Contacts of the helix formed by residues 444 - 455 (chain B) in PDB entry 2P1N
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 THR 444 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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419B PRO* 3.5 26.5 - - + -
421B ASP* 2.7 26.0 + - - +
442B LEU* 5.5 3.6 - - + -
443B LEU* 1.3 78.2 - - - +
445B ASP* 1.3 59.2 + - - +
446B LYS* 2.6 23.7 + - - +
447B VAL* 3.3 15.8 + - - +
448B PHE* 3.8 2.9 - - - -
467B GLY* 4.1 3.8 - - - -
468B ASP* 3.5 18.6 - - - +
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Residues in contact with ASP 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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444B THR* 1.3 73.9 - - - +
446B LYS* 1.3 62.9 + - - +
447B VAL 3.6 0.2 - - - -
448B PHE* 3.2 19.4 + - - +
449B GLU* 3.2 10.7 + - - +
467B GLY* 3.7 3.6 - - - -
468B ASP* 2.8 35.1 + - - +
469B SER* 2.7 43.3 + - - +
471B LEU* 3.7 15.1 - - + +
472B GLY* 3.6 15.7 + - - +
475B HIS* 4.3 4.9 - - + +
493B PHE* 4.3 0.2 - - - -
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Residues in contact with LYS 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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421B ASP* 3.9 9.4 - - + +
444B THR* 2.6 21.5 + - - +
445B ASP* 1.3 74.8 - - - +
447B VAL* 1.3 64.9 + - - +
449B GLU* 2.9 49.2 + - - +
450B TYR* 2.9 46.8 + - + +
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Residues in contact with VAL 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B ASP* 3.4 37.7 - - - +
424B PHE* 3.5 32.8 - - + -
425B GLY 4.5 2.7 - - - +
439B LEU* 3.8 13.9 - - + -
443B LEU* 3.6 24.0 - - + -
444B THR 3.3 11.1 + - - +
446B LYS* 1.3 74.6 - - - +
448B PHE* 1.3 70.2 + - + +
450B TYR* 2.8 25.5 + - - +
451B ILE* 2.8 21.5 + - + +
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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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439B LEU* 5.3 2.7 - - + -
443B LEU* 5.5 0.2 - - + -
444B THR 3.8 11.7 - - - -
445B ASP* 3.2 12.0 + - - +
446B LYS 3.1 0.8 - - - -
447B VAL* 1.3 87.3 - - + +
449B GLU* 1.3 62.3 + - - +
451B ILE* 2.8 26.5 + - + +
452B GLY* 2.9 10.4 + - - -
461B LEU* 5.0 4.3 - - + -
463B VAL* 4.1 33.9 - - + -
466B ALA* 4.2 6.7 - - + -
467B GLY* 3.8 28.3 - - - -
472B GLY* 3.2 26.9 - - - +
475B HIS* 3.7 8.2 - - - +
476B VAL* 3.5 25.5 - - + +
488B ILE* 6.5 0.2 - - + -
493B PHE* 3.9 25.8 - + - -
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Residues in contact with GLU 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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445B ASP 3.2 6.0 + - - +
446B LYS* 2.9 41.3 + - - +
448B PHE* 1.3 81.2 - - - +
450B TYR* 1.3 68.2 + - + +
452B GLY* 3.2 2.1 + - - -
453B THR* 2.7 40.8 + - + +
471B LEU* 5.9 1.2 - - - +
475B HIS* 3.6 38.0 + - + +
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Residues in contact with TYR 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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421B ASP 3.5 24.0 - - - -
422B ILE* 3.8 19.2 - - + +
425B GLY* 3.3 33.4 - - - +
428B VAL* 3.5 7.9 - - + +
446B LYS* 2.9 50.9 + - + +
447B VAL* 2.8 12.7 + - - +
449B GLU* 1.3 88.3 - - + +
451B ILE* 1.3 62.4 + - + +
453B THR* 4.4 2.2 - - + -
454B TYR* 2.9 43.6 + + + -
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Residues in contact with ILE 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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424B PHE* 5.9 1.3 - - + +
428B VAL* 4.2 13.5 - - + -
437B LEU* 3.8 25.8 - - + -
439B LEU* 4.3 17.3 - - + -
447B VAL* 2.8 22.5 + - + +
448B PHE* 2.8 25.1 + - + +
450B TYR* 1.3 78.6 - - - +
452B GLY* 1.3 54.3 + - - +
455B ALA* 2.9 34.8 + - + +
458B MET* 3.6 28.3 - - + -
461B LEU* 4.2 9.4 - - + -
476B VAL* 4.2 11.7 - - + -
480B CYS* 3.7 11.2 - - - -
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Residues in contact with GLY 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 PHE 2.9 10.3 + - - -
449B GLU 3.2 2.7 + - - -
451B ILE* 1.3 76.4 - - - +
453B THR* 1.3 60.4 + - - +
456B LYS* 3.1 24.8 + - - +
475B HIS* 3.4 28.4 - - - -
479B GLY* 3.2 14.8 - - - -
480B CYS* 4.3 4.7 - - - -
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Residues in contact with THR 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 GLU* 2.7 34.4 + - + +
450B TYR* 4.4 3.8 - - + -
452B GLY* 1.3 78.8 - - - +
454B TYR* 1.3 84.9 + - + +
456B LYS* 3.4 21.6 - - - +
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Residues in contact with TYR 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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425B GLY* 5.1 0.9 - - - -
428B VAL* 3.4 29.4 - - + +
429B GLU* 3.5 48.9 + - + -
431B CYS 5.7 0.2 - - - +
432B LYS* 5.4 5.9 - - - +
450B TYR* 2.9 39.2 + + + +
453B THR* 1.3 91.8 + - + +
455B ALA* 1.3 59.6 + - - +
456B LYS* 3.0 15.4 + - - +
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Residues in contact with ALA 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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428B VAL* 3.7 25.8 - - + -
434B LEU* 5.8 2.9 - - + -
451B ILE* 2.9 23.3 + - + +
453B THR 3.8 0.6 - - - -
454B TYR* 1.3 75.1 - - - +
456B LYS* 1.3 55.9 + - - +
457B LYS 3.2 10.3 + - - -
458B MET* 3.2 40.9 + - + +
480B CYS* 4.2 13.0 - - - -
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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