Contacts of the strand formed by residues 315 - 322 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249D LEU* 4.5 10.1 - - + -
277D TYR* 4.6 0.2 - - - -
311D ASP* 3.5 2.4 - - - -
312D ILE 2.9 35.9 + - - +
313D ASP* 4.1 5.8 - - + +
314D GLY* 1.3 81.6 - - - +
316D PRO* 1.3 71.7 - - + +
317D HIS* 3.2 28.5 - - + +
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Residues in contact with PRO 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D LEU* 3.9 27.8 - - + +
275D PHE* 3.7 30.0 - - + -
277D TYR* 3.8 34.9 - - + -
282D TYR* 5.1 4.9 - - + -
284D VAL* 6.0 0.5 - - - +
309D LEU* 3.8 11.0 - - + -
310D HIS 3.7 4.3 - - - +
311D ASP* 4.5 3.6 - - - -
314D GLY 4.0 1.6 - - - +
315D VAL* 1.3 94.8 - - + +
317D HIS* 1.3 66.0 + - - +
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Residues in contact with HIS 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D ILE* 3.8 22.5 - - + +
244D GLU* 2.7 28.7 + - - +
246D HIS* 6.3 0.4 - + - -
275D PHE* 5.7 0.9 - - - -
284D VAL* 6.0 1.8 - - - -
308D LYS 3.6 1.2 - - - +
309D LEU* 3.6 4.2 - - - +
310D HIS* 2.7 41.5 + - - +
312D ILE* 3.9 23.6 - - + +
315D VAL* 3.2 43.8 + - + +
316D PRO* 1.3 78.1 + - - +
318D LEU* 1.3 63.4 + - - +
319D ILE* 4.2 14.1 - - + -
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Residues in contact with LEU 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D GLU* 3.2 11.2 + - - +
245D TYR* 2.8 41.8 + - + +
273D TYR* 3.6 41.3 - - + -
275D PHE* 3.7 42.6 - - + -
284D VAL* 3.8 20.3 - - + +
307D THR* 4.1 10.3 - - + -
308D LYS 3.6 5.8 - - - +
309D LEU* 4.4 2.7 - - - -
317D HIS* 1.3 75.6 - - - +
319D ILE* 1.3 60.3 + - - +
22H LEU* 4.0 21.8 - - + -
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Residues in contact with ILE 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D ILE* 3.8 24.2 - - + -
210D ILE* 3.6 20.0 - - + -
241D PHE* 3.6 25.4 - - + -
243D VAL 3.8 3.1 - - - -
244D GLU* 4.4 3.8 - - + -
306D GLN 3.6 0.9 - - - +
307D THR* 3.3 1.8 - - - +
308D LYS* 2.7 51.7 + - + +
310D HIS* 3.7 23.6 - - + +
317D HIS* 4.2 9.0 - - + -
318D LEU* 1.3 80.4 - - - +
320D LEU* 1.3 64.3 + - - +
321D ILE* 3.7 26.6 + - + -
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Residues in contact with LEU 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D PHE* 4.0 1.0 - - - -
242D VAL* 2.8 32.9 + - + -
243D VAL* 2.8 28.0 + - + +
245D TYR* 4.2 27.1 - - + +
273D TYR* 5.2 0.2 - - + -
294D GLY* 5.3 1.1 - - - +
297D ILE* 3.6 28.0 - - + -
305D CYS* 4.2 20.2 - - + -
306D GLN 3.5 3.1 - - - -
307D THR* 3.7 22.7 - - + +
319D ILE* 1.3 76.1 - - - +
321D ILE* 1.3 58.4 + - - +
334D TYR* 3.6 31.6 - - + -
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Residues in contact with ILE 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D GLU* 6.0 0.4 - - - +
206D ILE* 5.1 7.6 - - + -
239D GLY* 3.4 29.8 - - - +
240D ASP 3.4 1.6 - - - -
241D PHE* 3.8 20.0 - - + +
242D VAL* 4.2 2.0 - - - -
305D CYS* 3.2 2.6 - - - -
306D GLN* 2.8 36.3 + - + +
308D LYS* 3.8 39.0 - - + +
319D ILE* 3.7 28.0 - - + -
320D LEU* 1.3 80.9 - - - +
322D ALA* 1.3 71.0 + - - +
323D SER 3.3 0.2 + - - -
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Residues in contact with ALA 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D PHE* 4.4 4.0 - - + -
237D SER 3.4 24.7 - - - +
238D ARG* 4.3 0.5 - - - +
239D GLY* 2.8 27.2 + - - -
240D ASP 2.9 14.0 + - - +
242D VAL* 3.6 10.6 - - + +
304D ASN 3.5 7.2 - - - -
321D ILE* 1.3 73.4 - - - +
323D SER* 1.3 57.6 + - - +
324D ARG 3.2 15.9 - - - +
326D ILE* 3.8 15.9 - - + -
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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