Contacts of the helix formed by residues 465 - 474 (chain E) in PDB entry 4CYM
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 465 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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456E PRO 3.4 22.4 + - - +
457E PHE* 5.4 1.3 + - - -
458E SER 3.5 4.4 + - - -
459E ARG* 3.8 23.7 + - - -
463E GLY 3.4 0.6 + - - -
464E HIS* 1.3 73.6 - - - +
466E PRO* 1.3 72.2 - - - +
467E LEU* 3.1 29.2 - - + +
468E HIS* 2.9 31.4 + - - +
469E VAL* 3.1 13.5 + - - +
487E ALA* 5.2 2.5 - - + -
488E MET* 5.0 4.3 - - + +
491E ALA* 3.9 13.0 - - + +
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Residues in contact with PRO 466 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454E VAL* 5.4 3.4 - - + -
455E THR 3.8 20.9 - - - +
456E PRO* 3.9 8.1 - - + +
458E SER* 3.4 22.9 - - - +
464E HIS 4.4 1.1 - - - +
465E THR* 1.3 85.1 - - + +
467E LEU* 1.3 58.0 + - - +
469E VAL* 2.8 12.2 + - + +
470E ALA* 2.7 30.8 + - - +
478E LEU* 5.8 0.2 - - - +
482E LEU* 3.5 26.2 - - + +
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Residues in contact with LEU 467 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465E THR* 3.1 16.7 - - + +
466E PRO* 1.3 79.9 - - - +
468E HIS* 1.3 64.1 + - - +
470E ALA* 4.2 0.4 - - - -
471E ALA* 3.0 23.0 + - - +
479E ILE* 4.1 31.2 - - + -
482E LEU* 3.4 28.1 - - + +
483E VAL* 4.3 6.1 - - + -
487E ALA* 4.4 10.3 - - + -
488E MET 3.8 9.2 - - - +
489E VAL* 3.7 35.7 - - + +
499E PRO* 3.9 19.4 - - + +
515E LEU* 4.7 7.2 - - + -
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Residues in contact with HIS 468 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463E GLY 3.9 9.4 - - - -
464E HIS* 3.8 22.0 - + + +
465E THR* 2.9 37.9 + - - +
467E LEU* 1.3 77.7 - - - +
469E VAL* 1.3 63.8 + - - +
471E ALA* 3.2 1.6 + - - +
472E VAL* 3.0 20.0 + - - +
491E ALA* 3.4 28.5 + - + -
492E THR 4.0 0.4 - - - -
493E ASP* 3.7 11.5 + - + -
497E ALA 2.7 29.6 + - - -
498E THR 3.8 0.2 - - - -
499E PRO* 3.5 23.9 - - + +
502E LEU* 3.5 32.6 - - + +
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Residues in contact with VAL 469 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464E HIS* 4.7 13.7 - - + -
465E THR 3.6 12.6 - - - +
466E PRO* 2.8 12.2 + - + +
468E HIS* 1.3 73.6 - - + +
470E ALA* 1.3 66.8 + - - +
472E VAL* 3.0 20.1 + - + +
473E CYS* 3.0 31.3 + - - -
475E GLN* 5.7 1.3 - - - +
478E LEU* 6.3 1.1 - - + -
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Residues in contact with ALA 470 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466E PRO 2.7 18.9 + - - +
467E LEU* 3.9 3.6 - - - +
469E VAL* 1.3 73.8 - - - +
471E ALA* 1.3 60.9 + - - +
473E CYS* 3.9 4.2 - - - +
474E GLY* 3.1 17.7 + - - -
475E GLN* 3.2 12.7 + - - +
478E LEU* 3.9 33.3 - - + +
479E ILE* 4.0 17.8 - - + +
482E LEU* 3.9 13.7 - - + -
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Residues in contact with ALA 471 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467E LEU 3.0 19.1 + - - +
468E HIS 3.6 4.3 - - - +
469E VAL 3.1 0.4 - - - -
470E ALA* 1.3 76.5 - - - +
472E VAL* 1.3 63.8 + - - +
474E GLY* 3.2 13.7 + - - -
479E ILE* 4.3 11.2 - - + -
499E PRO* 3.8 31.9 - - + +
502E LEU* 4.8 1.1 - - + -
503E ALA* 4.7 6.4 - - - +
508E TYR* 3.8 10.0 - - - -
511E VAL* 4.3 17.6 - - + +
515E LEU* 4.6 2.0 - - + -
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Residues in contact with VAL 472 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468E HIS 3.0 11.9 + - - +
469E VAL* 3.0 17.2 + - + +
471E ALA* 1.3 77.7 - - - +
473E CYS* 1.3 67.2 + - - +
502E LEU* 4.2 26.5 - - + -
505E GLN* 6.2 1.1 - - - +
506E LYS* 3.2 54.9 - - + -
508E TYR* 3.4 4.1 + - - -
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Residues in contact with CYS 473 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469E VAL* 3.0 34.2 + - - +
470E ALA 3.9 2.9 - - - +
472E VAL* 1.3 83.7 - - - +
474E GLY* 1.3 57.1 - - - +
475E GLN* 3.5 35.4 - - + +
508E TYR* 3.2 14.5 + - - -
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Residues in contact with GLY 474 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470E ALA 3.1 5.5 + - - -
471E ALA 3.2 6.1 + - - -
473E CYS* 1.3 79.0 - - - +
475E GLN* 1.3 61.6 + - - +
476E ALA* 2.8 12.1 + - - +
508E TYR* 3.4 23.3 - - - -
511E VAL* 4.0 12.8 - - - +
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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