Contacts of the strand formed by residues 326 - 332 (chain C) in PDB entry 1K4R
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 326 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318C PRO* 3.8 27.8 - - + -
319C THR 3.5 12.3 - - - +
325C THR* 1.3 79.7 - - - +
327C VAL* 1.3 62.7 + - - +
328C MET* 3.9 14.6 - - + +
372C ILE 3.8 0.9 - - - +
373C GLU* 3.2 4.9 - - - +
374C MET* 2.7 41.7 + - + +
376C LEU* 4.0 16.2 - - + +
383C ILE* 4.4 3.6 - - + -
392C TRP* 3.5 36.3 - - + +
394C GLN* 3.6 10.5 - - - +
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Residues in contact with VAL 327 (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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101B TRP* 3.7 13.5 - - + -
108B PHE* 3.9 16.8 - - + -
4C THR* 4.8 6.5 - - + -
150C TYR* 6.3 0.4 - - + -
318C PRO* 3.3 1.4 - - - +
319C THR* 2.9 58.8 + - + +
321C SER* 4.0 17.5 - - - -
325C THR 4.2 0.2 - - - -
326C VAL* 1.3 78.4 - - - +
328C MET* 1.3 62.5 + - - +
371C PHE* 3.8 23.8 - - + -
372C ILE 3.4 3.4 - - - -
373C GLU* 3.8 22.9 - - + -
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Residues in contact with MET 328 (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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101B TRP* 3.7 8.7 - - - -
314C TRP* 3.8 31.6 - - + -
316C ARG 3.5 13.9 - - - +
318C PRO* 3.9 8.1 - - + -
326C VAL* 3.9 30.5 - - + +
327C VAL* 1.3 76.9 - - - +
329C GLU* 1.3 64.2 + - - +
330C VAL* 5.2 0.4 - - + -
371C PHE* 3.4 8.1 - - - -
372C ILE* 3.0 51.1 + - + +
374C MET* 3.9 43.7 - - + -
383C ILE* 4.2 11.7 - - + -
385C VAL* 5.1 1.1 - - - -
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Residues in contact with GLU 329 (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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101B TRP* 5.0 0.7 - - + -
150C TYR* 4.9 5.7 - - - +
314C TRP* 3.7 2.8 - - - -
315C LYS* 2.7 56.5 + - + +
316C ARG* 3.0 55.7 + - + +
328C MET* 1.3 77.7 - - - +
330C VAL* 1.3 63.3 + - - +
369C GLY 5.1 4.5 - - - +
370C GLY* 3.2 18.8 - - - +
371C PHE* 4.1 12.1 - - + +
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Residues in contact with VAL 330 (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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312C PHE* 3.7 30.1 - - + -
313C THR 3.3 11.2 - - - +
314C TRP* 3.6 33.9 - - + -
315C LYS* 4.5 2.3 - - - +
328C MET* 5.2 2.5 - - + -
329C GLU* 1.3 81.4 - - - +
331C THR* 1.3 64.5 + - - +
340C ILE* 4.3 8.5 - - + -
364C ILE* 4.6 3.3 - - + +
369C GLY 4.8 1.4 - - - +
370C GLY* 2.9 36.9 + - - +
372C ILE* 4.9 4.7 - - + -
385C VAL* 4.1 20.6 - - + -
388C LEU* 4.1 4.5 - - + -
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Residues in contact with THR 331 (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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311C LYS 3.6 1.0 - - - +
312C PHE* 3.3 8.2 - - - -
313C THR* 2.9 45.0 + - - +
315C LYS* 3.3 43.7 + - - +
330C VAL* 1.3 73.6 - - - +
332C PHE* 1.3 69.5 + - - +
333C SER* 5.2 1.6 - - - +
364C ILE* 5.7 0.2 - - - -
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Residues in contact with PHE 332 (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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307C CYS* 3.5 13.2 - - + -
308C ASP* 3.3 43.7 - - + -
311C LYS* 3.4 17.3 - - + -
312C PHE* 3.5 31.2 - + + -
330C VAL 4.5 0.2 + - - -
331C THR* 1.3 83.8 - - - +
333C SER* 1.3 58.5 + - - +
334C GLY* 3.3 42.6 - - - -
335C THR 3.6 7.4 - - - -
336C LYS* 3.7 22.7 + - + -
338C CYS* 3.5 20.0 - - - -
364C ILE* 3.9 28.3 - - + +
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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