Contacts of the strand formed by residues 315 - 322 (chain A) in PDB entry 1ZKK
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 VAL 315 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A LEU* 4.6 9.9 - - + -
277A TYR* 4.6 0.2 - - - -
311A ASP* 3.5 1.7 - - - -
312A ILE* 2.9 38.9 + - + +
313A ASP 4.6 4.3 - - - +
314A GLY* 1.3 79.9 - - - +
316A PRO* 1.3 72.8 - - + +
317A HIS* 3.3 26.1 - - + +
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Residues in contact with PRO 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A LEU* 3.9 29.1 - - + +
275A PHE* 3.7 19.0 - - + -
277A TYR* 3.8 27.5 - - + -
282A TYR* 5.1 5.8 - - + -
309A LEU* 3.7 21.5 - - + -
310A HIS 3.8 3.1 - - - +
311A ASP* 4.5 3.8 - - - -
314A GLY 3.7 8.1 - - - +
315A VAL* 1.3 94.1 - - + +
317A HIS* 1.3 66.8 + - - +
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Residues in contact with HIS 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ILE* 3.6 33.1 - - + +
244A GLU* 2.6 31.1 + - - +
246A HIS* 6.2 0.7 - + - -
275A PHE* 5.7 0.4 - - - -
284A VAL* 6.0 1.1 - - - -
309A LEU* 3.5 5.9 - - - +
310A HIS* 2.8 41.3 + - - +
312A ILE* 4.0 22.1 - - + +
315A VAL* 3.3 35.7 + - + +
316A PRO* 1.3 76.7 + - - +
318A LEU* 1.3 62.8 - - - +
319A ILE* 3.9 3.8 + - + -
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Residues in contact with LEU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A GLU* 3.3 10.6 + - - +
245A TYR* 2.8 42.7 + - + +
273A TYR* 3.6 40.2 - - + -
275A PHE* 3.8 38.4 - - + -
284A VAL* 3.8 20.3 - - + +
307A THR* 4.1 9.6 - - + -
308A LYS 3.5 5.6 - - - +
309A LEU* 4.3 5.4 - - + -
317A HIS* 1.3 76.8 - - - +
319A ILE* 1.3 60.4 + - - +
22E LEU* 4.0 21.3 - - + -
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Residues in contact with ILE 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ILE* 3.8 24.2 - - + -
210A ILE* 3.8 27.8 - - + -
241A PHE* 3.9 18.4 - - + -
243A VAL 3.7 3.6 - - - -
244A GLU* 4.5 4.3 - - + -
306A GLN 3.6 0.9 - - - +
307A THR* 3.2 3.6 - - - -
308A LYS* 2.8 52.6 + - + +
310A HIS* 3.8 23.3 - - + +
317A HIS* 4.4 4.0 - - + -
318A LEU* 1.3 78.8 - - - +
320A LEU* 1.3 64.7 + - - +
321A ILE* 3.8 24.2 + - + -
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Residues in contact with LEU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A PHE* 3.9 1.4 - - - -
242A VAL* 2.9 29.7 + - + +
243A VAL* 2.8 29.7 + - + +
245A TYR* 4.2 30.1 - - + +
273A TYR* 5.2 0.2 - - + -
294A GLY 5.4 1.1 - - - +
297A ILE* 3.7 26.7 - - + -
305A CYS* 4.1 20.6 - - + -
306A GLN 3.5 3.4 - - - +
307A THR* 3.7 22.2 - - + +
319A ILE* 1.3 78.2 - - - +
321A ILE* 1.3 63.9 + - - +
334A TYR* 3.6 31.0 - - + -
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Residues in contact with ILE 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A GLU* 5.1 4.3 - - - +
206A ILE* 4.6 9.4 - - + -
239A GLY* 3.4 28.5 - - - +
240A ASP 3.4 2.0 - - - +
241A PHE* 3.8 21.5 - - + +
242A VAL* 4.2 2.5 - - - -
305A CYS* 3.2 2.7 - - - -
306A GLN* 2.8 35.8 + - + +
308A LYS* 3.8 33.4 - - + -
319A ILE* 3.8 23.3 - - + -
320A LEU* 1.3 82.2 - - - +
322A ALA* 1.3 72.2 + - - +
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Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A PHE* 4.5 4.0 - - + -
237A SER 3.5 23.6 - - - +
238A ARG* 4.2 0.9 - - - +
239A GLY* 2.8 26.2 + - - -
240A ASP 2.9 14.0 + - - +
242A VAL* 3.7 10.8 - - + +
304A ASN 3.4 6.3 - - - -
305A CYS* 4.4 0.2 - - - +
321A ILE* 1.3 74.0 - - - +
323A SER* 1.3 60.2 + - - +
324A ARG 3.3 14.4 - - - +
326A ILE* 3.8 16.8 - - + -
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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