Contacts of the helix formed by residues 542 - 552 (chain Y) in PDB entry 5G04
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 ASP 542 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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513Y ARG* 5.1 0.5 - - - +
536Y LEU* 4.7 2.2 - - - +
539Y ASP* 2.8 40.4 + - + +
540Y PRO 3.1 3.2 + - - -
541Y ASN* 1.3 76.7 - - - +
543Y GLN* 1.3 74.4 + - - +
544Y LYS* 3.1 46.0 + - - +
545Y SER* 3.3 17.7 + - - +
546Y LEU* 3.2 24.8 + - - +
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Residues in contact with GLN 543 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541Y ASN 3.5 4.8 + - - -
542Y ASP* 1.3 76.1 + - - +
544Y LYS* 1.3 63.2 - - + +
546Y LEU* 3.6 17.5 + - - +
547Y GLU* 3.2 41.7 + - - +
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Residues in contact with LYS 544 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510Y VAL* 4.4 21.8 - - - +
513Y ARG* 3.4 52.5 - - + +
532Y TYR* 3.8 10.7 - - - -
542Y ASP* 3.1 30.9 + - - +
543Y GLN* 1.3 78.2 - - + +
545Y SER* 1.3 64.0 + - - +
547Y GLU* 3.3 28.9 - - - +
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Residues in contact with SER 545 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513Y ARG* 4.0 6.4 - - - +
532Y TYR* 3.1 32.1 - - - +
535Y ALA* 3.4 25.7 - - - +
536Y LEU* 3.7 32.4 - - - +
539Y ASP* 3.7 5.0 + - - -
542Y ASP* 3.3 22.2 + - - -
544Y LYS* 1.3 74.9 - - - +
546Y LEU* 1.3 64.2 + - - +
547Y GLU 3.4 0.2 + - - -
548Y GLY 3.5 1.7 + - - -
549Y MET 4.0 3.6 + - - -
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Residues in contact with LEU 546 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536Y LEU* 4.1 12.7 - - + +
541Y ASN* 5.9 1.8 - - - -
542Y ASP 3.2 20.1 + - - +
543Y GLN* 3.9 20.2 - - - +
545Y SER* 1.3 74.6 - - - +
547Y GLU* 1.3 64.9 + - - +
548Y GLY 3.3 0.2 - - - -
549Y MET* 3.3 19.0 + - + +
550Y GLN* 3.2 54.9 + - + +
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Residues in contact with GLU 547 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513Y ARG* 4.7 7.6 + - - -
517Y ASP* 5.8 0.5 - - - +
532Y TYR* 5.3 1.6 - - + +
543Y GLN* 3.2 37.9 + - - +
544Y LYS* 3.3 24.9 - - - +
545Y SER 3.2 0.2 - - - -
546Y LEU* 1.3 78.1 - - - +
548Y GLY* 1.3 60.4 + - - +
550Y GLN* 3.3 8.2 + - - +
551Y LYS* 3.2 27.2 + - - +
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Residues in contact with GLY 548 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529Y MET* 4.8 7.4 - - - +
532Y TYR* 3.5 40.8 + - - -
545Y SER 3.5 4.4 + - - -
546Y LEU 3.3 0.8 - - - -
547Y GLU* 1.3 76.5 - - - +
549Y MET* 1.3 62.8 + - - +
551Y LYS* 3.3 27.5 + - - +
552Y MET* 4.2 5.5 + - - +
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Residues in contact with MET 549 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625F ARG* 3.7 34.1 - - - +
645F TYR* 4.5 10.3 - - - +
529Y MET* 4.2 32.1 - - - +
532Y TYR* 5.0 4.2 - - + -
533Y SER* 5.3 2.0 - - - +
536Y LEU* 4.2 26.7 - - + -
545Y SER 4.0 2.2 + - - +
546Y LEU* 3.3 21.5 + - + +
548Y GLY* 1.3 76.1 - - - +
550Y GLN* 1.3 62.6 + - + +
552Y MET* 3.3 24.9 - - - +
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Residues in contact with GLN 550 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546Y LEU* 3.2 49.2 - - + +
547Y GLU* 3.3 7.5 + - - +
548Y GLY 3.3 0.2 - - - -
549Y MET* 1.3 80.8 - - - +
551Y LYS* 1.3 63.2 + - - +
552Y MET* 3.3 17.2 - - - +
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Residues in contact with LYS 551 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520Y VAL* 4.3 21.5 - - + -
525Y TYR* 3.4 40.2 + - + -
532Y TYR* 5.5 2.0 - - + +
547Y GLU 3.2 19.0 + - - +
548Y GLY* 3.3 26.0 - - - +
550Y GLN* 1.3 74.7 - - - +
552Y MET* 1.3 71.6 + - + +
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Residues in contact with MET 552 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645F TYR* 5.4 2.2 - - + -
650F LYS* 3.3 43.5 - - - +
653F LEU* 4.8 11.7 - - + -
525Y TYR* 4.7 11.4 - - + -
529Y MET* 3.7 31.0 - - + -
548Y GLY 4.2 2.7 + - - +
549Y MET* 3.3 21.1 - - - +
550Y GLN* 3.3 20.8 - - - +
551Y LYS* 1.3 94.8 - - + +
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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