Contacts of the strand formed by residues 307 - 311 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272F LYS* 3.0 37.3 + - + +
273F SER 3.4 6.9 + - - +
274F PRO* 3.3 13.5 - - + +
275F ASN 2.8 25.0 + - - -
305F GLY 3.3 1.5 - - - -
306F SER* 1.3 82.7 - - - +
308F THR* 1.3 61.8 + - - +
309F PHE* 3.4 31.9 + - + -
391F ASP* 5.6 3.2 + - - -
396F ALA* 3.5 25.8 - - - +
406F GLN* 4.0 0.4 - - + -
408F LEU* 4.0 17.3 - - + -
419F ARG 2.9 26.1 + - - -
420F ALA* 2.8 22.2 + - - +
422F ASN 4.0 7.4 + - - -
423F SER* 3.6 17.4 - - - -
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Residues in contact with THR 308 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275F ASN* 3.5 15.4 + - - +
277F ILE* 4.3 4.3 - - + -
290F ALA* 4.1 13.5 + - + +
305F GLY 3.6 15.2 + - - -
306F SER 5.0 0.2 - - - -
307F ARG* 1.3 69.5 - - - +
309F PHE* 1.3 55.0 + - - +
310F VAL* 3.8 5.7 + - + -
318F PHE* 3.9 33.0 - - + -
405F MET* 4.0 17.1 - - + +
406F GLN 2.9 17.3 + - - -
407F ILE* 3.4 9.8 - - + +
408F LEU* 2.8 32.4 + - - +
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Residues in contact with PHE 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274F PRO* 3.9 16.2 - - + -
275F ASN 2.9 11.7 + - - +
276F ILE* 4.2 9.6 - - + -
277F ILE* 2.8 34.0 + - - +
307F ARG* 3.4 52.4 + - + -
308F THR* 1.3 71.0 - - - +
310F VAL* 1.3 58.2 + - - +
391F ASP* 4.3 2.5 - - - -
408F LEU* 3.4 29.8 - - + -
410F PHE* 3.7 7.4 - + + -
416F VAL* 3.8 26.5 - - + -
419F ARG* 3.8 53.6 - - + -
420F ALA* 4.2 4.9 - - - -
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Residues in contact with VAL 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277F ILE* 3.8 9.9 - - + +
308F THR* 4.1 3.8 - - + +
309F PHE* 1.3 77.7 - - - +
311F GLN* 1.3 74.9 + - - +
312F GLU 3.4 0.5 + - - -
314F ILE* 3.7 23.3 - - + -
315F TYR* 3.7 23.5 - - + -
318F PHE* 3.5 39.9 - - + -
407F ILE* 3.8 17.5 - - + -
408F LEU 2.8 12.0 + - - +
409F LYS* 3.5 6.9 - - - +
410F PHE* 3.2 22.4 + - - -
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Residues in contact with GLN 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277F ILE 3.1 5.6 + - - +
278F MET* 3.4 27.9 - - - +
279F SER* 2.7 56.6 + - - +
310F VAL* 1.3 71.6 - - - +
312F GLU* 1.3 69.4 + - + +
313F ASP* 3.3 3.4 - - + +
314F ILE* 3.1 15.3 + - - +
315F TYR 3.2 9.0 + - - -
410F PHE* 3.1 24.3 - - + +
411F LYS 3.1 28.3 + - - +
412F THR* 4.5 4.0 - - - +
413F ILE 4.8 1.2 - - - +
438F LYS* 5.4 2.4 + - - +
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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