Contacts of the helix formed by residues 327 - 332 (chain A) in PDB entry 2W8D
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 SER 327 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305A GLU* 3.3 15.4 + - - -
306A ASN* 3.1 16.4 + - - -
325A LEU* 3.7 4.7 + - - +
326A GLN* 1.3 74.1 - - - +
328A VAL* 1.3 54.3 + - - +
329A PRO* 3.7 9.2 - - - -
330A ALA* 3.0 6.6 + - - +
331A ILE* 2.7 37.1 + - - +
359A GLU* 3.4 47.2 - - - +
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Residues in contact with VAL 328 (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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249A TYR* 5.8 2.0 - - - +
304A MSE 4.0 4.5 - - - +
305A GLU 3.1 14.1 + - - +
327A SER* 1.3 67.4 - - - +
329A PRO* 1.3 74.4 - - + +
330A ALA 2.9 1.5 + - - -
331A ILE* 3.0 7.6 + - - +
332A LEU* 2.9 28.2 + - + +
403A TYR* 3.5 27.1 - - + +
527A ALA* 3.8 28.7 - - + +
530A ILE* 5.8 4.0 - - + -
531A LEU* 3.8 35.9 - - + -
543A MSE 4.2 6.0 - - + +
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Residues in contact with PRO 329 (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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305A GLU* 3.4 18.8 - - + +
327A SER* 3.7 6.7 - - - -
328A VAL* 1.3 94.3 - - + +
330A ALA* 1.3 57.5 + - - +
332A LEU* 3.7 7.5 + - + +
333A LYS* 3.5 24.2 + - - +
337A TYR* 5.0 2.9 - - - +
339A SER* 3.6 22.0 + - - +
359A GLU 3.6 12.3 - - - +
360A GLY 4.5 0.7 - - - +
361A ILE* 3.0 37.9 - - + -
403A TYR* 3.8 16.2 - - + -
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Residues in contact with ALA 330 (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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327A SER 3.0 13.7 + - - +
328A VAL 3.0 0.8 - - - -
329A PRO* 1.3 77.8 - - - +
331A ILE* 1.3 66.6 + - - +
333A LYS* 3.2 29.1 + - + +
334A SER 4.5 0.3 + - - -
359A GLU 3.8 11.4 + - - +
622A PHE* 3.7 17.7 - - + -
623A LYS* 5.3 5.1 + - - +
625A VAL* 3.5 31.9 - - + -
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Residues in contact with ILE 331 (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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326A GLN 3.8 8.7 - - - +
327A SER 2.7 24.4 + - - +
328A VAL* 3.6 5.4 - - - +
330A ALA* 1.3 73.3 - - - +
332A LEU* 1.3 61.2 + - + +
333A LYS 3.1 3.1 + - - -
334A SER* 2.9 26.8 + - - +
335A LYS* 5.8 0.2 - - - +
531A LEU* 4.2 14.6 - - + -
536A VAL* 4.1 22.0 - - + -
541A TYR* 3.4 47.8 - - + +
543A MSE 3.8 29.2 - - + -
622A PHE* 3.9 12.5 - - + -
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Residues in contact with LEU 332 (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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328A VAL* 2.9 25.7 + - + +
329A PRO* 4.0 5.4 - - + +
331A ILE* 1.3 76.8 - - + +
333A LYS* 1.3 62.6 + - - +
334A SER 3.2 0.7 - - - -
335A LYS* 3.0 21.6 + - + +
336A ASN 3.3 0.3 + - - -
337A TYR* 3.2 54.2 + - + -
403A TYR* 3.7 30.7 - - + -
531A LEU* 4.1 17.9 - - + -
534A LEU* 3.9 21.5 - - + -
536A VAL* 4.2 16.2 - - + -
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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