Contacts of the strand formed by residues 353 - 359 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A HIS* 5.5 4.3 - - + -
184A ILE* 4.0 29.8 - - + -
293A VAL* 4.4 10.8 - - + -
294A GLN 3.9 5.2 - - - -
295A CYS* 5.4 1.1 - - - -
348A TYR* 3.8 3.5 - - - -
349A ILE* 2.8 36.2 + - + +
350A TYR 2.7 25.6 + - - +
351A ALA 3.1 3.3 + - - +
352A ASN* 1.3 72.5 - - - +
354A TRP* 1.3 55.3 + - - +
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Residues in contact with TRP 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A LEU 3.2 1.2 - - - +
293A VAL* 3.1 8.7 - - - -
294A GLN 2.8 39.9 + - - +
296A ILE* 3.8 44.6 + - + +
346A SER* 4.0 20.9 - - - -
347A THR 3.5 12.6 - - - -
348A TYR* 3.2 58.8 - + + -
349A ILE* 4.2 2.7 - - - -
352A ASN* 3.6 16.3 + - - +
353A ALA* 1.3 75.0 - - - +
355A ALA* 1.3 59.6 + - - +
356A ILE* 3.7 6.6 + - + +
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Residues in contact with ALA 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A LEU* 4.1 13.2 - - + -
192A TYR* 4.2 20.9 - - + -
291A VAL* 4.7 6.3 - - + -
292A LEU 3.1 7.4 - - - +
293A VAL* 4.6 1.8 - - + +
345A LYS 3.6 2.6 - - - +
346A SER* 3.4 1.2 - - - -
347A THR* 2.8 45.3 + - - +
349A ILE* 3.7 20.7 - - + +
354A TRP* 1.3 71.4 - - - +
356A ILE* 1.3 60.7 + - - +
357A GLU* 4.0 1.6 + - - +
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Residues in contact with ILE 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A VAL 3.6 1.2 - - - +
291A VAL* 3.3 3.3 - - - +
292A LEU* 2.7 54.1 + - + +
294A GLN* 4.8 5.8 - - + -
296A ILE* 3.7 21.1 - - + -
329A GLU* 6.4 0.2 - - + -
332A PHE* 3.6 43.7 - - + -
344A VAL* 3.8 10.5 - - + -
345A LYS 3.5 2.0 - - - -
346A SER* 3.6 20.6 - - - +
354A TRP* 4.3 9.4 - - + +
355A ALA* 1.3 75.9 - - - +
357A GLU* 1.3 62.9 + - - +
358A PHE* 3.7 25.4 - - + -
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Residues in contact with GLU 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A TYR* 2.4 46.1 + - + +
194A GLY* 4.0 2.6 - - - -
289A LYS* 3.1 28.3 + - + +
290A VAL 3.4 3.8 - - - +
291A VAL* 4.1 8.1 - - + -
343A GLY 3.4 1.4 - - - +
344A VAL* 3.1 26.7 - - - +
345A LYS* 2.8 44.3 + - + +
355A ALA 5.4 0.9 - - - +
356A ILE* 1.3 73.1 - - - +
358A PHE* 1.3 62.3 + - - +
359A THR* 3.9 15.1 + - + +
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Residues in contact with PHE 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A LEU* 4.8 0.4 - - + -
277A LEU* 3.8 36.8 - - + -
289A LYS* 3.3 6.2 - - - +
290A VAL* 2.8 46.7 + - + -
292A LEU* 3.8 22.2 - - + -
332A PHE* 3.3 28.7 - + + -
335A LEU* 5.1 0.2 - - + -
336A ALA* 3.6 30.5 - - + -
341A PHE* 3.5 23.4 - + + -
343A GLY 3.4 2.9 - - - -
344A VAL* 3.9 12.6 - - + -
356A ILE* 3.7 24.7 - - + -
357A GLU* 1.3 79.5 - - - +
359A THR* 1.3 61.4 + - - +
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Residues in contact with THR 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A GLY 5.2 0.4 - - - -
289A LYS* 4.2 17.5 - - + -
341A PHE* 3.3 6.4 - - - +
342A THR* 2.8 30.8 + - - -
343A GLY* 2.8 35.4 + - - +
357A GLU* 4.1 22.4 - - + +
358A PHE* 1.3 76.6 - - - +
360A LYS* 1.3 57.8 + - - +
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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