Contacts of the strand formed by residues 360 - 366 (chain C) in PDB entry 1ZXN
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 MET 360 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C LEU* 3.9 20.6 - - + -
302C THR 4.0 1.8 - - - -
304C SER* 3.3 7.0 - - - -
308C PHE* 3.6 10.3 - - + -
309C GLN 3.1 23.5 + - - +
330C ALA* 3.8 18.6 - - + +
333C ILE* 3.5 42.2 - - + -
334C VAL* 3.6 25.8 - - - -
337C LEU* 5.0 7.9 - - + -
356C VAL* 3.5 15.5 - - + +
357C LYS* 2.9 18.4 + - - +
358C ASN 3.3 0.2 - - - -
359C HIS* 1.3 83.0 - - + +
361C TRP* 1.3 61.5 + - - +
362C ILE* 4.0 6.5 - - + +
407C ILE* 5.3 3.8 - - + -
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Residues in contact with TRP 361 (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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62C TRP* 3.7 35.9 - + - -
274C TYR* 4.3 8.1 - - + -
275C LEU* 3.7 17.9 - - + -
300C CYS 4.0 0.2 - - - +
301C LEU* 3.6 2.6 - - - +
302C THR* 2.9 67.5 + - + +
303C MET 4.1 8.1 - - - -
304C SER* 3.8 9.2 - - - -
309C GLN* 3.5 45.5 + - + +
311C ILE* 3.9 15.3 - - + +
360C MET* 1.3 73.4 - - - +
362C ILE* 1.3 65.4 + - - +
363C PHE* 3.3 32.6 - + - -
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Residues in contact with ILE 362 (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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299C VAL* 4.0 5.4 - - + -
300C CYS 3.3 11.4 - - - +
301C LEU* 4.3 9.0 - - + -
308C PHE* 4.0 16.8 - - + -
309C GLN 3.0 10.2 + - - +
310C GLN* 3.1 21.0 - - + -
311C ILE 3.0 23.7 + - - -
326C VAL* 5.2 3.1 - - + +
329C VAL* 3.3 33.9 - - + -
330C ALA* 4.1 15.0 - - + +
333C ILE* 4.0 15.5 - - + -
360C MET* 4.0 3.8 - - + -
361C TRP* 1.3 75.9 - - - +
363C PHE* 1.3 66.6 + - - +
364C VAL* 4.0 15.4 - - + +
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Residues in contact with PHE 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C PHE* 3.9 9.2 - + + -
270C TYR* 5.5 1.1 - + - -
271C VAL* 3.6 39.9 - - + -
274C TYR* 3.9 16.4 - + + -
275C LEU* 3.8 16.8 - - + -
288C VAL* 6.2 0.2 - - + -
298C GLU 3.9 0.3 - - - +
299C VAL* 3.4 5.0 - - - +
300C CYS* 2.8 54.8 + - + +
301C LEU 5.5 0.4 - - - -
302C THR* 4.1 10.8 - - + -
311C ILE* 3.2 40.2 - - + +
361C TRP* 3.3 45.3 - + - -
362C ILE* 1.3 74.1 - - - +
364C VAL* 1.3 63.9 + - - +
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Residues in contact with VAL 364 (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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267C PHE* 3.8 3.5 - - - -
297C TRP* 4.2 27.6 - - + -
298C GLU 3.5 6.1 - - - +
299C VAL* 4.6 2.7 - - + -
311C ILE 2.9 10.0 + - - +
312C SER* 3.0 14.9 - - - -
313C PHE* 2.9 26.3 + - - -
325C HIS* 4.4 15.0 - - + +
326C VAL* 4.7 11.0 - - + -
329C VAL* 4.2 16.4 - - + -
362C ILE* 4.0 29.8 - - + -
363C PHE* 1.3 79.7 - - - +
365C ASN* 1.3 66.6 + - - +
366C ALA* 4.6 0.2 - - + -
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Residues in contact with ASN 365 (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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248C GLY 4.4 2.8 + - - -
249C SER* 2.9 42.0 + - - +
267C PHE* 3.8 29.6 - - + +
296C ARG 3.7 0.9 - - - +
297C TRP* 3.6 2.8 - - - -
298C GLU* 2.9 38.2 + - + +
313C PHE* 3.2 23.8 - - - +
316C SER 5.2 1.9 + - - -
364C VAL* 1.3 74.6 - - - +
366C ALA* 1.3 66.4 + - - +
367C LEU* 6.2 2.8 - - - +
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Residues in contact with ALA 366 (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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296C ARG 3.2 5.6 - - - +
297C TRP* 3.7 28.0 - - + -
313C PHE 3.0 12.3 + - - +
314C VAL* 3.3 5.9 - - - -
315C ASN* 3.0 24.8 + - - +
325C HIS* 4.9 3.4 - - + -
364C VAL* 4.6 3.4 - - + -
365C ASN* 1.3 79.8 + - - +
367C LEU* 1.3 65.7 + - - +
368C ILE* 3.3 23.3 - - + -
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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