Contacts of the strand formed by residues 363 - 368 (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 GLU 363 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357G VAL* 5.0 0.9 - - + -
358G ILE 3.3 13.9 - - - +
359G TYR* 4.2 13.1 - - - +
360G THR 3.2 16.3 - - - +
361G HIS* 5.0 5.4 - - + -
362G PRO* 1.3 74.8 - - + +
364G VAL* 1.3 66.2 + - - +
421G LEU* 3.6 1.7 - - - +
422G GLY 2.9 32.9 + - - +
423G PRO* 5.5 0.7 - - + -
424G GLY* 3.7 10.1 - - - +
425G ALA* 3.3 19.8 + - + +
426G GLY* 2.9 26.9 + - - +
427G GLU* 4.6 0.5 + - - +
393H ARG* 2.8 32.8 + - - -
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Residues in contact with VAL 364 (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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218G ILE* 4.0 6.5 - - + -
222G ILE* 3.8 28.9 - - + -
226G PHE* 3.4 48.5 - - + -
357G VAL* 3.3 1.9 - - - +
358G ILE* 2.8 41.8 + - + +
363G GLU* 1.3 81.1 - - - +
365G ALA* 1.3 66.7 + - - +
366G TRP* 3.8 20.4 - - + -
420G ILE 3.3 6.3 - - - +
421G LEU* 3.9 4.7 - - + -
425G ALA* 4.0 0.9 - - - -
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Residues in contact with ALA 365 (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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356G SER 3.2 11.9 - - - +
357G VAL* 3.8 7.6 - - + -
364G VAL* 1.3 79.4 - - - +
366G TRP* 1.3 66.7 + - - +
419G HIS* 3.5 0.3 - - - -
420G ILE* 2.8 41.7 + - + +
425G ALA* 3.4 33.8 - - + +
426G GLY 4.0 0.2 - - - +
429G VAL* 3.6 14.6 - - + -
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Residues in contact with TRP 366 (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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188G VAL* 5.6 3.1 - - + -
214G GLY 4.5 5.4 - - - -
216G VAL 3.9 9.9 - - - -
217G GLY* 3.7 14.5 + - - -
218G ILE* 3.7 42.6 - - + -
222G ILE* 5.7 1.1 - - + -
354G VAL 4.6 0.2 - - - +
355G PRO* 3.5 1.0 - - - +
356G SER* 2.9 63.5 + - - +
358G ILE* 4.2 22.7 - - + -
364G VAL* 3.8 24.7 - - + -
365G ALA* 1.3 84.7 - - - +
367G VAL* 1.3 68.4 + - - +
368G GLY 4.7 7.6 - - - -
418G ALA 3.1 6.7 - - - +
419G HIS* 3.3 37.9 - + + +
429G VAL* 3.7 6.1 - - - +
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Residues in contact with VAL 367 (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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352G ASN 3.8 0.7 - - - +
353G CYS* 3.5 37.7 - - - +
354G VAL 3.9 2.9 - - - -
355G PRO* 3.9 16.8 - - + -
366G TRP* 1.3 81.3 - - - +
368G GLY* 1.3 66.7 + - - +
417G GLY* 3.5 0.5 - - - -
418G ALA* 3.0 30.8 + - + +
419G HIS* 4.7 1.8 + - - -
429G VAL* 3.9 8.5 - - + -
432G ALA* 3.8 28.7 - - + -
433G ALA* 4.1 12.6 - - + +
436G LEU* 3.9 15.6 - - + +
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Residues in contact with GLY 368 (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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352G ASN* 3.1 39.8 + - - +
354G VAL 5.4 0.2 + - - -
366G TRP* 4.7 8.8 - - - -
367G VAL* 1.3 77.0 - - - +
369G LYS* 1.3 61.9 + - - -
373G GLN* 4.0 5.5 + - - +
416G LEU 3.5 11.0 - - - -
419G HIS* 5.2 0.2 - - - -
436G LEU* 3.5 9.6 - - - -
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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