Contacts of the helix formed by residues 465 - 478 (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 465 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462B ASP* 3.2 18.9 + - - +
463B THR 3.2 0.2 - - - -
464B SER* 1.3 80.6 + - - +
466B PRO* 1.3 68.5 - - - +
467B GLU* 3.0 24.2 + - - +
468B LYS* 3.0 36.1 + - + +
469B VAL* 3.1 16.4 + - - +
507B PHE* 4.5 0.4 - - - -
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Residues in contact with PRO 466 (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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464B SER 3.6 9.2 - - - +
465B ASP* 1.3 88.3 - - - +
467B GLU* 1.3 55.7 + - - +
469B VAL* 3.1 3.2 + - + +
470B VAL* 2.9 34.7 + - - +
507B PHE* 3.9 26.7 - - + -
508B ASN* 4.4 8.3 - - + +
511B THR* 3.4 31.0 - - + +
512B PHE* 4.3 11.3 - - - +
515B ARG* 5.5 3.6 - - + -
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Residues in contact with GLU 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B ASP* 3.0 14.1 + - - +
466B PRO* 1.3 79.8 - - - +
468B LYS* 1.3 59.8 + - + +
470B VAL* 3.4 4.4 + - - +
471B SER* 3.0 26.7 + - - -
515B ARG* 2.8 47.3 + - - +
519B HIS* 2.7 33.3 + - + -
529B VAL* 5.2 0.2 - - - +
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Residues in contact with LYS 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B THR* 4.1 7.0 - - + +
462B ASP* 3.9 36.2 + - + +
465B ASP* 3.0 30.3 + - + +
467B GLU* 1.3 75.8 - - + +
469B VAL* 1.3 61.1 + - - +
471B SER* 3.7 7.4 - - - -
472B ALA* 3.0 27.9 + - - +
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Residues in contact with VAL 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B THR* 4.5 6.7 - - + -
462B ASP 4.2 0.7 - - - +
463B THR* 3.7 33.9 - - + -
465B ASP 3.1 13.8 + - - +
466B PRO 3.1 6.5 + - - +
468B LYS* 1.3 77.6 - - - +
470B VAL* 1.3 59.7 + - - +
472B ALA* 3.3 1.3 + - - +
473B PHE* 2.8 28.9 + - - +
497B LEU* 4.0 7.8 - - + +
498B MET* 3.6 32.8 - - + -
501B ALA* 4.1 8.5 - - + -
507B PHE* 3.8 15.9 - - + -
512B PHE* 3.8 9.6 - - + -
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Residues in contact with VAL 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B PRO 2.9 20.7 + - - +
467B GLU* 3.7 6.5 - - - +
469B VAL* 1.3 77.0 - - - +
471B SER* 1.3 62.6 + - - +
473B PHE* 3.3 2.6 + - - +
474B LEU* 2.9 38.2 + - + +
512B PHE* 3.5 41.3 - - + +
515B ARG* 3.9 10.3 - - + -
516B LEU* 3.8 22.9 - - + +
519B HIS* 3.8 27.4 - - + -
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Residues in contact with SER 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B GLU* 3.0 17.7 + - - -
468B LYS* 3.7 9.0 - - - -
469B VAL 3.2 0.2 - - - -
470B VAL* 1.3 78.3 - - - +
472B ALA* 1.3 61.7 + - - +
474B LEU* 3.3 5.8 + - - +
475B LYS* 3.0 47.9 + - - +
519B HIS* 6.4 2.0 - - - -
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Residues in contact with ALA 472 (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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438B LEU* 4.3 21.3 - - + -
457B ILE* 5.2 3.8 - - + -
461B THR* 3.9 22.7 - - + +
468B LYS 3.0 18.4 + - - +
469B VAL 3.9 0.4 - - - +
471B SER* 1.3 75.5 + - - +
473B PHE* 1.3 64.3 + - - +
475B LYS* 3.9 0.8 - - - +
476B VAL* 3.0 29.6 + - - +
497B LEU* 3.8 18.8 - - + -
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Residues in contact with PHE 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B VAL 2.8 19.2 + - - +
470B VAL* 3.6 5.8 - - - +
471B SER 3.3 0.2 - - - -
472B ALA* 1.3 77.1 - - - +
474B LEU* 1.3 76.0 + - + +
476B VAL* 4.0 3.7 - - - +
477B SER* 3.0 37.3 + - - -
494B VAL* 3.6 37.1 - - + +
497B LEU* 3.7 11.6 - - + +
498B MET* 4.2 16.6 - - + -
512B PHE* 4.6 6.5 - + + -
516B LEU* 4.3 14.8 - - + -
538B PRO* 4.2 8.3 - - + -
541B ALA* 3.5 24.9 - - + -
542B LEU* 3.9 28.0 - - + -
545B MET* 4.5 9.6 - - - -
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Residues in contact with LEU 474 (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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470B VAL* 2.9 29.2 + - + +
471B SER* 3.9 5.2 - - - +
473B PHE* 1.3 81.1 - - + +
475B LYS* 1.3 60.7 + - + +
477B SER* 3.1 3.3 + - - -
478B SER* 2.9 31.0 + - - -
516B LEU* 3.9 20.2 - - + -
519B HIS* 3.5 38.4 - - + +
520B MET* 4.1 2.2 - - + -
532B ILE* 4.1 26.4 - - + +
538B PRO* 3.9 30.2 - - + +
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Residues in contact with LYS 475 (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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437B PHE* 4.8 0.9 - - - -
438B LEU* 2.9 56.8 + - + +
439B ALA* 4.5 7.7 + - - +
441B PRO* 3.7 24.8 - - + +
471B SER* 3.0 38.5 + - - +
472B ALA* 3.9 0.7 - - - +
474B LEU* 1.3 76.3 - - + +
476B VAL* 1.3 61.8 + - - +
478B SER* 2.5 26.4 + - - -
479B VAL* 3.9 1.4 + - - +
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Residues in contact with VAL 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B PHE* 3.9 24.7 - - + -
438B LEU* 4.6 4.0 - - + -
446B LEU* 4.8 6.7 - - + -
457B ILE* 4.1 25.6 - - + -
472B ALA 3.0 19.0 + - - +
473B PHE* 4.0 3.4 - - - +
475B LYS* 1.3 76.6 - - - +
477B SER* 1.3 62.8 + - - +
478B SER 3.2 0.7 + - - -
479B VAL* 3.2 22.9 - - - +
490B VAL* 3.8 23.9 - - + +
493B ALA* 3.7 26.7 - - + -
494B VAL* 4.5 7.0 - - + +
497B LEU* 5.6 2.0 - - + -
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Residues in contact with SER 477 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B PHE* 3.0 23.8 + - - -
474B LEU* 3.1 10.9 + - - -
476B VAL* 1.3 77.3 - - - +
478B SER* 1.3 60.9 + - - +
479B VAL 3.1 0.9 - - - -
480B PHE* 3.1 9.5 + - - +
490B VAL* 4.1 11.4 - - - -
494B VAL* 5.1 0.7 - - - -
537B GLY* 3.1 30.3 - - - -
538B PRO* 3.4 19.0 - - - +
541B ALA* 3.5 29.4 - - - -
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Residues in contact with SER 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B PRO* 3.8 9.0 - - - +
474B LEU 2.9 17.9 + - - -
475B LYS* 2.5 21.3 + - - -
477B SER* 1.3 75.5 - - - +
479B VAL* 1.3 64.0 + - - +
480B PHE 3.3 3.2 + - - +
481B LYS* 5.2 4.2 + - - -
532B ILE* 6.5 1.6 - - - -
534B ASN* 6.0 1.5 + - - -
537B GLY* 4.9 1.9 - - - -
538B PRO* 4.8 8.5 - - - -
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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