Contacts of the helix formed by residues 323 - 333 (chain A) in PDB entry 6YBO
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 ASP 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319A ALA 3.1 15.4 + - - +
320A PHE 3.4 9.1 + - - +
322A ALA* 1.3 76.0 - - - +
324A PRO* 1.3 73.3 - - - +
325A GLU* 2.9 19.9 + - - +
326A VAL* 3.0 19.4 + - + +
327A GLN* 3.0 13.4 + - - +
382A HIS* 2.7 27.4 + - + +
387A ARG* 2.8 25.2 + - - -
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Residues in contact with PRO 324 (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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322A ALA 3.3 9.2 - - - +
323A ASP* 1.3 89.2 - - - +
325A GLU* 1.3 55.6 + - - +
327A GLN* 3.3 15.6 + - - +
328A GLU* 3.0 28.6 + - - +
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Residues in contact with GLU 325 (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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323A ASP* 2.9 12.4 + - - +
324A PRO* 1.3 78.3 - - - +
326A VAL* 1.3 58.0 + - - +
328A GLU* 3.4 13.6 + - - +
329A ALA* 3.0 25.8 + - - +
374A ARG* 2.6 33.2 + - - +
378A LEU* 4.1 13.3 - - + +
387A ARG* 2.9 31.8 + - - +
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Residues in contact with VAL 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A PHE* 3.2 68.6 - - + +
321A ARG* 4.9 2.7 - - - -
323A ASP* 3.0 21.3 + - + +
325A GLU* 1.3 74.5 - - - +
327A GLN* 1.3 59.8 + - - +
329A ALA* 3.0 6.5 + - - +
330A LEU* 2.8 44.1 + - + +
375A LEU* 4.5 3.1 - - + -
378A LEU* 4.1 15.3 - - + -
382A HIS* 4.1 6.7 - - + -
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Residues in contact with GLN 327 (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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321A ARG 3.0 25.9 + - - +
322A ALA* 3.7 15.9 + - - +
323A ASP 3.0 11.8 + - - +
324A PRO* 3.3 16.7 + - - +
326A VAL* 1.3 76.2 - - + +
328A GLU* 1.3 61.9 + - - +
330A LEU* 3.4 14.7 + - + +
331A ARG* 3.2 47.2 + - - +
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Residues in contact with GLU 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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324A PRO 3.0 16.1 + - - +
325A GLU* 3.8 16.0 - - - +
326A VAL 3.2 0.4 - - - -
327A GLN* 1.3 78.8 - - - +
329A ALA* 1.3 55.9 + - - +
331A ARG* 3.4 13.8 + - - +
332A ALA* 3.0 26.3 + - + +
374A ARG* 5.0 9.2 + - - +
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Residues in contact with ALA 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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325A GLU 3.0 14.7 + - - +
326A VAL 3.0 8.0 + - - +
328A GLU* 1.3 75.4 - - - +
330A LEU* 1.3 63.6 + - - +
332A ALA* 3.2 9.1 + - - +
333A SER* 3.0 27.4 + - - -
371A ALA* 5.4 0.8 - - - +
374A ARG* 3.9 14.8 - - + +
375A LEU* 4.0 20.4 - - + +
378A LEU* 3.8 20.6 - - + -
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Residues in contact with LEU 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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320A PHE* 5.3 1.8 - - + -
321A ARG* 3.8 32.1 - - - +
326A VAL* 2.8 31.7 + - + +
327A GLN* 3.6 15.9 - - + +
328A GLU 3.3 0.2 - - - -
329A ALA* 1.3 76.4 - - - +
331A ARG* 1.3 59.4 + - + +
333A SER* 3.3 2.7 + - - -
334A ARG 3.1 4.0 + - - -
335A LEU* 3.0 56.9 + - + +
336A ASP 5.1 0.9 - - - -
375A LEU* 3.9 25.1 - - + -
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Residues in contact with ARG 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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327A GLN* 3.2 41.0 + - - +
328A GLU* 3.7 12.3 - - + +
330A LEU* 1.3 74.7 - - + +
332A ALA* 1.3 65.9 + - - +
334A ARG* 3.0 19.2 + - - +
336A ASP* 3.8 28.4 - - + +
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Residues in contact with ALA 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 GLU* 3.0 16.3 + - + +
329A ALA* 3.2 13.2 + - - +
331A ARG* 1.3 76.2 - - - +
333A SER* 1.3 56.7 + - - +
334A ARG* 2.9 26.0 + - - +
370A MET 4.2 1.7 - - - +
371A ALA* 4.5 15.8 - - + +
374A ARG* 6.1 1.6 - - - +
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Residues in contact with SER 333 (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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329A ALA 3.0 15.1 + - - -
330A LEU 3.3 0.4 + - - -
331A ARG 3.1 0.2 - - - -
332A ALA* 1.3 74.7 - - - +
334A ARG* 1.3 70.7 + - - +
335A LEU* 3.3 22.9 + - - +
370A MET* 2.8 38.8 + - - +
371A ALA* 3.3 17.7 + - - +
372A PHE* 3.8 13.7 - - - -
375A LEU* 4.1 7.7 - - - +
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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