Contacts of the helix formed by residues 460 - 467 (chain B) in PDB entry 5J1T
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 VAL 460 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B LYS 4.3 2.5 - - - +
266B PHE* 3.9 18.4 - - + -
267B PRO* 3.6 43.1 - - + +
269B GLN* 3.8 6.7 - - - +
307B THR* 2.9 22.7 + - + +
458B GLN 3.4 0.2 + - - -
459B PRO* 1.3 70.9 - - - +
461B SER* 1.3 69.2 + - - +
462B SER* 3.7 19.7 - - - +
463B ILE* 3.0 31.6 + - + +
464B GLU* 3.0 12.4 + - - +
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Residues in contact with SER 461 (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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459B PRO* 3.9 5.2 + - - +
460B VAL* 1.3 71.8 - - - +
462B SER* 1.3 58.9 + - - +
464B GLU* 3.2 8.8 + - - +
465B GLU* 2.9 30.5 + - - +
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Residues in contact with SER 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B VAL* 3.2 14.5 + - - +
461B SER* 1.3 79.5 - - - +
463B ILE* 1.3 63.0 + - - +
465B GLU* 4.3 5.2 - - - -
466B GLN* 2.8 54.4 + - - +
467B GLY 4.3 0.3 - - - +
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Residues in contact with ILE 463 (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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265B LYS 4.2 2.9 - - - +
266B PHE* 3.5 34.3 - - + -
306B GLU* 3.7 32.0 - - + +
307B THR* 4.0 5.8 - - + +
310B CYS* 4.1 9.0 - - + -
460B VAL* 3.0 30.3 + - + +
462B SER* 1.3 78.1 + - - +
464B GLU* 1.3 64.7 + - - +
467B GLY* 2.8 47.2 + - - +
468B CYS 4.3 0.2 - - - +
470B PHE* 4.0 25.4 - - + -
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Residues in contact with GLU 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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303B GLU 3.3 24.0 - - - +
304B GLY* 3.2 12.0 - - - -
305B ARG* 3.7 6.1 + - - +
306B GLU* 3.0 37.6 + - - +
307B THR* 2.6 32.2 + - - -
459B PRO* 3.8 10.5 - - + +
460B VAL 3.0 16.6 + - - +
461B SER* 3.8 7.9 - - - +
463B ILE* 1.3 77.0 - - - +
465B GLU* 1.3 62.0 + - - +
467B GLY 4.7 0.5 + - - -
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Residues in contact with GLU 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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461B SER 2.9 18.2 + - - +
462B SER* 3.9 5.2 - - - +
464B GLU* 1.3 81.5 - - - +
466B GLN* 1.3 72.5 + - + +
467B GLY 3.7 0.2 - - - -
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Residues in contact with GLN 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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462B SER* 2.8 36.6 + - - +
465B GLU* 1.3 88.2 - - + +
467B GLY* 1.3 60.6 + - - +
469B LEU* 3.5 40.4 - - + +
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Residues in contact with GLY 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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306B GLU* 5.1 10.8 - - - -
462B SER 4.3 0.2 - - - +
463B ILE* 2.8 35.6 + - - +
464B GLU 4.6 0.6 + - - -
465B GLU 3.7 0.8 - - - -
466B GLN* 1.3 82.5 - - - +
468B CYS* 1.3 61.4 + - - -
469B LEU* 3.2 11.9 + - - +
470B PHE* 5.4 0.5 - - - -
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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