Contacts of the strand formed by residues 399 - 405 (chain B) in PDB entry 3IXK
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 ARG 399 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238B TYR* 3.6 48.2 + - + -
239B THR 3.3 11.9 - - - +
240B PRO* 4.3 0.9 - - + -
241B ILE* 3.5 5.9 - - - +
338B GLU* 3.0 40.1 + - - +
394B ASP* 2.8 63.9 + - + +
397B ARG* 3.5 52.8 - - - +
398B LYS* 1.3 80.3 - - - +
400B ILE* 1.3 65.6 + - - +
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Residues in contact with ILE 400 (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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237B TRP 3.8 0.5 - - - +
238B TYR* 3.3 3.5 - - - -
239B THR* 2.7 49.0 + - + +
241B ILE* 3.7 24.0 - - + +
247B TYR* 3.8 26.2 - - + +
249B VAL* 3.9 19.7 - - + -
275B VAL* 4.3 9.2 - - + -
391B VAL* 3.8 17.3 - - + -
392B VAL 3.2 11.0 - - - +
393B PHE* 4.3 13.0 - - + -
399B ARG* 1.3 78.4 - - - +
401B GLY* 1.3 62.7 + - - +
402B PHE* 3.8 24.4 - - + -
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Residues in contact with GLY 401 (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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236B LEU* 4.2 6.7 - - - -
237B TRP 3.1 9.0 - - - -
238B TYR* 3.3 24.6 - - - -
391B VAL* 3.3 11.3 - - - +
392B VAL* 2.8 36.4 + - - -
400B ILE* 1.3 75.9 - - - +
402B PHE* 1.3 61.6 - - - -
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Residues in contact with PHE 402 (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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235B SER 3.5 1.7 - - - +
236B LEU* 3.4 3.8 - - - +
237B TRP 2.8 30.8 + - - -
239B THR* 4.2 5.6 - - + -
249B VAL* 5.6 0.2 - - + -
275B VAL* 4.4 11.7 - - + -
335B LEU* 3.6 15.5 - - + -
344B PHE* 3.9 29.2 - + + -
346B ILE* 4.1 24.9 - - + -
381B MET* 3.6 29.6 - - + -
385B ILE* 4.8 6.7 - - + -
386B MET* 5.6 0.9 - - + -
389B PHE* 4.1 13.2 - + + -
390B TYR 3.6 2.7 - - - -
391B VAL* 3.7 26.7 - - + -
400B ILE* 3.8 24.5 - - + -
401B GLY* 1.3 75.9 - - - -
403B ALA* 1.3 61.4 + - - +
418B VAL* 3.8 9.4 - - + +
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Residues in contact with ALA 403 (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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232B TYR* 3.6 34.1 - - + -
233B THR 4.2 1.3 - - - +
235B SER 3.5 17.7 - - - +
236B LEU* 3.6 11.2 - - + -
389B PHE* 3.3 6.1 - - - +
390B TYR 2.8 31.9 + - - +
402B PHE* 1.3 76.3 - - - +
404B VAL* 1.3 60.8 + - - +
418B VAL* 3.7 10.1 - - - -
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Residues in contact with VAL 404 (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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232B TYR* 3.0 26.7 - - - +
233B THR* 3.2 35.7 + - - +
234B GLY* 5.4 2.2 - - - -
235B SER 6.0 0.7 - - - +
388B GLY 4.1 6.1 - - - +
389B PHE* 4.3 4.5 - - + -
403B ALA* 1.3 71.1 - - - +
405B SER* 1.3 72.2 + - - +
408B HIS* 4.1 18.2 - - + -
415B THR* 6.1 2.2 - - + -
416B ALA* 4.6 16.2 - - + +
417B ALA* 4.7 7.0 - - - -
418B VAL* 3.8 20.0 - - + +
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Residues in contact with SER 405 (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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201B GLN* 3.0 34.5 + - - +
231B LEU 3.6 5.2 - - - -
232B TYR* 4.5 0.2 - - - -
233B THR* 5.0 1.2 + - - -
387B GLU 4.2 4.7 - - - -
388B GLY 3.0 26.0 + - - -
389B PHE 3.6 15.7 - - - -
390B TYR 3.8 3.6 - - - +
403B ALA 3.4 1.6 + - - -
404B VAL* 1.3 77.5 - - - +
406B ALA* 1.3 57.8 + - - +
407B CYS* 3.3 10.2 + - - -
408B HIS* 3.0 30.6 + - - -
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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