Contacts of the strand formed by residues 346 - 356 (chain C) in PDB entry 1XKH
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 LEU 346 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338C PHE* 3.2 45.0 + - + +
340C LEU* 5.4 6.3 - - + +
343C ASP 5.3 0.4 + - - -
345C MSE 1.3 70.7 - - - +
347C THR* 1.3 61.7 + - - +
348C VAL* 3.8 16.3 + - + +
400C ALA* 5.3 2.0 - - + -
401C ASN* 3.5 12.1 - - - +
402C LEU* 3.5 33.7 - - + -
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Residues in contact with THR 347 (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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136C GLN* 6.3 0.4 - - - +
272C LYS* 4.3 11.8 + - - +
335C ILE* 4.1 14.7 - - - +
336C LEU 2.7 21.7 + - - -
337C GLU* 3.7 23.7 + - - +
345C MSE 3.2 9.6 - - + +
346C LEU* 1.3 71.4 - - - +
348C VAL* 1.3 63.9 + - - +
399C PHE* 5.3 0.7 - - - -
401C ASN* 2.8 77.3 + - - +
403C GLU* 5.3 7.4 - - + +
413C LYS* 5.5 0.4 - - - +
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Residues in contact with VAL 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C ILE* 3.6 0.7 - - - +
336C LEU* 2.8 40.6 + - + +
338C PHE* 4.5 19.5 - - + -
346C LEU* 3.9 17.0 - - + +
347C THR* 1.3 86.6 + - - +
349C GLY* 1.3 57.7 + - - +
399C PHE* 3.5 18.4 - - - +
400C ALA* 3.5 22.7 - - + -
401C ASN 4.1 1.3 - - - +
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Residues in contact with GLY 349 (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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334C GLY 3.0 15.9 - - - -
336C LEU* 5.6 1.6 - - - -
348C VAL* 1.3 79.8 - - - +
350C ALA* 1.3 61.7 + - - +
398C VAL* 3.7 3.6 - - - +
399C PHE* 3.0 44.3 + - - +
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Residues in contact with ALA 350 (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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332C TYR 4.9 0.2 - - - -
333C TYR* 3.5 6.3 - - - -
334C GLY* 3.0 27.1 + - - +
349C GLY* 1.3 75.5 - - - +
351C ASP* 1.3 59.4 + - - +
397C THR 3.1 16.6 - - - +
398C VAL* 3.3 22.7 - - + -
399C PHE* 4.4 2.0 - - - -
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Residues in contact with ASP 351 (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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242C ILE* 4.4 9.6 - - + -
243C TYR* 5.6 0.7 - - - -
270C ARG* 2.5 33.1 + - - +
331C VAL* 5.5 0.8 - - + +
332C TYR 3.4 6.5 - - - +
333C TYR* 3.6 24.9 - - + +
350C ALA* 1.3 74.8 - - - +
352C TYR* 1.3 70.8 + - - +
353C GLN* 4.8 0.9 + - - +
395C THR* 4.4 6.2 + - - +
396C ARG* 3.4 1.0 - - - +
397C THR* 2.7 58.9 + - - +
399C PHE* 4.7 1.8 - - - -
419C LYS* 5.1 0.3 + - - -
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Residues in contact with TYR 352 (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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330C SER* 3.7 2.0 - - - +
331C VAL* 3.3 4.4 - - - +
332C TYR* 2.9 59.7 + + + +
351C ASP* 1.3 81.3 + - - +
353C GLN* 1.3 59.5 + - - +
354C ASP* 2.5 40.2 + - + +
394C TYR* 5.2 0.9 - + + -
395C THR 3.3 8.7 - - - -
396C ARG* 2.5 55.4 - - + +
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Residues in contact with GLN 353 (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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237C LEU 3.3 8.7 - - - +
238C SER* 3.1 16.6 - - - +
239C ASP* 2.8 54.9 + - + +
242C ILE* 5.2 4.6 - - - +
243C TYR* 5.3 0.8 + - - -
329C THR* 5.3 2.4 - - - -
330C SER 3.3 6.3 - - - +
331C VAL* 3.5 25.7 - - + +
351C ASP* 4.8 1.5 + - - +
352C TYR* 1.3 75.3 - - - +
354C ASP* 1.3 66.6 + - - +
355C ASN* 3.9 16.2 + - - +
394C TYR* 3.6 1.6 - - - -
395C THR* 2.7 45.9 + - - +
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Residues in contact with ASP 354 (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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328C LYS 3.8 1.6 - - - +
329C THR* 3.1 22.9 - - - -
330C SER* 2.9 21.1 + - - +
352C TYR* 2.5 46.4 + - + +
353C GLN* 1.3 73.2 - - - +
355C ASN* 1.3 63.3 + - - +
356C ASP* 3.8 3.2 + - - +
392C GLU* 3.0 25.1 - - - +
393C GLN 4.3 1.1 - - - -
394C TYR* 3.4 15.2 - - - +
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Residues in contact with ASN 355 (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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234C GLY* 4.6 5.3 - - - -
237C LEU* 3.6 43.6 + - + +
327C ARG* 4.7 2.7 - - - -
328C LYS 4.1 3.1 - - - -
329C THR* 3.5 24.1 - - + +
353C GLN* 3.9 18.5 + - - +
354C ASP* 1.3 75.6 - - - +
356C ASP* 1.3 59.4 + - - +
357C PRO* 3.0 16.9 - - + +
392C GLU* 3.2 6.5 - - - +
393C GLN* 2.9 49.6 + - + +
394C TYR* 4.7 1.8 - - - +
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Residues in contact with ASP 356 (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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326C GLU 4.6 0.9 - - - +
327C ARG* 4.2 0.9 - - - +
328C LYS* 3.1 52.7 + - + +
354C ASP* 3.8 3.3 + - - +
355C ASN* 1.3 72.8 - - - +
357C PRO* 1.3 65.2 - - - +
358C LYS* 4.4 19.2 - - - +
390C SER* 5.6 0.3 + - - -
392C GLU* 3.8 29.9 - - - +
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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