Contacts of the strand formed by residues 319 - 325 (chain B) in PDB entry 1ZKC
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 THR 319 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315B TYR 3.6 20.0 - - - +
316B TYR* 2.7 37.3 + - + +
317B ASP 4.0 4.0 - - - +
318B GLY* 1.3 80.3 - - - +
320B ILE* 1.3 63.4 + - - +
333B GLY 4.7 2.1 + - - -
334B ASP 4.3 12.8 - - - -
335B PRO* 3.7 28.0 - - + +
427B ARG* 3.2 1.6 - - - -
428B ILE* 2.8 38.5 + - - +
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Residues in contact with ILE 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B GLY 4.4 4.9 - - - +
319B THR* 1.3 78.9 + - - +
321B PHE* 1.3 65.7 + - - +
322B HIS* 3.7 22.6 + - + +
332B GLY* 3.5 16.3 - - - -
333B GLY 3.9 4.9 + - - -
334B ASP 4.8 4.8 + - - +
337B GLY* 4.1 18.6 - - - +
421B ARG* 3.6 26.7 - - - +
425B GLU* 3.4 42.2 - - + +
426B ILE 3.2 9.9 - - - +
427B ARG* 4.2 2.0 - - + -
428B ILE* 5.9 1.1 - - - +
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Residues in contact with PHE 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B LEU* 4.5 12.6 - - + -
286B THR* 4.3 16.6 - - + -
291B LEU* 5.0 6.3 - - + -
320B ILE* 1.3 74.9 - - - +
322B HIS* 1.3 58.7 + - - +
323B ARG 3.4 1.3 - - - -
330B ILE* 3.7 37.0 - - + -
331B GLN 3.2 26.9 - - - +
332B GLY* 3.7 3.8 - - - -
380B PHE* 4.1 21.3 - + - -
382B ILE* 5.0 8.1 - - + -
410B MET* 5.0 4.5 - - - -
422B PRO* 3.4 23.9 - - - +
426B ILE* 2.8 40.8 + - + +
427B ARG* 4.5 1.8 - - - -
428B ILE* 3.7 34.8 - - + -
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Residues in contact with HIS 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B ILE* 3.7 16.5 + - + +
321B PHE* 1.3 73.1 - - - +
323B ARG* 1.3 74.8 + - + +
331B GLN* 3.0 31.1 + - + -
332B GLY* 3.9 10.5 - - - -
334B ASP* 4.3 9.8 - - + +
337B GLY 3.9 9.0 - - - +
338B THR 4.8 0.4 - - - -
339B GLY* 3.4 27.7 + - - -
379B GLN* 3.2 33.7 + - - -
419B THR 4.8 0.7 - - - +
420B ASP 3.6 0.3 - - - +
421B ARG* 3.2 47.5 + - - +
422B PRO* 3.9 5.6 - - - -
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Residues in contact with ARG 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B PHE 3.4 1.2 - - - -
322B HIS* 1.3 101.1 + - + +
324B SER* 1.3 62.5 + - - +
325B ILE* 3.9 20.7 - - + +
328B PHE* 6.2 0.2 - - - -
329B VAL* 4.7 6.1 - - + -
330B ILE* 3.4 4.0 - - - +
331B GLN* 2.9 58.6 + - + +
419B THR 3.7 18.0 + - - -
420B ASP* 2.9 31.7 + - + -
422B PRO* 4.7 0.2 - - - -
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Residues in contact with SER 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B ARG* 1.3 76.0 - - - +
325B ILE* 1.3 65.8 + - - +
326B ARG 4.2 0.7 + - - -
329B VAL 3.6 4.3 - - - -
330B ILE* 3.8 24.6 - - - +
384B PHE* 4.1 10.4 - - - -
410B MET 4.5 7.1 + - - -
411B GLU 4.6 6.4 + - - -
413B VAL 4.9 2.1 + - - -
415B SER* 3.5 29.5 + - - -
420B ASP* 2.8 16.9 + - - +
422B PRO* 3.9 12.1 - - - -
426B ILE* 5.2 0.2 - - - -
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Residues in contact with ILE 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B ARG* 3.9 30.7 - - + +
324B SER* 1.3 79.2 + - - +
326B ARG* 1.3 70.4 + - - +
327B ASN 3.3 0.5 + - - -
328B PHE* 3.0 54.7 + - + -
329B VAL* 2.9 18.2 + - + +
384B PHE* 3.4 4.9 - - - -
420B ASP* 3.7 28.5 - - + +
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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