Contacts of the strand formed by residues 381 - 390 (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 HIS 381 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228B GLN* 3.6 10.7 + - - -
234B CYS* 3.4 27.1 - - + +
349B ALA* 3.2 5.5 - - - +
350B PHE* 3.1 37.8 + - + +
352B VAL* 3.5 32.4 - - + +
379C THR* 4.8 0.4 - - - -
380C ASN* 1.3 83.3 + - - +
382C ALA* 1.3 61.4 + - - +
383C VAL* 3.4 17.7 - - + +
403C ASN* 2.7 31.4 + - - -
404C SER* 4.1 0.2 + - - -
405C TRP* 3.3 32.8 + + - -
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Residues in contact with ALA 382 (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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234B CYS* 3.5 28.7 - - - +
235B TYR* 3.7 31.2 - - + +
238B ALA* 3.9 9.4 - - + +
277B GLY 5.7 0.4 - - - +
279B PRO* 4.1 14.1 - - + -
348B VAL 3.4 9.0 - - - +
349B ALA* 4.2 5.8 - - + +
381C HIS* 1.3 73.6 + - - +
383C VAL* 1.3 66.9 + - - +
404C SER* 4.5 3.1 + - - -
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Residues in contact with VAL 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ALA* 3.6 12.1 - - - +
347B ALA* 3.4 5.9 - - - -
348B VAL* 2.8 47.4 + - + +
350B PHE* 3.8 23.6 - - + -
381C HIS* 3.4 28.9 - - + +
382C ALA* 1.3 80.0 - - - +
384C LEU* 1.3 60.4 + - - +
401C VAL* 3.3 21.8 - - + -
402C LYS 3.5 13.7 - - - +
403C ASN* 3.6 13.9 - - - +
404C SER 4.9 0.9 - - - +
415C PHE* 4.2 2.5 - - + -
426C ILE* 5.0 0.2 - - + -
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Residues in contact with LEU 384 (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* 4.6 6.3 - - + -
238B ALA* 4.2 9.2 - - - +
241B GLY* 3.9 18.2 - - - +
242B MET* 3.7 24.5 - - + +
245B ALA* 5.0 0.4 - - + -
345B PRO* 3.6 23.8 - - + -
346B MET 3.3 26.7 - - - +
347B ALA* 4.1 0.4 - - - +
383C VAL* 1.3 75.8 - - - +
385C LEU* 1.3 63.0 + - - +
386C VAL* 3.5 26.1 + - + +
401C VAL* 3.3 3.7 - - - +
402C LYS* 2.8 58.3 + - + +
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Residues in contact with LEU 385 (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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336B MET* 3.8 22.0 - - + -
340B LEU* 3.6 11.8 - - + +
345B PRO* 3.1 28.4 - - - +
346B MET* 2.9 39.3 + - + +
348B VAL* 4.0 14.2 - - + +
383C VAL 4.2 1.0 + - - -
384C LEU* 1.3 71.4 - - - +
386C VAL* 1.3 58.6 + - - +
387C GLY 3.8 2.5 - - - +
399C TRP* 3.4 60.1 - - + -
400C ILE 3.8 10.8 - - - +
401C VAL* 4.2 9.1 - - + +
426C ILE* 5.8 1.6 - - + -
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Residues in contact with VAL 386 (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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212B ASP* 4.5 7.0 - - - +
213B TRP* 2.9 35.4 + - + +
214B ARG* 4.6 1.6 - - - +
222B VAL* 4.1 28.5 - - + -
340B LEU* 4.0 9.0 - - - -
345B PRO* 4.1 4.9 - - + -
384C LEU* 3.6 31.6 - - + +
385C LEU* 1.3 79.3 - - - +
387C GLY* 1.3 58.7 + - - +
400C ILE* 2.9 32.1 + - + +
402C LYS* 4.3 4.5 - - + -
414C TYR* 3.7 23.8 - - + -
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Residues in contact with GLY 387 (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 3.0 14.6 - - - -
212B ASP* 4.1 1.1 - - - -
340B LEU* 3.5 16.2 - - - +
385C LEU* 3.8 1.1 - - - +
386C VAL* 1.3 80.9 - - - +
388C TYR* 1.3 64.1 + - - +
399C TRP* 3.5 10.7 - - - -
400C ILE* 2.8 33.6 + - - +
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Residues in contact with TYR 388 (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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207B LEU* 4.0 4.2 - - - +
208B PRO* 2.7 42.7 + - - +
209B THR 3.5 24.9 - - - -
210B SER* 3.5 5.6 + - - -
211B TRP* 2.7 51.3 + - + +
337B LYS* 3.6 39.0 - - + -
340B LEU* 4.0 12.8 - - + -
341B VAL* 3.7 14.0 - - + +
387C GLY* 1.3 73.3 - - - +
389C GLY* 1.3 60.2 + - - +
398C TYR* 3.3 18.6 - - - +
399C TRP* 3.8 9.9 - + + +
400C ILE* 4.1 6.3 - - - +
419C ARG* 3.6 22.9 - - - +
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Residues in contact with GLY 389 (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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209B THR 4.3 5.2 - - - -
210B SER* 3.9 12.8 - - - -
388C TYR* 1.3 76.2 - - - +
390C THR* 1.3 63.0 + - - -
397C ASP* 3.5 0.2 - - - -
398C TYR* 2.9 41.2 + - - -
419C ARG* 2.8 19.7 + - - -
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Residues in contact with THR 390 (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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209B THR* 4.3 8.7 + - - -
210B SER* 5.0 0.6 + - - -
389C GLY* 1.3 73.0 - - - -
391C ASP* 1.3 69.5 + - - +
392C SER* 3.1 7.1 + - - -
395C GLY* 3.7 24.5 - - - +
396C MET 3.6 4.3 - - - +
397C ASP* 2.7 24.7 + - - +
398C TYR* 3.5 9.0 + - - -
419C ARG* 3.8 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