ASN* 4.4 16.2 + - - +
434D THR* 5.5 1.2 + - - +
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Residues in contact with LEU 458 (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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387B PHE* 4.5 12.8 - - + -
390B LEU* 4.0 19.3 - - + -
392B LEU* 3.8 25.4 - - + -
396B GLU* 4.1 18.4 - - + +
400B VAL* 4.9 14.7 - - + +
437B LEU* 4.1 17.0 - - + -
441B ILE* 3.8 23.6 - - + -
454B ARG* 3.0 33.2 + - + +
455B LEU* 3.7 4.3 - - - +
456B ALA 3.2 0.2 - - - -
457B ASN* 1.3 78.1 - - - +
459B LEU* 1.3 67.2 + - + +
461B LEU* 3.3 18.6 + - - +
462B LEU* 4.0 6.2 + - - +
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Residues in contact with LEU 459 (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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400B VAL* 5.5 5.4 - - + -
403B MET* 3.8 27.1 - - + -
437B LEU* 4.6 7.6 - - + -
455B LEU* 3.1 24.7 + - + +
456B ALA 4.0 2.0 - - - +
458B LEU* 1.3 74.4 - - + +
460B MET* 1.3 58.0 + - - +
461B LEU 3.0 5.6 - - - -
462B LEU* 2.8 50.6 + - + +
463B SER 4.3 0.3 + - - -
456D ALA* 3.6 46.2 - - + +
459D LEU* 4.3 21.4 - - + +
460D MET* 4.3 7.2 - - + -
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Residues in contact with MET 460 (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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456B ALA* 2.9 33.7 + - + +
457B ASN* 4.4 13.7 - - - +
458B LEU 3.4 0.2 - - - -
459B LEU* 1.3 76.0 - - - +
461B LEU* 1.3 60.6 + - - +
462B LEU 3.1 0.6 + - - -
463B SER* 3.6 11.9 + - - -
464B HIS* 4.0 1.9 + - - -
403D MET* 3.7 24.0 - - + -
407D ASN* 2.9 41.6 + - - +
430D LEU* 3.8 30.7 - - + -
434D THR* 3.2 25.1 - - + +
459D LEU* 4.4 15.5 - - + -
462D LEU* 5.6 6.1 - - + -
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Residues in contact with LEU 461 (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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383B THR* 4.9 3.1 - - + -
386B ARG* 3.4 48.7 - - + +
387B PHE* 3.3 44.6 - - + -
390B LEU* 3.8 21.1 - - + -
457B ASN 3.6 10.0 + - - +
458B LEU 3.3 10.0 + - - +
459B LEU 3.0 1.0 - - - -
460B MET* 1.3 75.4 - - - +
462B LEU* 1.3 65.6 + - - +
463B SER 3.1 2.7 - - - -
464B HIS* 3.1 24.1 + - + +
465B VAL* 3.1 23.3 + - - +
407D ASN* 5.8 0.2 - - - +
410D MET* 4.5 3.8 - - + -
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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