Contacts of the helix formed by residues 447 - 455 (chain B) in PDB entry 2GPP
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 447 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266B THR* 6.6 0.4 - - + -
269B CYS 5.4 0.6 + - - -
270B ASP* 2.7 40.8 + - + +
273B ASP* 3.2 28.7 + - - +
445B PRO 5.3 3.4 - - - -
446B MET* 1.3 81.1 - - - +
448B LYS* 1.3 70.1 + - - +
449B LEU 3.5 1.1 - - - -
450B PHE* 3.4 7.5 + - - +
451B LEU* 3.2 14.6 + - - +
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Residues in contact with LYS 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 MET 3.9 0.4 + - - -
447B HIS* 1.3 73.4 - - - +
449B LEU* 1.3 64.9 + - - +
451B LEU* 2.8 25.0 + - + +
452B GLU* 2.8 22.9 + - + +
378D SER* 5.2 6.4 - - - -
379D LEU* 3.6 41.5 - - + +
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Residues in contact with LEU 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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273B ASP* 3.4 19.3 + - - +
276B LEU* 3.4 32.3 - - + -
277B VAL* 3.9 9.9 - - + +
280B ILE* 3.8 24.2 - - + -
448B LYS* 1.3 77.4 - - - +
450B PHE* 1.3 64.4 + - - +
452B GLU* 3.2 7.0 + - - +
453B MET* 3.0 37.0 + - + +
379D LEU* 3.5 17.0 - - + +
380D LEU* 3.9 27.6 - - + +
383D LEU* 3.8 16.2 - - + -
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Residues in contact with PHE 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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269B CYS* 3.8 28.9 - - - +
272B ALA* 3.6 33.0 - - + -
273B ASP* 2.9 22.4 + - + +
276B LEU* 3.9 17.7 - - + +
305B TRP* 4.0 24.8 - + - -
306B MET* 5.1 3.4 - - + -
309B LEU* 5.0 0.7 - - + -
435B PHE* 4.5 18.4 - + + -
446B MET* 3.9 24.2 - - + -
447B HIS 3.5 10.3 - - - +
449B LEU* 1.3 77.5 - - - +
451B LEU* 1.3 53.2 + - - +
453B MET* 3.2 2.4 + - - +
454B LEU* 2.8 55.9 + - + +
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Residues in contact with LEU 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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439B LYS* 3.4 35.9 - - + -
446B MET* 3.5 39.3 - - + +
447B HIS 3.2 9.6 + - - +
448B LYS* 2.8 18.3 + - + +
450B PHE* 1.3 75.1 - - - +
452B GLU* 1.3 56.5 + - - +
454B LEU* 3.1 6.6 + - + +
455B GLU* 2.8 46.3 + - - +
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Residues in contact with GLU 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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302B GLN* 5.7 6.3 + - - +
448B LYS* 2.8 24.8 + - + +
449B LEU* 3.5 10.5 - - + +
451B LEU* 1.3 73.9 - - - +
453B MET* 1.3 64.7 + - + +
455B GLU* 3.7 13.3 + - - +
456B ALA* 3.7 13.3 - - - +
378D SER* 3.1 15.4 + - - -
379D LEU* 2.9 36.4 + - - +
380D LEU* 2.9 32.0 + - + +
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Residues in contact with MET 453 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276B LEU* 4.0 21.8 - - + -
280B ILE* 5.6 2.5 - - + -
301B LEU* 3.3 41.7 - - + +
302B GLN* 3.9 10.1 - - + +
305B TRP* 3.1 47.7 + - + +
449B LEU* 3.0 28.7 + - + +
450B PHE 3.6 3.1 - - - +
452B GLU* 1.3 77.1 - - - +
454B LEU* 1.3 67.1 + - - +
456B ALA* 3.5 18.0 + - - +
380D LEU* 4.1 30.7 - - + -
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Residues in contact with LEU 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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305B TRP* 3.8 24.2 - - + -
432B VAL* 4.1 33.9 - - + +
435B PHE* 3.8 22.4 - - + +
436B TYR* 4.2 21.4 - - + +
439B LYS* 4.1 22.7 - - + -
446B MET* 4.4 2.5 - - - -
450B PHE* 2.8 42.0 + - + +
451B LEU* 3.4 6.7 - - + +
453B MET* 1.3 80.1 - - - +
455B GLU* 1.3 58.1 + - + +
456B ALA 3.0 11.1 + - - +
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Residues in contact with GLU 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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436B TYR* 4.4 8.3 - - + +
439B LYS* 2.9 49.1 + - + +
451B LEU* 2.8 31.3 + - - +
452B GLU* 3.9 8.0 + - - +
453B MET 3.3 0.2 - - - -
454B LEU* 1.3 73.7 - - - +
456B ALA* 1.3 59.3 + - - +
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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