Contacts of the helix formed by residues 452 - 460 (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 LYS 452 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449B LEU 4.9 0.4 + - - +
450B GLY 3.1 1.4 - - - -
451B PRO* 1.3 90.1 - - + +
453B SER* 1.3 64.4 + - - +
454B SER* 3.2 4.9 - - - -
455B VAL* 3.0 27.2 + - + +
456B LEU* 3.1 27.5 + - + +
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Residues in contact with SER 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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446B LEU* 4.0 18.1 + - - +
449B LEU* 3.5 33.3 + - - -
450B GLY 3.1 18.2 + - - -
451B PRO 3.3 2.2 + - - -
452B LYS* 1.3 77.5 - - - +
454B SER* 1.3 65.1 + - - +
456B LEU* 3.3 6.0 + - - +
457B ILE* 3.0 29.7 + - - +
489B ALA* 4.8 13.2 + - - +
493B ALA* 5.5 0.6 - - - +
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Residues in contact with SER 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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451B PRO 5.0 3.7 + - - -
452B LYS* 4.4 2.3 + - - -
453B SER* 1.3 82.4 + - - +
455B VAL* 1.3 76.8 + - - +
457B ILE* 3.5 2.9 + - - +
458B ALA 3.4 11.1 + - - -
492B ASP* 3.5 42.1 - - - +
493B ALA* 3.9 12.1 - - - +
496B ALA* 3.3 21.8 - - - +
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Residues in contact with VAL 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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452B LYS* 3.0 18.3 + - + +
454B SER* 1.3 84.2 - - - +
456B LEU* 1.3 61.6 + - + +
458B ALA* 3.4 3.6 + - - +
459B GLN* 2.8 40.2 + - + +
496B ALA* 4.7 4.9 - - - -
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Residues in contact with LEU 456 (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 0.7 - - - +
434B VAL* 3.9 17.5 - - + -
449B LEU* 3.8 32.3 - - + +
452B LYS* 3.1 25.2 + - + +
453B SER* 3.3 7.8 + - - +
455B VAL* 1.3 79.0 - - + +
457B ILE* 1.3 59.9 + - + +
459B GLN* 3.8 23.3 - - - +
460B GLN* 2.9 36.6 + - + +
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Residues in contact with ILE 457 (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* 3.9 20.0 - - + +
437B PHE* 4.1 19.1 - - + -
438B LEU* 5.3 3.4 - - + -
446B LEU* 4.9 2.9 - - + -
449B LEU* 3.6 27.1 - - + -
453B SER 3.0 19.8 + - - +
454B SER 3.7 4.5 - - - +
455B VAL 3.3 0.2 - - - -
456B LEU* 1.3 78.5 - - - +
458B ALA* 1.3 59.8 + - - +
460B GLN* 3.5 1.6 + - - +
461B THR* 2.7 35.7 + - - +
472B ALA* 5.2 3.1 - - + -
476B VAL* 4.1 18.4 - - + -
493B ALA* 4.3 20.0 - - + +
497B LEU* 4.7 16.6 - - + -
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Residues in contact with ALA 458 (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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454B SER 3.4 6.9 + - - +
455B VAL* 3.9 6.7 - - - +
456B LEU 3.3 0.2 - - - -
457B ILE* 1.3 77.0 - - - +
459B GLN* 1.3 64.6 + - - +
461B THR* 3.3 12.3 + - - +
463B THR* 4.6 0.2 - - - +
496B ALA* 3.5 36.3 - - + +
497B LEU* 3.8 14.4 - - - +
500B LYS* 2.9 31.7 + - + +
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Residues in contact with GLN 459 (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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455B VAL* 2.8 26.9 + - + +
456B LEU* 3.7 25.3 - - - +
458B ALA* 1.3 78.6 - - - +
460B GLN* 1.3 83.9 + - - +
461B THR 3.5 2.3 + - - +
500B LYS* 3.8 13.8 + - - +
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Residues in contact with GLN 460 (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* 3.8 32.8 - - + +
438B LEU* 5.6 2.9 - - - +
456B LEU* 2.9 21.3 + - + +
459B GLN* 1.3 108.4 + - - +
461B THR* 1.3 61.4 + - - +
462B ASP 4.1 0.9 + - - -
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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