Contacts of the helix formed by residues 453 - 463 (chain B) in PDB entry 4U7D
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 CYS 453 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451B SER 3.4 3.2 + - - -
452B LYS* 1.3 74.1 - - - +
454B ARG* 1.3 68.4 + - - +
455B ARG* 3.7 14.4 - - - -
456B VAL* 3.1 34.3 + - + +
457B LEU* 3.2 12.3 + - - +
466B TRP* 5.4 0.9 - - - -
471B CYS* 3.4 30.5 - - - -
475B CYS* 3.7 7.4 - - - -
477B ASN* 4.4 0.4 - - - -
478B CYS* 3.3 32.3 - - - -
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Residues in contact with ARG 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B TYR* 3.9 14.4 - - + +
290B VAL* 3.7 25.8 + - - +
446B TYR* 2.9 63.1 + - + +
447B CYS 4.9 1.2 + - - -
449B ASN* 3.0 27.3 + - - +
450B ILE* 4.9 0.6 - - - +
452B LYS 3.4 1.2 + - - -
453B CYS* 1.3 71.8 - - - +
455B ARG* 1.3 61.9 + - - +
457B LEU* 3.3 12.8 + - - +
458B MET* 3.2 23.6 + - - +
475B CYS* 3.4 31.9 - - + -
476B ASP* 3.0 33.1 + - - +
477B ASN* 3.3 20.1 + - - +
480B LYS* 5.4 0.8 - - - +
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Residues in contact with ARG 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B PHE* 3.4 20.8 - - + -
282B ASN* 2.8 28.1 + - - +
283B ARG 2.9 26.1 + - - -
284B PRO* 3.6 12.4 + - - +
286B LEU* 2.8 22.6 + - - +
288B TYR* 3.7 23.0 - - + -
453B CYS* 3.2 9.5 - - - -
454B ARG* 1.3 75.0 - - - +
456B VAL* 1.3 62.4 + - - +
457B LEU 3.2 0.2 - - - -
458B MET* 3.4 2.5 + - - -
459B ALA* 3.0 22.9 + - - +
466B TRP* 4.0 18.8 - - + -
470B ALA 5.0 0.7 - - - -
471B CYS* 3.7 25.5 + - - +
474B MET* 2.7 41.5 + - - +
475B CYS* 4.6 0.2 - - - +
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Residues in contact with VAL 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B LYS* 4.1 24.0 - - + -
453B CYS* 3.1 30.2 + - + +
455B ARG* 1.3 76.9 - - - +
457B LEU* 1.3 62.2 + - + +
459B ALA* 3.7 2.9 + - - +
460B GLN* 3.4 34.2 + - + +
466B TRP* 3.2 37.3 - - + +
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Residues in contact with LEU 457 (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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395B MET* 5.7 2.5 - - - +
445B SER 6.0 0.2 - - - +
446B TYR* 4.1 30.1 - - + +
449B ASN* 3.6 45.5 - - + +
452B LYS* 3.6 21.3 - - + +
453B CYS 3.2 13.9 + - - +
454B ARG* 3.4 14.8 - - - +
455B ARG 3.2 0.2 - - - -
456B VAL* 1.3 76.7 - - - +
458B MET* 1.3 64.6 + - - +
460B GLN* 3.4 34.5 + - - +
461B HIS* 3.6 9.4 + - - +
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Residues in contact with MET 458 (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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281B PHE* 3.6 34.3 - - + -
288B TYR* 4.1 29.6 - - + +
395B MET* 3.7 27.3 - - + +
398B TYR* 4.2 13.0 - - + -
399B TYR* 3.6 39.0 - - + -
446B TYR* 5.4 5.2 - - + +
454B ARG 3.2 13.7 + - - +
455B ARG* 3.7 2.7 - - - +
457B LEU* 1.3 76.4 - - - +
459B ALA* 1.3 59.3 + - - +
461B HIS* 2.8 23.9 + - - +
462B PHE* 3.1 27.0 - - + -
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Residues in contact with ALA 459 (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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281B PHE* 3.6 20.5 - - + -
455B ARG 3.0 15.9 + - - +
456B VAL 3.9 2.9 - - - +
458B MET* 1.3 76.0 - - - +
460B GLN* 1.3 56.8 + - - +
462B PHE 3.4 1.2 + - - +
463B ASP 2.9 6.4 + - - -
464B GLU* 2.8 43.5 + - + +
466B TRP* 3.6 34.3 - - + -
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Residues in contact with GLN 460 (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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452B LYS* 5.1 7.3 - - - +
456B VAL* 3.4 27.1 + - + +
457B LEU* 3.4 29.2 + - - +
458B MET 3.1 0.6 - - - -
459B ALA* 1.3 77.8 - - - +
461B HIS* 1.3 61.5 + - + +
463B ASP* 3.5 18.0 + - - +
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Residues in contact with HIS 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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395B MET* 3.5 40.6 - - + +
396B GLU* 3.2 29.9 + - - -
442B GLU* 3.0 42.0 + - + +
457B LEU 3.6 6.0 + - - +
458B MET* 2.8 15.9 + - - +
460B GLN* 1.3 78.3 - - + +
462B PHE* 1.3 70.8 + - + +
463B ASP* 3.1 15.2 + - - +
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Residues in contact with PHE 462 (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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255B ALA 5.7 4.9 - - - -
281B PHE* 4.1 29.2 - + + -
395B MET* 5.5 4.5 - - + -
396B GLU* 5.5 13.2 - - + -
399B TYR* 4.1 33.4 - + + -
458B MET* 3.1 39.2 + - + -
459B ALA 3.4 4.2 + - - +
461B HIS* 1.3 84.1 - - + +
463B ASP* 1.3 73.9 + - - +
464B GLU* 3.3 16.7 + - + +
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Residues in contact with ASP 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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459B ALA 2.9 6.1 + - - -
460B GLN* 3.5 13.8 + - - +
461B HIS 3.1 11.4 - - - +
462B PHE* 1.3 83.5 - - - +
464B GLU* 1.3 59.7 + - - +
465B VAL* 4.2 2.1 + - - +
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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