Contacts of the strand formed by residues 305 - 312 (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 CYS 305 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242D VAL* 4.0 31.4 - - - -
303D GLY 3.7 2.1 - - - -
304D ASN* 1.3 97.7 + - - +
306D GLN* 1.3 62.2 + - - +
320D LEU* 4.2 19.5 - - + -
321D ILE 3.2 6.7 - - - +
323D SER* 4.1 4.9 + - - +
326D ILE* 4.2 0.9 - - - -
332D LEU* 4.1 20.2 - - - -
333D LEU 3.0 9.4 + - - +
334D TYR* 3.3 26.8 - - + +
335D ASP 4.5 1.6 + - - -
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Residues in contact with GLN 306 (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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305D CYS* 1.3 75.7 - - - +
307D THR* 1.3 76.2 + - - +
308D LYS* 3.7 25.8 + - - +
319D ILE 3.6 0.7 - - - +
320D LEU* 3.5 2.0 - - - -
321D ILE* 2.8 37.5 + - + +
323D SER* 4.5 12.8 - - - -
334D TYR* 4.8 0.7 - - - -
23H ARG 4.8 10.9 + - - -
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Residues in contact with THR 307 (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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273D TYR* 2.8 38.7 + - + +
306D GLN* 1.3 90.4 + - - +
308D LYS* 1.3 65.0 + - - +
318D LEU* 4.1 22.9 - - + -
319D ILE 3.3 10.8 - - - +
320D LEU* 3.7 14.1 - - + +
334D TYR* 3.5 17.0 - - - +
335D ASP 5.9 0.2 - - - -
22H LEU* 3.4 25.7 - - + +
23H ARG 5.5 0.2 - - - +
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Residues in contact with LYS 308 (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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306D GLN* 3.7 26.7 - - + +
307D THR* 1.3 84.5 - - - +
309D LEU* 1.3 66.9 + - - +
310D HIS* 5.7 0.2 - - + -
317D HIS 3.6 0.2 - - - +
318D LEU* 3.6 5.2 - - - -
319D ILE* 2.7 44.0 + - + +
321D ILE* 3.8 35.5 - - + +
22H LEU* 4.6 1.8 - - - -
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Residues in contact with LEU 309 (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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275D PHE* 3.7 29.8 - - + -
276D GLN 3.5 23.8 - - - +
277D TYR* 3.9 18.2 - - + -
308D LYS* 1.3 76.3 - - - +
310D HIS* 1.3 65.1 + - - +
311D ASP* 5.4 1.1 - - + +
316D PRO* 3.8 17.9 - - + -
317D HIS 3.6 6.3 - - - +
318D LEU* 4.4 2.9 - - + -
22H LEU* 3.9 21.4 - - + +
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Residues in contact with HIS 310 (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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203D ARG* 3.5 32.8 + - + -
206D ILE* 3.6 20.7 - - + +
207D ASP* 2.5 29.6 + - - -
210D ILE* 3.7 19.5 - - + -
308D LYS* 5.7 0.2 - - + -
309D LEU* 1.3 76.6 + - - +
311D ASP* 1.3 59.5 + - - +
312D ILE* 3.8 9.2 - - + -
316D PRO* 3.6 1.3 - - - -
317D HIS* 2.7 48.0 + - + +
319D ILE* 3.7 28.1 - - + +
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Residues in contact with ASP 311 (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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203D ARG* 2.8 37.0 + - - +
277D TYR* 2.6 39.8 + - + +
278D LEU* 5.8 0.3 - - - +
309D LEU* 5.4 1.3 - - + +
310D HIS* 1.3 74.6 + - - +
312D ILE* 1.3 56.3 + - - +
313D ASP 3.5 1.4 + - - -
314D GLY* 2.8 29.7 + - - -
315D VAL 3.5 5.4 - - - -
316D PRO* 4.5 1.1 - - - -
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Residues in contact with ILE 312 (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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203D ARG* 4.1 3.1 - - - +
207D ASP* 3.5 47.3 - - + +
210D ILE* 3.9 27.6 - - + -
211D GLU* 5.7 6.5 - - + -
310D HIS* 3.8 6.5 + - + -
311D ASP* 1.3 74.0 - - - +
313D ASP* 1.3 78.7 + - + +
314D GLY 3.1 0.7 - - - -
315D VAL* 2.9 28.8 + - - +
317D HIS* 3.9 20.2 - - + +
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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