Contacts of the strand formed by residues 353 - 359 (chain D) in PDB entry 3P9K
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 ALA 353 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180D HIS* 5.5 4.0 - - + -
184D ILE* 4.1 30.1 - - + -
293D VAL* 4.3 10.3 - - + -
294D GLN 3.7 6.3 - - - -
295D CYS* 5.3 2.5 - - - -
348D TYR* 3.7 5.0 - - - -
349D ILE* 3.0 25.0 + - + -
350D TYR 2.8 20.1 + - - +
351D ALA 3.1 3.2 + - - +
352D ASN* 1.3 79.4 - - - +
354D TRP* 1.3 59.7 + - - +
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Residues in contact with TRP 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D LEU 3.3 0.9 - - - +
293D VAL* 3.2 8.7 - - - +
294D GLN 2.8 34.5 + - - +
296D ILE* 3.5 47.0 + - + +
329D GLU* 5.6 2.0 - - - -
346D SER* 3.9 25.6 - - - -
347D THR 3.4 8.5 - - - -
348D TYR* 3.3 54.2 - + + -
349D ILE* 4.1 4.3 - - - -
352D ASN* 3.5 17.5 + - - +
353D ALA* 1.3 75.7 - - - +
355D ALA* 1.3 60.4 + - - +
356D ILE* 3.8 5.9 + - + +
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Residues in contact with ALA 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D LEU* 4.0 15.0 - - + -
192D TYR* 4.1 21.9 - - + -
291D VAL* 4.6 5.6 - - + -
292D LEU 3.3 6.7 - - - +
293D VAL* 4.7 1.6 - - + +
345D LYS 3.7 1.6 - - - +
346D SER* 3.3 2.1 - - - -
347D THR* 2.7 46.4 + - - +
349D ILE* 3.7 19.0 - - + +
354D TRP* 1.3 72.1 - - - +
356D ILE* 1.3 59.3 + - - +
357D GLU* 5.4 0.4 - - - +
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Residues in contact with ILE 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D VAL 3.6 1.4 - - - +
291D VAL* 3.4 4.7 - - - -
292D LEU* 2.7 52.5 + - + +
294D GLN* 4.4 11.2 - - + -
296D ILE* 4.0 20.2 - - + -
329D GLU* 6.5 0.2 - - + -
332D PHE* 3.9 44.0 - - + -
344D VAL* 4.0 11.0 - - + -
345D LYS 3.5 1.6 - - - +
346D SER* 3.4 21.5 - - - +
354D TRP* 4.3 6.5 - - + +
355D ALA* 1.3 76.0 - - - +
357D GLU* 1.3 62.8 + - - +
358D PHE* 3.6 24.4 + - + -
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Residues in contact with GLU 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D TYR* 2.6 41.5 + - + +
194D GLY* 4.6 1.8 - - - -
289D LYS* 3.4 31.8 - - + +
290D VAL 3.5 5.4 - - - +
291D VAL* 4.5 0.9 - - + +
343D GLY 3.5 0.9 - - - +
344D VAL* 3.1 8.0 - - - +
345D LYS* 2.7 58.8 + - + +
355D ALA 4.1 0.9 + - - +
356D ILE* 1.3 73.1 - - - +
358D PHE* 1.3 63.5 + - - +
359D THR* 3.7 17.6 + - + +
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Residues in contact with PHE 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265D LEU* 5.0 0.2 - - + -
277D LEU* 4.0 31.9 - - + -
289D LYS* 3.4 4.3 - - - +
290D VAL* 2.9 43.7 + - + +
292D LEU* 3.5 25.6 - - + -
332D PHE* 3.4 29.6 - + - -
335D LEU* 5.3 0.2 - - + -
336D ALA* 3.7 29.6 - - + -
341D PHE* 3.6 23.4 - + + -
343D GLY 3.2 4.5 - - - +
344D VAL* 4.0 9.9 - - + -
356D ILE* 3.6 26.7 - - + -
357D GLU* 1.3 78.6 - - - +
359D THR* 1.3 63.2 + - - +
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Residues in contact with THR 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288D GLY 4.6 0.7 - - - -
289D LYS* 4.2 13.0 - - + -
341D PHE* 3.6 4.4 - - - +
342D THR* 3.1 7.6 + - - -
343D GLY* 2.7 51.7 + - - +
345D LYS* 6.4 1.3 - - + -
357D GLU* 3.7 31.0 - - + +
358D PHE* 1.3 77.4 - - - +
360D LYS* 1.3 64.6 + - - +
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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