Contacts of the helix formed by residues 463 - 470 (chain B) in PDB entry 5X61
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395B LEU* 5.4 3.1 - - + -
455B VAL* 4.2 18.7 - - + +
462B GLU* 1.3 76.1 - - - +
464B PRO* 1.3 68.3 - - + +
465B GLN* 4.1 12.7 - - - +
466B ARG* 2.8 51.2 + - - +
467B SER* 2.9 23.4 + - - -
804B SO4 5.9 1.8 - - - +
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Residues in contact with PRO 464 (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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368B LEU* 4.1 18.4 - - + -
371B LEU* 3.7 25.6 - - + -
389B PRO* 3.6 34.3 - - + +
390B THR* 5.0 2.5 - - - -
395B LEU* 3.5 30.1 - - + -
460B LEU* 4.8 2.9 - - + -
462B GLU 3.6 3.8 - - - +
463B THR* 1.3 86.2 - - - +
465B GLN* 1.3 53.3 + - + +
467B SER* 3.9 0.4 - - - -
468B LEU* 2.8 40.8 + - + +
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Residues in contact with GLN 465 (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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390B THR* 3.1 31.7 + - - +
463B THR* 4.1 12.8 - - - +
464B PRO* 1.3 79.0 - - + +
466B ARG* 1.3 58.8 + - + +
468B LEU* 3.8 5.5 - - - +
469B ALA* 3.1 27.4 + - - +
566B GLU* 3.8 11.1 - - - +
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Residues in contact with ARG 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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323A GLU* 5.2 8.7 + - - -
462B GLU* 4.4 20.6 - - + +
463B THR* 2.8 52.9 + - - +
465B GLN* 1.3 78.4 - - + +
467B SER* 1.3 60.8 + - - +
469B ALA* 3.7 7.7 - - - +
470B SER* 3.0 31.8 + - - -
472B ARG* 4.4 1.9 + - - +
803B SO4 4.9 0.5 + - - -
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Residues in contact with SER 467 (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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371B LEU* 3.7 24.6 + - - +
462B GLU* 3.4 27.3 + - - +
463B THR 2.9 16.2 + - - -
464B PRO* 3.7 4.5 - - - -
466B ARG* 1.3 76.9 - - - +
468B LEU* 1.3 60.8 + - - +
470B SER* 3.8 0.9 - - - -
471B GLY 3.2 3.3 + - - -
472B ARG* 2.9 54.5 + - - +
473B PHE* 3.8 2.8 - - - -
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Residues in contact with LEU 468 (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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371B LEU* 4.0 19.5 - - + -
389B PRO* 4.6 3.4 - - + -
390B THR* 4.5 13.7 - - - -
464B PRO 2.8 20.2 + - - +
465B GLN* 3.8 4.7 - - - +
467B SER* 1.3 75.6 - - - +
469B ALA* 1.3 64.7 + - - +
471B GLY* 3.2 10.2 + - - -
473B PHE* 3.8 11.8 - - + -
566B GLU* 4.2 20.2 - - - +
567B PHE* 3.7 47.6 - - + +
570B ARG* 3.2 44.5 + - + +
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Residues in contact with ALA 469 (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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465B GLN 3.1 17.9 + - - +
466B ARG* 3.4 8.9 + - - +
468B LEU* 1.3 79.1 - - - +
470B SER* 1.3 57.5 + - - +
570B ARG* 3.5 18.6 + - - +
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Residues in contact with SER 470 (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 ARG 3.0 16.8 + - - -
467B SER* 3.5 5.9 + - - -
469B ALA* 1.3 75.5 - - - +
471B GLY* 1.3 61.4 + - - +
472B ARG* 3.1 34.9 + - - +
570B ARG* 5.3 0.2 - - - -
574B GLU* 5.4 0.9 - - - +
803B SO4 3.4 30.5 - - - -
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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