Contacts of the helix formed by residues 464 - 469 (chain D) in PDB entry 3GUT
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 464 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394D ILE* 4.3 1.0 - - - +
396D GLN* 3.1 12.5 + - - -
462D GLY 3.2 4.8 + - - -
463D TYR* 1.3 72.2 - - - +
465D PRO* 1.4 68.6 - - - +
466D GLY 3.2 3.8 + - - -
467D LEU* 3.5 13.3 + - + +
468D LEU* 3.3 25.5 + - + +
477D GLN* 5.1 3.3 + - - +
513D MET* 3.7 19.0 - - + +
515D THR* 2.9 28.4 + - - +
528D ARG* 2.5 46.9 - - - +
531D PRO* 3.8 11.9 - - - +
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Residues in contact with PRO 465 (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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458D ALA* 2.8 24.7 - - + +
459D CYS* 3.5 28.7 - - - -
462D GLY* 3.4 10.5 - - - +
463D TYR 3.2 3.4 - - - +
464D ASN* 1.4 88.3 - - - +
466D GLY* 1.3 56.5 + - - +
469D VAL* 3.1 32.5 + - + +
470D HIS 3.2 10.6 + - - +
473D LEU* 3.9 18.5 - - + +
476D LEU* 3.6 19.1 - - + +
477D GLN* 4.3 5.6 - - - +
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Residues in contact with GLY 466 (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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464D ASN 3.3 0.8 - - - -
465D PRO* 1.3 77.2 - - - +
467D LEU* 1.3 68.9 + - - +
470D HIS* 3.1 29.1 + - - +
471D SER* 3.6 9.1 + - - -
474D ALA* 3.8 31.0 - - - +
477D GLN* 5.1 0.8 - - - +
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Residues in contact with LEU 467 (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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404D ILE* 3.4 19.8 - - + +
405D HIS* 4.8 1.4 - - - -
464D ASN* 3.5 14.3 + - + +
466D GLY* 1.3 85.9 - - - +
468D LEU* 1.3 69.2 + - + +
474D ALA* 5.6 4.0 - - + -
477D GLN* 5.9 2.2 - - - +
513D MET* 5.2 4.0 - - + -
528D ARG* 3.9 27.6 - - - +
530D GLU* 5.1 5.6 - - - +
531D PRO* 4.1 26.7 - - + -
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Residues in contact with LEU 468 (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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396D GLN* 3.4 29.2 - - - +
398D VAL* 3.7 17.9 - - + -
404D ILE* 3.4 33.7 - - + -
405D HIS* 3.6 17.3 - - - +
406D LEU* 3.5 36.3 + - + +
455D MET* 4.5 1.0 - - - +
463D TYR 4.5 1.8 - - - +
464D ASN* 3.3 16.9 + - + +
467D LEU* 1.3 83.5 - - + +
469D VAL* 1.3 63.5 + - + +
501D GLN* 3.6 8.7 - - - +
513D MET* 3.7 27.8 - - + -
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Residues in contact with VAL 469 (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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405D HIS* 5.1 1.5 - - - -
406D LEU* 4.6 9.4 - - + -
455D MET* 3.4 56.1 - - + +
458D ALA* 4.8 3.1 - - + -
459D CYS* 4.0 10.8 - - - -
465D PRO* 3.1 18.7 + - + +
468D LEU* 1.3 80.2 - - + +
470D HIS* 1.3 66.5 + - + +
473D LEU* 3.9 18.6 - - + -
494D ILE* 3.9 9.0 - - + -
497D ALA* 3.2 13.5 - - + +
501D GLN* 3.0 22.3 + - - -
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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