Contacts of the strand formed by residues 482 - 486 (chain G) in PDB entry 6MZL
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 SER 482 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477G ASP* 3.3 12.6 - - - +
478G VAL 4.5 0.5 + - - -
479G THR 5.8 0.2 - - - -
480G ASP 3.3 3.9 + - - -
481G ASP* 1.3 90.1 + - - +
483G SER* 1.3 60.0 + - - +
494G VAL* 4.5 8.3 - - - -
495G ARG 3.1 14.8 - - - -
496G VAL* 4.1 8.1 - - - +
551G PHE* 3.1 43.8 - - - -
555G ARG* 5.9 1.0 + - - +
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Residues in contact with SER 483 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466G PHE* 4.5 6.8 - - - -
475G ALA* 5.9 0.9 - - - -
476G VAL 3.8 7.6 - - - -
477G ASP* 4.1 11.4 - - - -
482G SER* 1.3 74.8 - - - +
484G LEU* 1.3 66.9 + - - +
485G ILE* 3.9 12.2 + - - +
494G VAL* 3.5 4.0 - - - +
495G ARG* 2.9 45.1 + - - +
551G PHE* 4.3 0.2 - - - -
781G VAL* 5.7 9.0 - - - -
789G ASN* 5.4 12.6 + - - +
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Residues in contact with LEU 484 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474G THR 3.4 0.5 - - - +
475G ALA* 2.8 31.7 - - - -
476G VAL 2.9 23.2 + - - +
483G SER* 1.3 77.3 - - - +
485G ILE* 1.3 56.8 + - - +
486G ALA* 3.3 4.0 + - - +
493G THR 3.7 2.2 - - - +
494G VAL* 3.7 26.9 - - + -
549G ALA* 4.5 11.5 - - + +
550G SER* 3.5 11.2 - - - +
551G PHE* 3.5 61.7 - - + +
558G LEU* 3.7 22.4 - - + -
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Residues in contact with ILE 485 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466G PHE* 4.7 1.6 - - + -
472G GLY* 5.2 0.7 - - - -
475G ALA* 3.9 14.6 - - + -
483G SER* 3.9 11.6 - - - +
484G LEU* 1.3 69.9 - - - +
486G ALA* 1.3 59.3 + - - +
487G GLY* 3.0 18.1 + - - +
492G SER 4.8 0.4 - - - -
493G THR* 2.9 48.0 + - - +
495G ARG* 3.7 28.0 - - + +
781G VAL* 5.2 5.6 - - + -
783G LEU* 4.3 15.7 - - + -
787G ARG* 3.7 52.7 - - + +
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Residues in contact with ALA 486 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472G GLY* 4.0 0.2 - - - -
473G LEU* 2.6 32.1 + - - +
474G THR* 2.6 44.2 + - + +
484G LEU 3.3 2.6 + - - +
485G ILE* 1.3 69.7 - - - +
487G GLY* 1.3 51.8 + - - +
491G ASP 4.5 3.4 - - - -
492G SER* 4.7 4.0 - - - +
546G VAL* 3.7 33.2 - - + -
549G ALA* 4.8 9.4 - - + -
767G GLU* 5.0 0.2 - - - +
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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