Contacts of the strand formed by residues 307 - 311 (chain J) in PDB entry 1ZUM
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 ARG 307 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272J LYS* 2.9 43.5 + - + +
273J SER 3.4 7.1 + - - +
274J PRO* 3.4 9.8 - - + +
275J ASN 2.8 27.2 + - - -
305J GLY 3.2 1.7 - - - -
306J SER* 1.3 84.1 - - - +
308J THR* 1.3 62.1 + - - +
309J PHE* 3.5 35.7 + - + -
391J ASP* 6.1 1.4 - - - -
396J ALA* 3.5 27.1 - - - +
406J GLN* 4.0 2.9 - - + -
408J LEU* 4.0 13.7 - - + -
419J ARG 3.1 25.7 + - - -
420J ALA 3.1 21.0 + - - -
422J ASN 4.4 4.2 + - - -
423J SER* 3.6 20.2 + - - -
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Residues in contact with THR 308 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275J ASN* 3.5 14.2 - - - +
277J ILE* 4.3 4.0 - - + -
290J ALA* 4.2 15.6 + - + +
294J LEU* 5.6 0.2 - - - +
305J GLY 3.7 14.0 + - - -
307J ARG* 1.3 72.9 - - - +
309J PHE* 1.3 58.1 + - - +
310J VAL* 3.6 6.1 + - + -
318J PHE* 3.9 33.0 - - + -
405J MET* 4.1 13.5 - - - +
406J GLN 2.8 18.8 + - - -
407J ILE* 3.4 9.8 - - + +
408J LEU* 2.8 28.2 + - - +
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Residues in contact with PHE 309 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274J PRO* 3.9 15.9 - - + -
275J ASN 2.9 9.2 + - - +
276J ILE* 4.3 6.3 - - + -
277J ILE* 2.7 34.0 + - - +
307J ARG* 3.5 52.9 - - + -
308J THR* 1.3 70.4 - - - +
310J VAL* 1.3 57.0 + - - +
391J ASP* 4.1 2.2 - - - -
408J LEU* 3.5 36.8 - - + -
410J PHE* 3.6 18.8 - + + -
416J VAL* 3.8 21.5 - - + -
419J ARG* 3.8 40.6 - - + -
420J ALA* 4.2 4.5 - - - -
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Residues in contact with VAL 310 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277J ILE* 3.7 7.2 - - + -
308J THR* 3.8 6.5 - - + +
309J PHE* 1.3 78.1 - - - +
311J GLN* 1.3 65.8 + - - +
312J GLU 3.4 0.2 + - - -
314J ILE* 3.7 26.7 - - + -
315J TYR* 3.8 24.3 - - + -
318J PHE* 3.7 32.5 - - + -
407J ILE* 3.6 26.0 - - + -
408J LEU 2.8 11.6 + - - +
409J LYS* 3.4 7.6 - - - +
410J PHE* 3.1 23.2 + - - -
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Residues in contact with GLN 311 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277J ILE 3.1 14.1 + - - +
278J MET* 3.5 21.1 - - - +
279J SER* 2.7 49.7 + - - +
310J VAL* 1.3 70.2 - - - +
312J GLU* 1.3 69.3 + - + +
313J ASP* 3.3 4.9 - - - +
314J ILE* 3.0 20.5 + - - +
315J TYR 3.2 5.1 + - - -
410J PHE* 3.1 27.9 - - + +
411J LYS 3.0 28.5 + - - +
412J THR* 4.5 4.2 - - - +
413J ILE 4.8 0.6 - - - +
438J LYS* 5.2 4.3 + - - +
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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