Contacts of the strand formed by residues 396 - 402 (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 ILE 396 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296B HIS* 4.4 8.5 - - + +
300B THR* 3.4 21.3 - - - +
353B GLU 4.7 1.5 + - - +
354B PHE* 5.5 0.8 - - - +
358B LEU* 3.5 28.7 - - + +
359B SER* 3.2 48.5 - - - +
360B HIS* 3.4 23.1 - - + +
365B ILE* 3.7 19.1 - - + -
366B LEU 3.9 1.8 - - - +
367B SER* 3.3 18.2 - - - +
391B ASP* 4.3 1.8 - - - +
394B HIS 3.2 2.3 + - - +
395B THR* 1.3 71.5 - - - +
397B PHE* 1.3 61.5 + - - +
398B GLY 4.0 9.9 - - - +
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Residues in contact with PHE 397 (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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295B LEU* 3.3 10.5 - - + -
296B HIS* 2.9 26.8 + - - -
300B THR* 3.5 19.3 - - - +
303B THR* 3.5 31.6 - - + -
304B CYS* 3.5 11.1 - - - -
307B PHE* 3.6 41.7 - + + -
366B LEU* 2.9 45.5 + - + -
367B SER 3.6 17.5 - - - -
368B MET* 3.5 23.8 - - - -
380B PHE* 4.2 3.4 - - + -
395B THR* 3.8 8.5 - - + -
396B ILE* 1.3 74.4 - - - +
398B GLY* 1.3 58.2 + - - +
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Residues in contact with GLY 398 (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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294B GLU 3.0 14.1 - - - -
295B LEU* 4.0 1.3 - - - -
296B HIS* 3.6 19.4 + - - -
365B ILE* 3.9 3.1 - - - +
366B LEU* 3.0 32.8 + - - +
396B ILE* 4.0 6.1 - - - +
397B PHE* 1.3 80.3 - - - +
399B ARG* 1.3 65.2 + - - +
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Residues in contact with ARG 399 (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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293B LEU* 3.5 6.4 - - - -
294B GLU* 2.8 62.1 + - + -
296B HIS* 4.4 15.4 - - + +
364B GLY 3.2 14.4 - - - +
365B ILE* 4.5 12.3 - - + -
366B LEU* 3.9 4.3 - - - +
398B GLY* 1.3 77.6 - - - +
400B VAL* 1.3 69.0 + - - +
401B VAL* 3.5 22.1 - - + +
404B PHE* 5.7 2.2 - - - -
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Residues in contact with VAL 400 (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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291B LEU* 4.4 13.7 - - + -
292B ASN 3.5 5.8 - - - +
293B LEU* 3.9 17.0 - - + -
364B GLY* 2.7 28.9 + - - +
366B LEU* 5.9 0.4 - - + -
382B ILE* 3.7 28.0 - - + -
399B ARG* 1.3 79.5 + - - +
401B VAL* 1.3 62.1 + - - +
402B GLY 3.3 28.3 - - - +
403B GLY 4.7 1.8 - - - -
404B PHE* 3.4 32.9 - - + -
407B LEU* 4.6 6.3 - - + -
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Residues in contact with VAL 401 (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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435A VAL* 3.9 45.2 - - + +
436A ASP 4.4 9.4 + - - +
437A PRO* 5.9 0.3 - - - +
281B TYR* 4.5 1.1 - - + -
292B ASN* 2.8 23.2 + - + +
293B LEU 4.2 1.1 - - - -
294B GLU* 3.6 33.4 - - + +
399B ARG* 3.4 37.4 + - - +
400B VAL* 1.3 75.7 - - - +
402B GLY* 1.3 57.9 + - - +
404B PHE* 3.7 17.0 - - - -
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Residues in contact with GLY 402 (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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435A VAL* 6.0 0.2 - - - -
436A ASP 5.7 0.7 - - - -
439A GLU* 3.3 17.5 - - - -
291B LEU* 3.6 1.4 - - - -
292B ASN* 2.9 39.3 + - - -
400B VAL* 3.3 14.6 - - - +
401B VAL* 1.3 81.3 - - - +
403B GLY* 1.3 62.4 + - - -
404B PHE* 3.4 3.8 - - - -
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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