Contacts of the helix formed by residues 463 - 471 (chain A) in PDB entry 5YDJ
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 THR 463 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395A LEU* 5.7 1.8 - - + -
455A VAL* 4.2 12.1 - - + +
462A GLU* 1.3 76.1 - - - +
464A PRO* 1.4 69.9 - - + +
465A GLN* 4.3 15.9 + - - +
466A ARG* 2.9 64.3 + - - +
467A SER 3.3 7.4 + - - -
804A SO4 4.3 16.8 - - - +
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Residues in contact with PRO 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A LEU* 4.4 5.4 - - + -
371A LEU* 3.5 27.4 - - + +
389A PRO* 3.5 37.7 - - + +
390A THR* 4.8 1.8 - - - +
395A LEU* 3.6 32.8 - - + -
460A LEU* 4.9 3.4 - - + -
462A GLU 3.7 1.8 - - - +
463A THR* 1.4 85.8 - - - +
465A GLN* 1.3 62.2 + - - +
467A SER* 3.6 4.1 + - - +
468A LEU* 2.9 34.8 + - - +
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Residues in contact with GLN 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A PRO 5.6 0.2 - - - +
390A THR* 3.9 29.4 + - - +
463A THR* 3.1 13.5 + - - +
464A PRO* 1.3 83.9 - - - +
466A ARG* 1.3 54.2 + - + +
468A LEU* 3.2 6.6 + - - +
469A ALA* 2.7 37.7 + - - +
566A GLU* 5.1 6.5 - - - +
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Residues in contact with ARG 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A GLU* 3.6 22.1 - - + +
463A THR* 2.9 56.1 + - - +
465A GLN* 1.3 74.8 - - + +
467A SER* 1.3 56.3 + - - +
469A ALA* 4.0 5.1 - - - +
470A SER* 2.7 39.2 + - - -
472A ARG* 4.1 2.8 + - - +
804A SO4 5.5 1.6 + - - -
806A SO4 4.4 3.8 + - - +
323B GLU* 5.6 7.0 + - - -
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Residues in contact with SER 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A LEU* 3.8 24.6 + - - +
462A GLU* 2.7 36.1 + - - +
463A THR 3.3 3.4 + - - -
464A PRO* 3.6 9.9 - - - +
466A ARG* 1.3 78.7 - - - +
468A LEU* 1.3 56.5 + - - -
470A SER* 3.7 2.5 - - - -
471A GLY 2.9 7.8 + - - -
472A ARG* 2.7 46.2 + - - -
473A PHE* 3.8 1.7 - - - -
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Residues in contact with LEU 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A LEU* 4.4 7.2 - - + -
389A PRO* 4.6 5.2 - - + -
390A THR* 4.4 23.3 - - + -
464A PRO 2.9 24.1 + - - +
465A GLN* 3.2 6.5 + - - +
467A SER* 1.3 75.2 - - - +
469A ALA* 1.3 52.9 + - - +
471A GLY 3.5 2.9 + - - -
473A PHE* 3.6 28.9 - - + -
566A GLU* 4.9 11.0 - - + +
567A PHE* 3.7 45.8 - - + -
570A ARG* 2.6 55.3 + - + +
571A TYR* 5.0 1.6 - - + -
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Residues in contact with ALA 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465A GLN 2.7 21.9 + - - +
466A ARG* 4.0 6.1 - - - +
468A LEU* 1.3 73.0 - - - +
470A SER* 1.3 61.8 + - - +
570A ARG* 3.4 17.0 + - - +
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Residues in contact with SER 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466A ARG 2.7 22.7 + - - -
467A SER 3.3 4.7 + - - -
469A ALA* 1.3 77.1 - - - +
471A GLY* 1.3 60.6 + - - +
472A ARG* 3.1 41.1 + - - +
570A ARG* 4.8 0.2 - - - -
574A GLU* 5.3 2.2 - - - +
806A SO4 3.5 15.5 - - - -
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Residues in contact with GLY 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A SER 2.9 6.7 + - - -
468A LEU 3.5 2.9 + - - -
469A ALA 3.3 3.4 - - - -
470A SER* 1.3 77.9 - - - +
472A ARG* 1.3 60.5 + - - +
473A PHE* 3.2 20.6 + - - -
475A LYS* 2.8 27.7 + - - -
570A ARG* 4.2 6.3 - - - -
574A GLU* 4.4 10.3 - - - +
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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