Contacts of the helix formed by residues 477 - 488 (chain D) in PDB entry 2GL7
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 GLU 477 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436D MET* 3.8 20.4 - - + +
439D CYS* 4.8 14.4 - - + -
440D GLN* 5.3 13.8 + - + +
475D HIS* 2.9 19.7 + - + +
476D GLN* 1.3 82.6 - - + +
478D ALA* 1.3 61.8 + - - +
479D GLU 3.3 2.7 - - - -
480D MET* 3.2 46.5 + - + +
481D ALA* 3.1 20.1 + - - +
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Residues in contact with ALA 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471D LEU 4.1 2.2 - - - -
472D THR* 4.1 3.8 - - - -
473D SER* 4.0 9.9 - - - +
474D ARG 3.9 12.6 - - - +
475D HIS* 2.9 42.5 + - + +
476D GLN 3.4 0.4 - - - -
477D GLU* 1.3 78.7 - - - +
479D GLU* 1.3 58.0 + - - +
481D ALA* 3.4 4.0 + - - +
482D GLN* 3.1 35.9 + - - +
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Residues in contact with GLU 479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476D GLN 4.9 3.0 + - - +
477D GLU* 3.3 0.6 - - - +
478D ALA* 1.3 77.4 - - - +
480D MET* 1.3 63.7 + - - +
482D GLN* 3.3 20.8 + - - +
483D ASN* 2.9 33.5 + - - +
520D CYS* 6.2 0.4 - - + -
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Residues in contact with MET 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477D GLU* 3.2 46.5 + - + +
479D GLU* 1.3 80.0 - - - +
481D ALA* 1.3 52.1 + - - +
483D ASN* 3.3 10.4 + - + +
484D ALA* 2.8 34.6 + - - +
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Residues in contact with ALA 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439D CYS* 4.2 7.4 - - - -
444D ILE* 3.8 23.9 - - + +
471D LEU 3.3 28.3 - - - +
472D THR* 4.1 3.4 - - + -
477D GLU 3.1 11.8 + - - +
478D ALA 3.6 5.2 - - - +
480D MET* 1.3 73.3 - - - +
482D GLN* 1.3 64.7 + - - +
484D ALA* 3.8 7.4 - - - +
485D VAL* 3.1 29.5 + - - +
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Residues in contact with GLN 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472D THR* 2.9 32.9 - - - +
473D SER* 5.0 0.2 - - - -
478D ALA* 3.1 24.0 + - - +
479D GLU* 3.4 21.7 + - - +
481D ALA* 1.3 76.9 - - - +
483D ASN* 1.3 61.4 + - - +
485D VAL 3.8 2.9 + - - -
486D ARG 3.9 4.5 + - - -
516D ASN 3.5 22.7 - - - +
517D LEU* 3.8 17.8 - - + +
519D LEU* 4.0 14.6 + - - +
520D CYS* 3.6 33.5 - - + +
523D ASN* 3.2 19.5 - - - +
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Residues in contact with ASN 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479D GLU* 2.9 29.9 + - - +
480D MET* 3.6 11.5 - - + +
482D GLN* 1.3 76.7 - - - +
484D ALA* 1.3 63.1 + - - +
485D VAL 3.2 0.4 - - - -
486D ARG* 3.1 39.1 + - - +
487D LEU* 3.0 33.5 + - + +
520D CYS* 3.5 20.7 - - - -
522D ALA* 4.0 4.2 - - - +
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Residues in contact with ALA 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444D ILE* 3.8 21.9 - - + +
480D MET 2.8 20.4 + - - +
481D ALA* 3.3 5.6 + - - +
483D ASN* 1.3 70.5 - - - +
485D VAL* 1.3 65.2 + - - +
487D LEU* 4.3 11.9 - - + +
488D HIS* 3.1 42.7 + - + +
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Residues in contact with VAL 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444D ILE* 3.7 18.2 - - + -
448D VAL* 4.6 7.7 - - + +
468D LEU* 4.2 18.4 - - + -
472D THR* 4.3 7.9 - - + -
481D ALA 3.1 15.6 + - - +
482D GLN 4.0 0.7 - - - +
484D ALA* 1.3 77.4 - - - +
486D ARG* 1.3 58.9 + - - +
488D HIS* 3.7 4.0 + - - +
490D GLY* 2.9 38.3 + - - -
491D LEU* 4.3 7.4 - - + -
494D VAL* 4.8 6.7 - - + -
513D LEU* 5.2 4.3 - - + -
517D LEU* 3.7 39.3 - - + -
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Residues in contact with ARG 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482D GLN 3.9 1.4 + - - -
483D ASN* 3.1 41.0 + - - +
485D VAL* 1.3 80.6 - - - +
487D LEU* 1.3 78.1 + - + +
489D TYR* 3.0 24.3 + - - -
490D GLY 4.7 0.2 - - - +
491D LEU* 3.6 21.9 - - + +
522D ALA* 3.8 29.1 + - - +
523D ASN* 2.9 39.3 + - - +
526D PRO* 3.8 15.0 - - + -
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Residues in contact with LEU 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483D ASN* 3.0 31.4 + - + +
484D ALA* 3.2 9.8 + - + +
486D ARG* 1.3 96.2 - - + +
488D HIS* 1.3 65.9 + - + +
489D TYR* 3.3 17.9 + - - -
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Residues in contact with HIS 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444D ILE* 4.6 0.4 - - + +
445D GLU* 3.3 62.4 + - + +
448D VAL* 3.5 20.4 - - + +
449D ARG* 5.4 2.5 - - - +
452D LEU* 5.0 3.3 - - - +
484D ALA* 3.1 36.4 + - + +
485D VAL 4.5 1.1 - - - +
486D ARG 3.2 0.2 - - - -
487D LEU* 1.3 83.0 - - + +
489D TYR* 1.3 73.3 + - - +
490D GLY 3.3 3.0 + - - -
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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