Contacts of the helix formed by residues 519 - 528 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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516A PRO 4.6 4.0 - - - +
517A PRO 2.9 9.6 + - - +
518A VAL* 1.3 74.8 - - - +
520A PRO* 1.3 86.2 - - + +
521A SER* 3.4 20.4 - - - -
522A ASP* 3.3 30.3 + - - +
523A GLU* 2.9 19.7 + - - +
553A LYS* 5.0 2.5 - - - +
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Residues in contact with PRO 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A LEU* 4.0 16.8 - - + -
458A MET* 4.0 33.3 - - + +
459A GLU* 5.7 7.2 - - + -
462A GLU* 4.9 13.5 - - - +
519A CYS* 1.3 89.2 - - + +
521A SER* 1.3 66.4 + - - +
523A GLU* 2.7 20.4 + - + +
524A PHE* 2.9 11.3 + - - +
553A LYS* 4.6 20.9 - - + -
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Residues in contact with SER 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A LYS* 4.3 14.0 + - - +
455A LEU* 3.8 22.4 - - - +
519A CYS* 3.4 11.2 - - - -
520A PRO* 1.3 79.1 - - - +
522A ASP* 1.3 63.5 + - - +
524A PHE* 3.9 7.9 - - - -
525A GLU* 3.1 29.0 + - - +
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Residues in contact with ASP 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517A PRO 4.3 4.3 - - - +
518A VAL* 4.6 8.5 - - + -
519A CYS* 3.3 36.9 + - - +
520A PRO 2.7 5.7 + - - -
521A SER* 1.3 76.2 - - - +
523A GLU* 1.3 56.6 + - - +
525A GLU* 3.7 2.7 - - - +
526A PHE* 2.8 51.3 + - + -
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Residues in contact with GLU 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A MET* 5.7 1.1 - - - -
518A VAL* 4.1 24.0 - - + +
519A CYS 2.9 16.7 + - - +
520A PRO* 2.7 11.5 + - + +
522A ASP* 1.3 69.1 - - - +
524A PHE* 1.3 67.3 + - - +
526A PHE* 2.8 23.0 - - + +
527A TYR* 2.8 5.9 + - - +
550A LYS 4.2 6.3 - - - +
551A TYR* 2.9 35.2 - - + +
552A PRO* 3.1 22.5 - - + +
553A LYS* 2.8 31.9 + - - +
554A LEU* 3.0 28.8 + - + +
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Residues in contact with PHE 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A PHE* 3.5 30.3 - + - -
435A PHE* 5.7 0.2 - + - -
447A VAL* 4.5 6.5 - - + -
450A ILE* 4.1 2.9 - - + -
451A LYS* 3.5 64.8 - - + -
454A CYS* 3.7 26.2 - - + -
455A LEU* 4.9 4.0 - - + -
458A MET* 5.9 0.2 - - + -
520A PRO 2.9 15.1 + - - +
521A SER* 3.8 5.6 - - - +
523A GLU* 1.3 72.3 - - - +
525A GLU* 1.3 58.5 + - - +
526A PHE 2.6 3.5 + - - -
527A TYR* 2.6 37.9 + - + +
528A ARG* 3.2 31.7 + - + +
554A LEU* 4.5 17.2 - - + +
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Residues in contact with GLU 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A LYS* 2.7 32.6 + - - +
521A SER* 3.1 18.5 + - - +
522A ASP* 3.7 3.8 - - - +
524A PHE* 1.3 79.4 - - - +
526A PHE* 1.3 61.7 + - + +
527A TYR 3.4 0.2 - - - -
528A ARG* 3.9 36.5 + - - +
529A LYS* 3.5 25.1 + - - +
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Residues in contact with PHE 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518A VAL* 4.8 17.9 - - + -
522A ASP* 2.8 35.1 + - + +
523A GLU* 2.8 17.5 - - - +
524A PHE 2.6 2.4 + - - -
525A GLU* 1.3 80.0 - - + +
527A TYR* 1.3 63.6 - - - +
529A LYS* 3.6 20.2 + - + +
530A GLU* 3.7 5.2 - - - +
550A LYS* 4.5 24.7 - - + -
551A TYR* 3.1 17.8 + + + -
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Residues in contact with TYR 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A PHE* 3.3 52.5 + + + -
435A PHE* 3.7 3.6 - + - -
437A PRO* 3.0 41.1 - - + +
439A ALA* 4.5 11.1 - - + +
523A GLU 2.8 8.9 + - - +
524A PHE* 2.6 16.7 + + - +
526A PHE* 1.3 67.8 - - - +
528A ARG* 1.3 52.5 + - + +
529A LYS 3.0 4.5 - - - -
530A GLU* 2.6 39.7 + - + +
543A TRP* 3.2 33.4 - + - -
544A TRP* 3.4 25.1 - + - -
551A TYR* 3.5 12.1 - + + -
554A LEU* 4.0 16.2 - - + -
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Residues in contact with ARG 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A PHE* 3.9 13.9 - - + -
439A ALA* 5.6 7.6 - - - +
443A GLN* 5.0 16.2 - - - +
447A VAL* 3.6 37.6 - - - +
524A PHE* 3.8 35.1 - - + +
525A GLU* 3.9 36.7 + - - +
527A TYR* 1.3 78.2 - - + +
529A LYS* 1.3 62.0 + - + +
530A GLU 3.1 5.8 + - - +
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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