Contacts of the helix formed by residues 433 - 440 (chain B) in PDB entry 2GRN
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 433 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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432B ALA* 1.3 77.4 - - - +
434B VAL* 1.3 63.4 + - - +
435B SER* 2.9 13.6 + - - -
436B THR* 2.6 49.3 + - - -
437B PHE* 3.2 16.1 + - - +
449B LEU* 3.4 12.4 - - - +
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Residues in contact with VAL 434 (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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433B ASP* 1.3 74.7 - - - +
435B SER* 1.3 58.9 + - - +
437B PHE* 3.2 4.7 + - - +
438B LEU* 2.9 47.7 + - + +
449B LEU* 4.1 12.8 - - + -
456B LEU* 3.7 38.1 - - + +
457B ILE* 3.9 25.4 - - + +
460B GLN* 3.8 30.5 - - + -
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Residues in contact with SER 435 (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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433B ASP* 2.9 8.7 + - - +
434B VAL* 1.3 77.8 - - - +
436B THR* 1.3 57.4 + - - +
438B LEU* 3.4 8.5 + - - +
439B ALA* 2.9 29.6 + - - +
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Residues in contact with THR 436 (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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432B ALA* 5.8 2.7 - - + -
433B ASP* 2.6 42.7 + - - -
435B SER* 1.3 70.8 - - - +
437B PHE* 1.3 65.4 + - - +
439B ALA* 3.3 7.0 + - - +
440B PHE* 3.1 27.2 + - + +
445B LYS* 3.6 27.4 - - - +
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Residues in contact with PHE 437 (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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432B ALA* 6.0 0.9 - - + +
433B ASP 3.2 10.9 + - - +
434B VAL* 3.2 9.8 + - - +
436B THR* 1.3 80.4 - - - +
438B LEU* 1.3 73.9 + - + +
440B PHE 3.1 0.9 - - - -
441B PRO* 2.8 44.6 - - + +
442B SER 3.6 26.5 - - - -
445B LYS* 3.8 20.2 - - + +
446B LEU* 3.6 38.8 - - + -
449B LEU* 4.4 10.5 - - + -
457B ILE* 4.1 17.7 - - + -
475B LYS 4.8 0.7 - - - -
476B VAL* 3.9 40.6 - - + -
479B VAL* 4.3 7.2 - - + -
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Residues in contact with LEU 438 (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 VAL* 2.9 38.2 + - + +
435B SER* 3.9 6.3 - - - +
437B PHE* 1.3 94.1 - - + +
439B ALA* 1.3 60.3 + - - +
441B PRO* 3.5 5.8 - - - +
457B ILE* 5.3 2.9 - - + -
460B GLN 5.6 2.9 - - - +
461B THR* 4.9 11.2 - - - +
472B ALA* 4.3 19.5 - - + +
475B LYS* 2.9 61.3 + - + +
476B VAL* 4.6 4.5 - - + -
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Residues in contact with ALA 439 (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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435B SER 2.9 17.9 + - - +
436B THR* 3.6 7.0 - - - +
437B PHE 3.1 0.2 - - - -
438B LEU* 1.3 79.0 - - - +
440B PHE* 1.3 89.4 + - + +
441B PRO* 3.7 3.6 - - - +
475B LYS* 4.5 6.8 + - - +
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Residues in contact with PHE 440 (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 THR* 3.1 14.5 + - + +
437B PHE 3.1 2.7 - - - -
439B ALA* 1.3 97.9 - - + +
441B PRO* 1.3 66.7 - - - +
442B SER* 4.4 1.0 - - - -
445B LYS* 3.1 31.6 - - - +
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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