Contacts of the strand formed by residues 325 - 330 (chain D) in PDB entry 4O9U
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 GLU 325 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437B GLN* 5.1 7.5 + - - +
293D GLY 2.8 15.2 + - - +
294D LYS* 3.1 48.7 + - + +
295D VAL 2.9 29.1 + - - +
320D GLU* 5.6 0.4 - - - -
323D GLY 3.2 6.5 + - - +
324D VAL* 1.3 66.3 - - - +
326D VAL* 1.3 61.6 + - - +
327D LYS* 3.7 25.3 - - - +
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Residues in contact with VAL 326 (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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295D VAL* 3.5 7.0 - - + +
297D PHE* 3.9 16.8 - - + -
316D ALA* 3.8 34.8 - - + +
319D LEU* 3.7 34.8 - - + -
320D GLU* 4.2 9.9 + - + +
324D VAL* 3.1 20.0 + - + +
325D GLU* 1.3 74.3 - - - +
327D LYS* 1.3 70.1 + - - +
328D PHE* 3.9 11.9 - - + -
354D LYS* 3.4 23.6 - - + +
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Residues in contact with LYS 327 (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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311B LYS* 3.8 13.5 - - - +
437B GLN* 5.0 5.5 - - - +
294D LYS* 5.1 0.6 - - - +
295D VAL 3.1 6.4 + - - +
296D VAL* 3.2 14.8 - - + +
297D PHE* 3.1 24.1 + - - +
325D GLU* 3.7 21.4 + - + +
326D VAL* 1.3 80.4 - - - +
328D PHE* 1.3 66.0 + - - +
329D ALA 4.0 0.4 - - - -
353D ASP 5.1 3.8 - - - +
354D LYS* 3.7 12.3 - - - +
356D LYS* 4.3 25.3 - - + +
361D ILE* 3.8 13.9 - - + -
364D GLU* 2.9 38.6 + - - +
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Residues in contact with PHE 328 (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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297D PHE* 3.6 35.4 - + + +
299D PRO* 5.0 2.7 - - + -
312D LEU* 3.9 22.2 - - + -
313D LYS* 5.1 1.1 - - - -
316D ALA* 3.5 27.1 - - + -
326D VAL* 3.9 15.7 - - + -
327D LYS* 1.3 73.0 - - - +
329D ALA* 1.3 61.5 + - - +
330D ILE* 3.4 15.2 + - + +
345D LEU* 3.9 18.2 - - + -
350D VAL* 3.6 24.7 - - + -
354D LYS* 2.6 34.5 + - + +
355D LEU* 3.9 7.9 - - + -
356D LYS 2.8 31.1 + - - +
361D ILE* 4.3 2.9 - - - -
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Residues in contact with ALA 329 (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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296D VAL* 3.8 25.0 - - + +
297D PHE 3.1 6.3 + - - -
298D VAL* 4.0 15.4 - - + +
299D PRO* 3.4 24.1 - - - +
328D PHE* 1.3 68.8 - - - +
330D ILE* 1.3 60.5 + - - +
331D HIS 3.9 2.4 + - - -
356D LYS 3.4 4.7 - - - -
358D LEU* 6.1 0.2 - - - -
361D ILE* 3.9 22.6 - - + +
365D PHE* 3.9 10.1 - - + -
397D LEU* 4.2 11.4 - - + -
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Residues in contact with ILE 330 (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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28C VAL* 4.8 7.1 - - + +
299D PRO* 4.2 7.4 - - + -
328D PHE* 3.4 20.0 - - + +
329D ALA* 1.3 78.8 - - - +
331D HIS* 1.3 69.4 + - - +
332D PRO* 3.4 7.7 - - + +
341D MET* 4.0 13.5 - - + -
342D ASN* 3.5 27.8 - - - +
345D LEU* 3.3 31.6 - - + -
355D LEU* 3.7 20.0 - - + -
356D LYS 2.5 19.5 + - - +
357D ASP* 3.2 22.4 - - - +
358D LEU* 3.6 3.0 + - - +
397D LEU* 5.1 0.9 - - - -
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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