Contacts of the helix formed by residues 508 - 520 (chain B) in PDB entry 2GRR
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 ASN 508 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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466B PRO* 4.3 9.4 - - + +
506B SER 3.4 5.7 + - - +
507B PHE* 1.3 77.8 - - - +
509B SER* 1.3 61.5 + - - +
510B ASN* 3.0 17.6 + - - +
511B THR* 2.9 45.2 + - - +
512B PHE* 3.1 19.9 + - - +
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Residues in contact with SER 509 (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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502B PHE* 3.3 39.0 + - - -
507B PHE* 3.2 13.0 + - - -
508B ASN* 1.3 71.8 + - - +
510B ASN* 1.3 58.5 + - - +
512B PHE* 3.3 3.9 + - - +
513B LEU* 3.0 28.1 + - - +
552B PRO* 4.0 10.4 - - - +
555B LEU* 3.9 18.1 - - - +
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Residues in contact with ASN 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLU* 5.6 2.6 - - - +
508B ASN* 3.0 11.2 + - - +
509B SER* 1.3 75.3 - - - +
511B THR* 1.3 61.6 + - - +
513B LEU* 3.3 2.9 + - - +
514B THR* 2.9 33.7 + - - +
554B ALA* 6.1 0.7 - - - +
555B LEU* 3.7 19.9 - - - +
558B LEU* 4.8 11.5 - - + +
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Residues in contact with THR 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B PRO* 3.9 20.2 - - + -
508B ASN* 2.9 35.8 + - - +
510B ASN* 1.3 72.9 - - - +
512B PHE* 1.3 66.6 + - - +
514B THR* 3.7 5.1 - - + -
515B ARG* 2.9 36.7 + - + +
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Residues in contact with PHE 512 (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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466B PRO* 4.2 10.0 - - - +
469B VAL* 3.8 22.4 - - + -
470B VAL* 3.5 36.8 - - + +
473B PHE* 4.7 10.5 - + + -
498B MET* 3.3 30.5 - - + -
502B PHE* 3.9 20.0 - + - -
507B PHE* 3.8 26.5 - + + -
508B ASN 3.1 6.3 + - - -
509B SER 3.5 7.9 - - - +
510B ASN 3.2 0.2 - - - -
511B THR* 1.3 76.9 - - - +
513B LEU* 1.3 64.3 + - + +
516B LEU* 2.9 55.0 + - + +
545B MET* 4.7 9.0 - - + -
551B PHE* 6.5 0.2 - + - -
555B LEU* 5.0 2.2 - - + -
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Residues in contact with LEU 513 (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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131A ALA* 5.1 1.8 - - + -
509B SER 3.0 16.5 + - - +
510B ASN* 3.7 4.9 - - - +
512B PHE* 1.3 83.4 - - + +
514B THR* 1.3 63.9 + - - +
516B LEU* 3.2 14.8 + - + +
517B LEU* 3.0 46.8 + - + +
555B LEU* 4.0 27.1 - - + +
558B LEU* 3.4 43.3 - - + -
559B LEU* 4.0 28.9 - - + +
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Residues in contact with THR 514 (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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88A PRO* 5.5 14.2 - - + +
130A GLN* 6.5 0.4 - - - -
131A ALA* 4.6 14.5 + - - +
510B ASN* 2.9 19.4 + - - +
511B THR* 3.7 6.5 - - - -
513B LEU* 1.3 78.1 - - - +
515B ARG* 1.3 65.3 + - + +
517B LEU* 3.2 7.4 + - - +
518B VAL* 2.9 34.3 + - + +
523B LEU* 4.0 21.0 - - + +
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Residues in contact with ARG 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B PRO* 5.4 0.4 - - + +
467B GLU* 2.8 49.0 + - - +
470B VAL* 3.9 14.6 - - + -
511B THR* 2.9 33.6 + - + +
512B PHE* 4.9 0.2 - - - -
514B THR* 1.3 81.1 - - + +
516B LEU* 1.3 59.8 + - - +
518B VAL* 3.6 12.5 - - - +
519B HIS* 2.9 44.1 + - + -
525B SER* 4.0 12.9 - - - -
527B ASP* 2.9 41.8 + - - -
529B VAL* 3.8 6.5 - - - +
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Residues in contact with LEU 516 (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* 3.8 14.1 - - + +
473B PHE* 3.7 28.9 - - + -
474B LEU* 3.9 15.0 - - + -
512B PHE* 2.9 39.6 + - + +
513B LEU* 3.2 17.9 + - + +
515B ARG* 1.3 76.9 - - - +
517B LEU* 1.3 59.5 + - + +
519B HIS* 3.3 2.1 + - - +
520B MET* 2.9 53.3 + - - +
542B LEU* 3.9 28.9 - - + -
559B LEU* 5.2 2.5 - - + -
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Residues in contact with LEU 517 (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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131A ALA* 4.4 8.5 - - + -
513B LEU* 3.0 38.6 + - + +
514B THR 3.6 6.3 - - - +
516B LEU* 1.3 77.2 - - + +
518B VAL* 1.3 61.2 + - - +
520B MET* 3.3 7.9 + - - -
521B GLY 3.1 3.6 + - - -
522B LEU* 2.9 43.0 + - + +
523B LEU* 3.4 18.6 + - + +
558B LEU 4.7 1.6 - - - +
559B LEU* 4.2 22.2 - - + -
562B PHE* 3.7 48.2 - - + -
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Residues in contact with VAL 518 (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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514B THR* 2.9 27.4 + - + +
515B ARG* 3.6 22.4 - - - +
517B LEU* 1.3 75.1 - - - +
519B HIS* 1.3 59.0 + - + +
521B GLY* 2.9 20.6 + - - -
523B LEU* 3.4 27.0 - - + +
524B LYS 3.9 13.0 - - - +
525B SER* 3.4 29.8 - - - +
529B VAL* 3.7 30.8 - - + +
531B ALA* 4.5 0.7 - - - +
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Residues in contact with HIS 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B GLU* 2.8 32.9 + - - -
470B VAL* 3.8 16.4 - - + -
471B SER* 6.5 1.1 - - - -
474B LEU* 3.5 24.1 - - + +
515B ARG* 2.9 36.6 + - - +
516B LEU 3.9 0.7 - - - +
518B VAL* 1.3 78.4 - - + +
520B MET* 1.3 58.6 + - - +
521B GLY 3.1 0.9 - - - -
529B VAL* 4.2 22.8 - - + +
530B LYS* 4.7 10.6 + - + +
531B ALA* 3.3 24.5 - - - +
532B ILE* 3.3 12.2 + - + +
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Residues in contact with MET 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B LEU* 4.1 19.1 - - + -
516B LEU* 2.9 42.5 + - - +
517B LEU* 3.8 8.7 - - - +
518B VAL 3.1 0.4 - - - -
519B HIS* 1.3 76.0 - - - +
521B GLY* 1.3 61.1 + - - +
522B LEU* 3.3 24.5 + - + +
531B ALA* 4.3 3.6 - - - +
532B ILE* 4.4 3.0 - - - +
535B LEU* 3.7 42.8 - - + +
538B PRO* 4.0 20.4 - - + -
539B LEU* 4.1 19.3 - - + -
542B LEU* 4.1 22.2 - - + -
559B LEU* 5.9 0.7 - - + -
563B VAL* 5.9 0.7 - - + -
569B ALA* 5.1 3.6 - - - +
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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