Contacts of the strand formed by residues 312 - 320 (chain B) 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 PHE 312 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B CYS* 3.4 38.6 - - + -
308B ASP 3.7 13.2 - - - -
309B LYS 4.6 5.8 + - - +
310B THR 3.6 4.6 - - - +
311B LYS* 1.3 77.8 - - - +
313B THR* 1.3 68.0 + - - +
330B VAL* 3.7 18.8 - - + -
331B THR 3.3 8.3 - - - -
332B PHE* 3.5 22.9 - + + -
340B ILE* 3.9 23.6 - - + -
341B PRO* 3.8 15.5 - - + -
364B ILE* 4.1 6.5 - - + -
385B VAL* 3.6 31.0 - - + +
388B LEU* 3.8 30.3 - - + +
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Residues in contact with THR 313 (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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311B LYS 5.1 3.0 + - - +
312B PHE* 1.3 80.1 - - - +
314B TRP* 1.3 64.2 + - - +
330B VAL* 3.3 7.3 - - - +
331B THR* 2.9 46.4 + - - +
388B LEU* 3.6 11.2 - - + -
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Residues in contact with TRP 314 (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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313B THR* 1.3 76.4 - - - +
315B LYS* 1.3 60.8 + - - +
316B ARG 4.0 9.0 - - - -
317B ALA* 4.4 16.6 - - + +
318B PRO* 4.0 21.5 - - + -
328B MET* 3.8 22.9 - - + -
329B GLU 3.9 1.1 - - - -
330B VAL* 3.6 27.4 - - + -
331B THR* 5.1 0.2 - - - -
383B ILE* 4.0 13.9 - - + -
385B VAL* 3.8 20.0 - - + -
388B LEU* 3.4 30.6 - - + +
389B SER* 3.2 23.9 + - - -
390B HIS* 3.5 32.8 - + + -
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Residues in contact with LYS 315 (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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313B THR 3.7 3.0 + - - -
314B TRP* 1.3 73.4 - - - +
316B ARG* 1.3 66.3 + - + +
317B ALA 4.2 0.4 - - - -
329B GLU* 2.7 45.7 + - + +
330B VAL 5.0 2.2 - - - -
331B THR* 3.3 32.9 + - - +
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Residues in contact with ARG 316 (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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150B TYR* 3.5 25.4 + - - +
314B TRP* 4.0 2.2 - - - -
315B LYS* 1.3 86.8 - - + +
317B ALA* 1.3 66.6 + - - +
328B MET* 3.5 3.5 - - - +
329B GLU* 3.0 53.6 + - - +
101C TRP* 3.6 72.2 + - + +
105C CYS 5.4 0.6 + - - -
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Residues in contact with ALA 317 (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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314B TRP* 4.4 12.8 - - + +
315B LYS 4.2 0.8 - - - -
316B ARG* 1.3 78.1 - - - +
318B PRO* 1.3 80.8 - - + +
319B THR* 3.3 10.0 + - - +
327B VAL 3.9 2.4 - - - +
390B HIS* 3.9 17.9 - - + +
101C TRP* 4.4 0.7 - - - -
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Residues in contact with PRO 318 (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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314B TRP* 4.0 24.0 - - + -
316B ARG 3.8 0.2 - - - -
317B ALA* 1.3 90.0 - - + +
319B THR* 1.3 60.6 + - - +
326B VAL* 3.8 18.2 - - + -
327B VAL 3.3 9.6 - - - +
328B MET* 3.9 4.9 - - + -
383B ILE* 3.9 23.1 - - + -
390B HIS* 3.6 31.9 - - + +
392B TRP* 3.5 21.6 - - + -
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Residues in contact with THR 319 (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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317B ALA 3.9 3.6 - - - -
318B PRO* 1.3 75.8 - - - +
320B ASP* 1.3 66.9 + - - +
321B SER 3.4 0.3 + - - -
326B VAL* 3.5 3.9 - - - +
327B VAL* 2.9 41.1 + - + -
392B TRP* 3.9 8.1 - - - -
101C TRP* 3.2 41.7 - - + +
106C GLY 4.0 5.2 + - - -
107C LEU* 3.6 28.1 - - - +
108C PHE* 4.0 7.0 - - + -
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Residues in contact with ASP 320 (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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319B THR* 1.3 76.6 + - - +
321B SER* 1.3 62.6 + - - +
322B GLY* 3.3 18.1 + - - +
324B ASP* 4.8 7.3 + - - +
325B THR 4.0 7.6 - - - +
392B TRP* 3.6 25.8 - - + -
394B GLN* 4.9 9.3 + - - -
395B LYS* 5.0 9.0 + - - +
107C LEU* 6.4 1.1 - - + -
108C PHE* 3.2 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