Contacts of the helix formed by residues 499 - 511 (chain B) 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 499 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360B SER 4.6 2.7 - - - -
361B ARG* 4.6 0.9 - - - +
362B MET* 3.0 51.4 - - - +
366B ASP* 3.7 22.4 + - - -
369B VAL* 5.5 3.1 - - - -
497B LEU 3.4 2.8 + - - -
498B VAL* 1.3 82.6 - - - +
500B THR* 1.3 68.2 + - - +
501B SER* 3.2 8.1 + - - -
502B GLY* 3.7 2.8 + - - -
503B PHE* 3.2 16.5 + - - +
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Residues in contact with THR 500 (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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365B SER 4.9 0.5 + - - -
366B ASP* 3.2 31.3 + - - -
368B TRP* 3.4 41.3 + - + +
369B VAL* 3.9 12.8 - - + +
415B HIS 5.6 0.2 + - - -
416B PRO* 5.7 10.1 - - + -
499B SER* 1.3 77.1 + - - +
501B SER* 1.3 61.1 + - - +
503B PHE* 3.4 3.8 + - + +
504B LEU* 2.9 35.2 + - + +
519B ILE* 6.4 1.6 - - + -
523B VAL* 5.9 0.4 - - + -
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Residues in contact with SER 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PHE* 5.4 7.3 - - - -
362B MET* 5.6 2.8 - - - -
499B SER* 3.2 7.0 + - - -
500B THR* 1.3 81.3 - - - +
502B GLY* 1.3 66.6 + - - +
504B LEU* 3.2 11.7 + - - +
505B LYS* 2.9 41.6 + - - +
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Residues in contact with GLY 502 (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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20B PHE* 6.3 0.9 - - - -
498B VAL* 6.1 0.9 - - - -
499B SER 3.7 3.7 + - - -
501B SER* 1.3 84.2 + - - +
503B PHE* 1.3 55.7 + - - +
505B LYS* 3.3 19.2 - - - +
506B SER* 2.9 28.1 + - - -
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Residues in contact with PHE 503 (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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368B TRP* 5.3 5.4 - + - -
369B VAL* 3.5 35.2 - - + -
373B ILE* 3.9 26.7 - - + -
457B MET* 5.4 6.5 - - + -
460B ILE* 5.3 7.9 - - + -
472B VAL* 3.8 25.4 - - + -
473B PHE* 5.0 2.5 - + - -
476B LEU* 4.0 23.1 - - + -
498B VAL* 3.9 12.6 + - + +
499B SER 3.2 20.5 + - - +
500B THR* 3.5 4.0 - - + +
502B GLY* 1.3 74.5 - - - +
504B LEU* 1.3 61.9 + - + +
506B SER* 3.1 6.6 + - - -
507B ILE* 2.9 55.2 + - + +
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Residues in contact with LEU 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B THR* 2.9 19.9 + - + +
501B SER* 3.3 13.2 - - - +
503B PHE* 1.3 76.3 - - + +
505B LYS* 1.3 65.8 + - + +
507B ILE* 3.2 16.0 + - + +
508B SER* 3.0 24.9 + - - +
515B ILE* 3.7 26.5 - - + -
516B GLN* 4.4 18.8 - - + +
519B ILE* 3.7 35.0 - - + -
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Residues in contact with LYS 505 (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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20B PHE* 3.3 36.6 - - - -
501B SER* 2.9 26.0 + - - +
502B GLY* 3.3 18.7 - - - +
504B LEU* 1.3 77.4 - - + +
506B SER* 1.3 54.4 + - - +
508B SER* 3.3 6.4 + - - -
509B ASN* 2.7 43.2 + - - +
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Residues in contact with SER 506 (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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472B VAL* 4.7 11.3 - - - +
475B LYS* 4.9 14.7 - - - +
476B LEU* 5.1 10.4 - - - +
502B GLY 2.9 14.0 + - - -
503B PHE* 3.1 10.3 + - - -
505B LYS* 1.3 73.0 - - - +
507B ILE* 1.3 60.0 + - - +
509B ASN* 3.3 12.3 + - - +
510B VAL* 2.9 34.1 + - - +
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Residues in contact with ILE 507 (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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460B ILE* 4.9 19.5 - - + -
464B ILE* 3.8 22.3 - - + +
472B VAL* 4.4 17.0 - - + +
503B PHE* 2.9 56.6 + - + +
504B LEU* 3.2 21.5 + - + +
506B SER* 1.3 76.1 - - - +
508B SER* 1.3 51.8 + - - +
510B VAL* 2.9 6.8 + - - +
511B SER* 2.7 34.0 + - - +
515B ILE* 3.7 20.2 - - + -
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Residues in contact with SER 508 (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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504B LEU* 3.0 16.6 + - - +
505B LYS* 3.9 5.8 - - - -
507B ILE* 1.3 77.9 - - - +
509B ASN* 1.3 61.9 + - - +
511B SER 3.4 10.1 - - - -
512B GLY* 2.8 31.9 + - - -
513B LYS 4.8 1.7 + - - -
515B ILE* 3.5 20.6 - - - +
516B GLN* 4.9 7.8 + - - -
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Residues in contact with ASN 509 (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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475B LYS* 5.3 4.1 + - - +
505B LYS* 2.7 37.7 + - - +
506B SER* 3.5 12.8 - - - +
507B ILE 3.1 0.2 - - - -
508B SER* 1.3 78.1 - - - +
510B VAL* 1.3 63.3 + - + +
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Residues in contact with VAL 510 (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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874A GLU* 5.3 5.7 - - - +
464B ILE* 5.9 0.4 - - + -
468B PHE* 3.9 31.0 - - + +
471B GLN* 3.3 24.7 - - - +
472B VAL* 3.7 21.5 - - + +
475B LYS* 3.6 34.3 - - + +
506B SER* 2.9 17.3 + - - +
507B ILE 2.9 8.9 + - - +
509B ASN* 1.3 80.5 - - + +
511B SER* 1.3 59.6 + - - +
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Residues in contact with SER 511 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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874A GLU* 5.5 5.2 + - - +
464B ILE* 4.0 20.3 - - - +
468B PHE* 4.3 24.1 - - - -
507B ILE* 2.7 18.1 + - - +
508B SER* 3.2 6.6 + - - -
510B VAL* 1.3 78.4 - - - +
512B GLY* 1.3 59.9 + - - +
513B LYS* 3.2 38.2 + - - +
515B ILE* 4.9 0.5 - - - +
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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