Contacts of the strand formed by residues 307 - 311 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C LYS* 3.0 38.5 + - + +
273C SER 3.4 7.0 + - - +
274C PRO* 3.3 13.3 - - + +
275C ASN 2.8 26.9 + - - -
305C GLY 3.3 1.5 - - - -
306C SER* 1.3 83.9 - - - +
308C THR* 1.3 61.8 + - - +
309C PHE* 3.5 32.7 + - + -
391C ASP* 5.5 2.8 + - - -
396C ALA* 3.3 30.3 - - - +
406C GLN* 4.0 2.7 - - + -
408C LEU* 4.0 13.9 - - + -
419C ARG 3.0 25.1 + - - -
420C ALA 2.8 22.8 + - - -
422C ASN 4.3 5.8 + - - -
423C SER* 3.9 15.7 - - - -
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Residues in contact with THR 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C ASN* 3.5 14.5 - - - +
277C ILE* 4.2 5.8 - - + -
290C ALA* 4.3 10.8 + - + +
305C GLY 3.7 14.4 + - - -
307C ARG* 1.3 69.2 - - - +
309C PHE* 1.3 55.1 + - - +
310C VAL* 3.7 6.8 + - + -
318C PHE* 3.8 34.1 - - + -
405C MET* 3.8 17.7 - - + +
406C GLN 2.8 17.4 + - - -
407C ILE* 3.3 10.0 - - - +
408C LEU* 2.7 32.3 + - - +
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Residues in contact with PHE 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C PRO* 3.9 19.5 - - + -
275C ASN 2.8 12.0 + - - +
276C ILE* 4.2 9.9 - - + -
277C ILE* 2.7 34.8 + - - +
307C ARG* 3.7 48.2 - - + -
308C THR* 1.3 70.8 - - - +
310C VAL* 1.3 56.5 + - - +
391C ASP* 4.2 2.7 - - - -
408C LEU* 3.4 24.2 - - + -
410C PHE* 3.7 15.9 - + + -
416C VAL* 3.7 20.4 - - + -
419C ARG* 3.6 52.7 - - + -
420C ALA* 4.2 4.5 - - + -
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Residues in contact with VAL 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C ILE* 3.7 6.7 - - + +
308C THR* 3.9 6.5 - - + +
309C PHE* 1.3 78.1 - - - +
311C GLN* 1.3 67.0 + - - +
312C GLU 3.5 0.2 + - - -
314C ILE* 3.8 26.0 - - + -
315C TYR* 3.8 25.1 - - + -
318C PHE* 3.5 43.7 - - + -
407C ILE* 3.7 16.4 - - + -
408C LEU 2.8 11.8 + - - +
409C LYS* 3.4 8.5 - - - +
410C PHE* 3.2 21.2 + - - -
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Residues in contact with GLN 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277C ILE 3.1 9.5 + - - +
278C MET* 3.5 27.4 - - - +
279C SER* 2.5 57.4 + - - +
310C VAL* 1.3 71.1 - - - +
312C GLU* 1.3 70.5 + - + +
313C ASP* 3.3 4.0 - - - +
314C ILE* 3.0 16.4 + - + +
315C TYR 3.2 8.7 + - - -
410C PHE* 3.1 22.5 - - + +
411C LYS 3.1 26.3 + - - +
412C THR* 4.5 4.0 - - - +
413C ILE 4.7 0.8 - - - +
438C LYS* 5.4 2.7 + - - +
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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