Contacts of the helix formed by residues 480 - 490 (chain B) in PDB entry 2P2J
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 ASP 480 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272B LYS* 6.0 0.7 - - - +
477B LEU* 2.9 19.0 + - + +
478B PHE 4.1 4.5 - - - +
479B GLY* 1.3 81.2 - - - +
481B HIS* 1.3 63.5 + - - +
482B GLU* 3.2 11.1 + - - +
483B ARG* 3.2 35.4 + - + +
484B PHE 3.2 13.5 + - - -
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Residues in contact with HIS 481 (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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65B VAL* 2.7 34.3 + - - +
66B SER* 5.1 2.9 - - - -
475B ARG 3.7 11.9 - - - -
476B THR* 2.9 28.1 + - - +
480B ASP* 1.3 75.1 - - - +
482B GLU* 1.3 74.6 + - - +
484B PHE* 3.2 25.5 - + - +
485B GLU* 2.9 33.7 + - + +
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Residues in contact with GLU 482 (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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480B ASP* 3.2 7.9 - - - +
481B HIS* 1.3 95.9 + - - +
483B ARG* 1.3 60.0 + - - +
485B GLU* 3.3 10.7 + - - +
486B GLN* 2.8 31.2 + - - +
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Residues in contact with ARG 483 (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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272B LYS* 5.0 15.7 - - + +
477B LEU* 4.0 13.0 - - + -
480B ASP* 3.2 36.3 + - + +
482B GLU* 1.3 74.9 - - - +
484B PHE* 1.3 53.1 + - - +
486B GLN* 3.1 17.0 + - - +
487B THR* 2.7 51.1 + - - +
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Residues in contact with PHE 484 (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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65B VAL* 4.0 8.3 - - + -
67B ILE* 4.2 3.4 - - + -
417B GLU* 5.7 2.7 - - + -
473B GLN* 5.2 0.9 - - + -
474B ALA* 3.5 30.5 - - + -
475B ARG 3.3 15.3 - - - -
476B THR* 3.6 22.4 - - - -
477B LEU* 3.5 27.9 - - + +
480B ASP 3.2 5.5 + - - +
481B HIS* 3.2 33.4 - + - +
482B GLU 3.2 0.2 - - - -
483B ARG* 1.3 77.8 - - - +
485B GLU* 1.3 62.1 + - - +
488B TYR* 3.2 56.0 + + - -
489B PHE* 3.6 29.8 - + - -
496B TYR* 5.8 1.3 - + - -
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Residues in contact with GLU 485 (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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62B PRO* 3.6 6.1 - - - +
63B GLY* 2.6 45.7 + - - +
65B VAL* 3.9 28.1 + - + +
481B HIS* 2.9 23.4 + - + +
482B GLU* 3.7 12.6 - - - +
484B PHE* 1.3 74.7 - - - +
486B GLN* 1.3 58.9 + - - +
489B PHE* 3.0 37.0 + - + +
490B SER* 3.4 9.2 + - - -
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Residues in contact with GLN 486 (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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482B GLU 2.8 17.3 + - - +
483B ARG* 3.5 15.2 + - - +
485B GLU* 1.3 74.5 - - - +
487B THR* 1.3 68.6 + - - +
488B TYR 3.5 0.3 + - - -
490B SER* 2.6 33.4 + - - +
491B THR* 4.8 2.4 + - - -
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Residues in contact with THR 487 (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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266B GLY* 6.2 4.3 - - - -
267B SER 6.2 0.9 - - - +
272B LYS* 6.0 0.3 - - - +
477B LEU* 4.3 5.4 - - + +
483B ARG* 2.7 40.8 + - - +
486B GLN* 1.3 77.4 + - - +
488B TYR* 1.3 95.4 + - + +
491B THR* 4.8 7.4 + - - -
497B PHE* 5.2 5.5 - - - +
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Residues in contact with TYR 488 (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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264B THR* 5.5 0.5 - - - +
272B LYS* 6.0 1.0 - - - +
274B VAL* 4.2 8.5 - - - +
417B GLU* 2.6 43.4 + - + +
477B LEU* 4.3 12.2 - - + +
484B PHE* 3.2 45.0 + + - -
487B THR* 1.3 105.5 - - + +
489B PHE* 1.3 72.3 + - + +
490B SER 3.7 1.6 - - - -
491B THR* 5.2 2.1 + - - -
492B PHE 5.3 0.3 + - - +
495B MET 3.2 2.8 - - - +
496B TYR* 3.7 31.2 - + + -
497B PHE* 2.9 46.9 + - - +
498B SER 5.7 3.1 - - - -
515B ARG* 6.0 2.0 - - - -
526B ARG* 4.3 5.9 + - - -
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Residues in contact with PHE 489 (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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60B PHE* 3.7 42.4 - + + +
62B PRO* 5.4 4.9 - - - +
65B VAL* 3.8 35.1 - - + +
67B ILE* 4.3 2.0 - - + -
473B GLN* 3.4 23.3 - - - -
484B PHE* 3.6 41.5 - + - -
485B GLU* 3.0 16.9 + - + +
488B TYR* 1.3 89.7 - - + +
490B SER* 1.3 58.9 + - - +
491B THR 3.8 0.7 - - - -
492B PHE 4.4 7.7 - - - +
493B LYS* 4.4 11.8 - - - +
494B ASN 4.5 3.3 + - - -
495B MET 3.6 19.3 - - - +
496B TYR* 3.7 16.8 - + + -
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Residues in contact with SER 490 (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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485B GLU* 3.4 8.0 + - - -
486B GLN* 2.6 36.0 + - - +
488B TYR 3.7 0.2 - - - -
489B PHE* 1.3 79.3 - - - +
491B THR* 1.3 70.0 + - - +
492B PHE* 3.5 2.0 - - - -
493B LYS* 3.1 34.0 + - - +
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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