Contacts of the helix formed by residues 469 - 480 (chain B) in PDB entry 2P1Q
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 469 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445B ASP* 2.6 22.6 + - - -
468B ASP* 1.3 80.4 - - - +
470B ASP* 1.3 65.3 + - - +
471B LEU* 3.0 14.7 + - - +
472B GLY 3.0 10.4 + - - -
492B PRO* 3.4 14.4 + - - +
493B PHE* 3.2 13.9 - - - -
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Residues in contact with ASP 470 (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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469B SER* 1.3 75.3 - - - +
471B LEU* 1.3 62.2 + - - +
472B GLY 3.0 0.6 + - - -
473B MET 3.2 1.7 + - - -
474B HIS* 3.0 21.2 + - - +
492B PRO 3.7 5.0 + - - +
493B PHE* 4.0 4.9 - - - -
494B GLY* 2.7 35.8 + - - +
496B LYS* 3.7 33.6 + - + -
497B ALA* 3.1 37.5 + - + +
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Residues in contact with LEU 471 (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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445B ASP* 3.7 13.2 - - + +
449B GLU* 6.0 0.4 - - - +
469B SER* 3.0 14.5 + - - +
470B ASP* 1.3 76.7 - - - +
472B GLY* 1.3 57.8 + - - +
474B HIS* 3.5 18.9 - - + +
475B HIS* 3.0 76.2 + - + +
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Residues in contact with GLY 472 (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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445B ASP* 3.6 21.0 + - - -
448B PHE* 3.2 38.2 - - - +
469B SER 3.0 8.3 + - - -
471B LEU* 1.3 81.1 - - - +
473B MET* 1.3 63.1 + - - +
475B HIS* 3.3 7.2 + - - -
476B VAL* 3.5 5.2 + - - +
493B PHE* 4.0 5.6 - - - -
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Residues in contact with MET 473 (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 PHE* 5.6 0.4 - - - -
470B ASP 3.2 3.0 + - - +
472B GLY* 1.3 74.6 - - - +
474B HIS* 1.3 62.5 + - - +
476B VAL* 3.2 7.5 + - + +
477B LEU* 3.0 39.5 + - + +
486B LEU* 4.5 7.2 - - + -
488B ILE* 3.5 30.3 - - + -
493B PHE* 3.7 27.4 - - + -
494B GLY 4.3 3.1 - - - +
497B ALA* 3.9 11.2 - - + -
498B LEU* 3.7 37.7 - - + +
511B LEU* 4.9 2.5 - - + -
513B MET* 3.7 33.9 - - + +
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Residues in contact with HIS 474 (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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470B ASP 3.0 18.1 + - - +
471B LEU* 3.5 25.1 - - + +
473B MET* 1.3 77.9 - - - +
475B HIS* 1.3 67.1 + + - +
477B LEU* 4.1 0.2 - - - +
478B SER* 2.8 57.0 + - - -
497B ALA* 3.6 9.2 - - + +
500B ALA* 4.8 9.6 - - + +
501B ASN* 3.1 31.9 + - - -
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Residues in contact with HIS 475 (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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445B ASP 4.2 7.0 - - - -
448B PHE 3.3 17.5 - - - +
449B GLU* 3.7 42.3 + - + +
452B GLY* 3.4 13.9 - - - -
471B LEU* 3.0 62.7 + - + +
472B GLY* 3.7 5.2 - - - +
473B MET 3.3 0.6 - - - -
474B HIS* 1.3 82.2 - + - +
476B VAL* 1.3 58.6 + - - +
478B SER* 4.1 2.6 - - - -
479B GLY* 2.9 23.7 + - - -
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Residues in contact with VAL 476 (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 PHE* 3.7 34.1 - - + +
451B ILE* 4.0 18.4 - - + -
452B GLY* 4.7 0.2 - - - -
461B LEU* 3.9 22.2 - - + -
472B GLY 3.5 4.2 + - - +
473B MET* 3.2 10.2 + - - +
474B HIS 3.2 0.4 - - - -
475B HIS* 1.3 74.5 - - - +
477B LEU* 1.3 65.7 + - - +
480B CYS* 3.0 43.6 + - - +
483B LEU* 4.0 20.2 - - + +
486B LEU* 4.1 13.0 - - + -
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Residues in contact with LEU 477 (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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473B MET* 3.0 43.0 + - + +
476B VAL* 1.3 75.9 - - - +
478B SER* 1.3 62.2 + - - +
483B LEU* 4.0 4.5 - - + -
486B LEU* 3.8 22.2 - - + -
497B ALA 4.0 9.9 - - - +
498B LEU* 4.8 3.4 - - - -
501B ASN* 3.7 37.1 + - + +
504B LYS* 3.4 36.2 - - + +
505B LEU* 4.6 11.9 - - + -
508B MET* 4.0 26.2 - - + -
511B LEU* 5.2 2.7 - - + -
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Residues in contact with SER 478 (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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474B HIS* 2.8 43.5 + - - -
475B HIS* 4.1 2.7 - - - -
477B LEU* 1.3 79.7 - - - +
479B GLY* 1.3 58.8 + - - +
480B CYS 3.8 0.2 - - - -
481B ASP* 5.0 2.4 - - - +
501B ASN* 3.9 8.2 - - - +
504B LYS* 5.9 0.2 + - - -
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Residues in contact with GLY 479 (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 GLY* 3.3 20.4 - - - +
456B LYS* 2.7 30.2 + - - +
475B HIS 2.9 14.7 + - - -
478B SER* 1.3 80.4 - - - +
480B CYS* 1.3 60.4 + - - +
481B ASP* 3.0 12.2 + - - +
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Residues in contact with CYS 480 (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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451B ILE* 3.7 29.6 - - - -
452B GLY* 4.1 1.3 - - - -
455B ALA 4.0 12.6 - - - +
458B MET* 3.6 26.9 - - + +
476B VAL* 3.0 29.5 + - - +
477B LEU 4.5 0.4 + - - -
478B SER 3.8 0.8 - - - -
479B GLY* 1.3 72.4 - - - +
481B ASP* 1.3 62.4 + - - +
482B SER 3.1 3.9 + - - -
483B LEU* 3.2 25.3 + - + +
504B LYS* 2.9 20.4 + - - -
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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