Contacts of the helix formed by residues 519 - 529 (chain B) in PDB entry 4D1Q
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 519 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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518B VAL* 1.3 87.6 - - + +
520B PRO* 1.4 81.6 - - + +
521B SER* 4.0 13.5 - - - -
522B ASP* 3.1 38.8 + - - -
523B GLU* 3.1 23.3 + - - +
553B LYS* 4.8 5.2 - - - +
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Residues in contact with PRO 520 (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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455B LEU* 3.9 12.6 - - + -
458B MET* 3.6 35.4 - - + +
459B GLU* 3.8 21.5 - - - +
462B GLU* 4.4 7.2 - - - +
519B CYS* 1.4 86.9 - - + +
521B SER* 1.3 73.0 + - - +
523B GLU* 2.8 18.6 + - + +
524B PHE* 2.8 13.0 + - - +
553B LYS* 4.1 18.1 - - + -
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Residues in contact with SER 521 (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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451B LYS* 4.0 22.2 - - - +
455B LEU* 4.0 15.8 - - - +
519B CYS* 3.6 7.0 - - - -
520B PRO* 1.3 81.1 - - - +
522B ASP* 1.3 64.1 + - - +
524B PHE* 3.2 7.8 + - - +
525B GLU* 2.8 36.8 + - - +
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Residues in contact with ASP 522 (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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513B SER* 2.7 29.2 - - - +
514B ARG* 3.5 14.3 - - - +
515B GLU 4.7 1.4 - - - +
517B PRO* 2.8 30.8 - - + +
518B VAL* 3.5 7.4 - - - +
519B CYS* 3.1 33.0 + - - +
520B PRO 3.1 0.2 - - - -
521B SER* 1.3 79.9 - - - +
523B GLU* 1.3 56.9 + - - +
525B GLU* 3.8 5.1 - - - +
526B PHE* 2.8 31.9 + - - +
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Residues in contact with GLU 523 (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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458B MET* 5.5 0.4 - - - -
517B PRO* 4.4 13.4 + - + +
518B VAL 4.4 5.9 - - - +
519B CYS 3.1 12.7 + - - +
520B PRO* 2.8 14.6 + - + +
522B ASP* 1.3 69.6 - - - +
524B PHE* 1.3 65.3 + - - +
526B PHE* 3.5 3.8 + - - -
527B TYR* 3.0 18.5 + - - +
550B LYS 4.4 3.1 - - - +
551B TYR* 2.8 49.2 - - + +
552B PRO* 3.4 15.4 - - + +
553B LYS* 3.0 32.0 + - - +
554B LEU* 2.7 34.3 + - + +
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Residues in contact with PHE 524 (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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434B PHE* 3.3 35.2 - + - -
447B VAL* 4.2 10.8 - - + -
450B ILE* 4.1 4.0 - - + -
451B LYS* 3.4 53.6 - - + -
454B CYS* 4.2 17.9 - - + -
455B LEU* 5.1 2.5 - - + -
458B MET* 5.4 1.1 - - + -
520B PRO 2.8 11.5 + - - +
521B SER* 3.3 12.3 - - - +
523B GLU* 1.3 76.5 - - - +
525B GLU* 1.3 74.0 + - - +
527B TYR* 2.8 32.2 + - + +
528B ARG* 3.1 32.0 + - + +
554B LEU* 4.4 15.8 - - + +
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Residues in contact with GLU 525 (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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451B LYS* 3.1 30.2 + - - +
521B SER* 2.8 22.2 + - - +
522B ASP* 4.1 4.7 - - - +
524B PHE* 1.3 93.5 - - + +
526B PHE* 1.3 61.3 + - - +
528B ARG* 3.2 46.2 + - - +
529B LYS* 3.2 14.1 + - - +
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Residues in contact with PHE 526 (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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515B GLU* 3.5 42.4 - - + +
516B PRO* 5.9 0.7 - - + -
517B PRO* 3.8 25.1 - - + -
522B ASP 2.8 20.5 + - - +
523B GLU* 3.8 5.4 - - - +
525B GLU* 1.3 75.0 - - - +
527B TYR* 1.3 62.7 + - - +
529B LYS* 3.7 19.7 + - + +
530B GLU* 3.8 6.4 + - - +
550B LYS* 3.2 32.5 - - + -
551B TYR* 3.3 20.2 + + - -
543G TRP* 4.6 4.0 - + - -
546G LEU* 4.1 8.5 - - + -
547G ASN* 3.1 41.7 - - - -
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Residues in contact with TYR 527 (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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434B PHE* 3.2 58.6 + + - -
435B PHE* 3.6 5.4 - + - -
436B TYR 3.4 0.3 - - - -
437B PRO* 3.0 40.1 + - + +
439B ALA* 4.1 10.7 - - + +
523B GLU 3.0 11.1 + - - +
524B PHE* 2.8 15.1 + - - +
526B PHE* 1.3 74.7 - - - +
528B ARG* 1.3 53.1 + - - +
530B GLU* 2.7 42.0 + - + +
543B TRP* 3.4 30.7 - + - -
544B TRP* 3.6 21.5 - + - -
551B TYR* 3.5 17.3 - + + -
554B LEU* 4.0 12.6 - - + -
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Residues in contact with ARG 528 (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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434B PHE* 4.6 10.3 - - + -
439B ALA* 5.6 8.6 - - - +
443B GLN* 2.9 42.3 + - - +
447B VAL* 3.6 28.6 - - - +
451B LYS* 6.0 0.6 - - - +
524B PHE* 3.6 31.1 - - + +
525B GLU* 3.2 37.6 + - - +
527B TYR* 1.3 75.0 - - - +
529B LYS* 1.3 58.6 + - + +
530B GLU 2.9 19.2 + - - +
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Residues in contact with LYS 529 (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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515B GLU* 3.0 31.0 + - - +
525B GLU 3.2 15.9 + - - +
526B PHE* 3.9 18.6 - - + +
527B TYR 3.2 0.8 + - - -
528B ARG* 1.3 79.3 - - + +
530B GLU* 1.3 59.2 + - - +
531B ILE* 4.4 1.7 - - - +
530G GLU* 3.2 39.4 + - - +
531G ILE* 3.1 32.8 + - + +
532G VAL* 4.3 0.4 - - - +
547G ASN* 5.9 0.4 - - - +
550G LYS* 2.7 32.7 + - - +
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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