Contacts of the strand formed by residues 397 - 402 (chain C) in PDB entry 1K3B
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 ASP 397 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B GLU* 4.9 1.6 - - - +
363B ILE* 4.6 0.2 - - - +
389C GLY 3.5 3.6 - - - -
390C THR* 2.7 33.1 + - - +
395C GLY 3.6 4.1 + - - +
396C MET* 1.3 82.4 - - - +
398C TYR* 1.3 61.1 + - - +
418C ARG* 3.5 8.3 - - - +
419C ARG* 3.0 60.7 + - - +
420C GLY* 5.9 0.5 - - - -
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Residues in contact with TYR 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B SER* 5.3 1.2 + - - -
363B ILE* 3.4 39.5 - - + -
388C TYR* 3.3 0.7 - - - -
389C GLY* 2.9 50.1 + - - -
390C THR 3.5 16.1 + - - -
391C ASP* 3.6 13.2 - - - -
396C MET 3.8 5.8 - - - -
397C ASP* 1.3 75.9 - - - +
399C TRP* 1.3 64.7 + - - +
400C ILE* 3.8 15.3 - - + +
416C ARG* 3.6 38.9 + - + -
417C ILE 3.1 13.2 - - - +
419C ARG* 3.1 16.9 + - - -
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Residues in contact with TRP 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B GLU* 3.5 31.0 - - + -
336B MET* 3.7 34.7 - - + +
337B LYS* 4.1 15.3 - - + -
340B LEU* 4.7 0.9 - - + -
385C LEU* 3.4 37.9 - - + -
387C GLY 3.5 11.4 - - - -
388C TYR* 3.8 11.7 - + + -
398C TYR* 1.3 74.3 - - - +
400C ILE* 1.3 61.7 + - - +
401C VAL* 3.9 2.2 - - + -
415C PHE 3.7 0.3 - - - +
416C ARG* 3.0 27.5 - - - +
417C ILE* 2.8 22.0 + - + +
418C ARG 4.0 3.6 - - - -
419C ARG* 3.6 36.2 - - + +
426C ILE* 3.9 20.8 - - + +
427C GLU* 2.7 29.4 + - + +
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Residues in contact with ILE 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B TRP 4.0 13.9 - - - +
212B ASP* 3.7 26.7 - - + +
214B ARG* 3.5 26.5 - - - +
385C LEU* 3.8 1.2 - - - +
386C VAL* 2.9 41.6 + - + +
387C GLY 2.8 22.4 + - - +
388C TYR 4.1 4.5 - - - +
398C TYR* 3.8 25.1 - - + +
399C TRP* 1.3 74.6 - - - +
401C VAL* 1.3 61.3 + - - +
414C TYR* 4.3 7.4 - - + -
415C PHE 3.7 4.0 - - - +
416C ARG* 4.1 11.2 - - + -
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Residues in contact with VAL 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B VAL* 4.7 1.3 - - + -
383C VAL* 3.3 35.9 - - + -
384C LEU 3.3 13.7 - - - +
385C LEU* 4.2 7.2 - - + +
399C TRP* 4.1 9.0 - - + -
400C ILE* 1.3 79.3 - - - +
402C LYS* 1.3 63.6 + - - +
414C TYR* 3.1 10.8 - - - +
415C PHE* 2.7 73.3 + - + +
417C ILE* 4.1 15.7 - - + -
426C ILE* 4.2 7.2 - - + -
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Residues in contact with LYS 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B VAL* 4.1 5.3 - - + +
223B SER* 2.9 42.2 + - - -
224B PRO 3.1 21.5 + - - -
225B VAL* 3.8 13.0 - - + +
226B ARG 5.1 1.1 - - - +
241B GLY* 4.6 12.8 - - - -
244B GLU* 4.8 0.6 + - - -
383C VAL* 3.5 5.5 - - - +
384C LEU* 2.8 55.0 + - + +
386C VAL* 4.3 3.6 - - + +
400C ILE 4.4 0.2 + - - -
401C VAL* 1.3 72.6 - - - +
403C ASN* 1.3 69.6 + - - +
414C TYR* 3.3 35.8 - - + +
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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