Contacts of the strand formed by residues 381 - 387 (chain G) in PDB entry 1ZMD
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 TYR 381 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371G GLU* 2.7 40.4 + - + +
374G LEU* 3.7 36.3 - - + -
375G LYS* 3.4 33.8 - - + -
379G ILE 3.1 22.4 - - - +
380G GLU* 1.3 76.1 + - - +
382G LYS* 1.3 72.1 + - - +
383G VAL* 3.8 16.1 - - + +
407G LEU* 3.9 13.9 - - + -
408G GLY 3.1 16.4 - - - +
410G LYS* 3.7 10.6 - - - +
416G LEU* 4.4 2.9 - - + -
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Residues in contact with LYS 382 (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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381G TYR* 1.3 76.4 - - - +
383G VAL* 1.3 66.7 + - - +
407G LEU* 3.4 5.7 - - - -
408G GLY* 2.8 41.3 + - - +
409G GLN 4.0 12.6 - - - -
410G LYS* 3.9 37.2 + - + +
413G ASP* 2.5 40.0 + - - +
442G CYS* 4.7 3.6 - - - -
466G ALA* 3.0 31.2 + - + +
467G SER* 3.7 11.1 + - - +
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Residues in contact with VAL 383 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371G GLU* 4.4 8.1 - - - +
381G TYR* 3.8 23.8 - - + +
382G LYS* 1.3 82.5 - - - +
384G GLY* 1.3 62.0 + - - +
385G LYS* 4.0 19.5 + - + -
405G LYS* 3.8 31.4 - - + -
406G ILE 3.4 3.1 - - - +
407G LEU* 3.9 6.5 - - + -
465G ALA 4.8 2.1 - - - +
466G ALA* 4.1 9.5 - - - -
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Residues in contact with GLY 384 (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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383G VAL* 1.3 74.9 - - - +
385G LYS* 1.3 62.8 + - - +
404G VAL 3.8 0.3 - - - +
405G LYS* 3.2 4.5 - - - +
406G ILE* 2.7 38.9 + - - +
462G ALA* 3.6 22.4 - - - +
465G ALA* 4.1 3.4 - - - -
466G ALA* 3.6 14.6 - - - +
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Residues in contact with LYS 385 (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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221G GLU* 2.7 39.5 + - - -
371G GLU* 5.4 0.4 - - - -
383G VAL* 4.0 11.9 - - + -
384G GLY* 1.3 79.0 - - - +
386G PHE* 1.3 62.4 + - - +
387G PRO* 4.6 3.3 - - + +
403G MET* 4.0 18.8 - - - -
404G VAL 3.4 4.7 - - - +
405G LYS* 4.0 18.2 - - + -
462G ALA* 4.3 2.9 - - - -
465G ALA* 4.2 7.2 - - - +
471G SER* 4.1 11.3 + - - -
474G PHE* 4.8 7.1 - - + -
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Residues in contact with PHE 386 (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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385G LYS* 1.3 73.6 - - - +
387G PRO* 1.4 88.7 - - - +
388G PHE 3.9 0.2 + - - -
390G ALA* 3.6 32.8 - - + -
391G ASN* 3.9 8.3 - - - -
403G MET* 3.2 5.2 - - - -
404G VAL* 2.9 33.7 + - - +
457G GLU 5.4 0.2 - - - -
458G ALA* 3.6 40.2 - - + +
461G GLU* 3.3 37.7 - - + -
462G ALA* 3.8 8.3 - - + +
471G SER* 3.5 13.0 - - - -
473G ASN* 3.8 13.5 - - + -
474G PHE* 3.5 24.2 - - + -
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Residues in contact with PRO 387 (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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385G LYS* 4.6 1.1 - - + -
386G PHE* 1.4 102.6 - - + +
388G PHE* 1.3 64.9 + - - +
389G ALA* 4.1 10.5 - - + +
390G ALA* 3.0 19.0 + - + +
402G GLY 3.4 10.3 - - - +
403G MET* 4.0 4.5 - - + -
458G ALA* 5.5 0.2 - - - -
474G PHE* 3.5 53.2 - - + -
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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