Contacts of the helix formed by residues 316 - 323 (chain A) in PDB entry 2X8Y
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 PRO 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314A LYS* 3.4 8.0 - - - +
315A LEU* 1.3 91.1 - - + +
317A GLN* 1.3 66.3 + - - +
318A ASP 4.3 1.1 - - - +
319A PHE* 3.0 21.7 + - + +
320A TRP* 3.6 5.8 - - - -
347A ASP* 3.3 50.9 - - + +
349A VAL* 3.8 17.9 - - + -
376A LEU* 4.0 18.8 - - + -
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Residues in contact with GLN 317 (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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315A LEU 4.0 0.2 + - - -
316A PRO* 1.3 74.1 - - - +
318A ASP* 1.3 58.0 + - - +
320A TRP* 3.1 23.6 + - - +
321A ASP* 2.9 58.4 + - - +
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Residues in contact with ASP 318 (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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316A PRO* 3.2 1.4 - - + +
317A GLN* 1.3 78.8 - - - +
319A PHE* 1.3 56.9 - - - +
321A ASP* 4.3 10.8 - - - +
322A LYS* 2.9 60.4 + - + +
346A THR 4.7 2.9 - - - +
347A ASP* 3.4 21.5 - - - +
348A ASP* 3.8 26.8 + - - +
349A VAL 4.3 1.7 - - - +
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Residues in contact with PHE 319 (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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300A PHE* 3.8 14.6 - + - -
315A LEU* 3.6 32.3 - - + -
316A PRO* 3.0 27.4 + - + +
318A ASP* 1.3 78.7 - - - +
320A TRP* 1.3 82.5 + + - +
323A SER* 2.7 61.5 + - - -
325A ILE* 5.2 2.0 - - + -
349A VAL* 3.3 26.3 + - + +
350A ARG* 4.0 2.5 - - - -
351A ILE* 3.7 39.0 - - + -
369A LEU* 3.8 10.3 - - + -
372A ILE* 4.1 10.1 - - + -
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Residues in contact with TRP 320 (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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297A LEU* 3.9 29.6 - - + -
300A PHE* 3.9 21.5 - - + -
301A GLN* 3.8 34.3 - - + -
304A ASP* 3.9 15.0 + - + -
315A LEU* 3.7 35.7 + - + +
316A PRO 3.6 13.5 - - - -
317A GLN* 3.1 30.3 + - - +
319A PHE* 1.3 91.3 - + - +
321A ASP* 1.3 63.3 + - - +
322A LYS 3.5 0.2 + - - -
323A SER* 4.3 7.3 + - - +
325A ILE* 5.3 4.7 - - + -
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Residues in contact with ASP 321 (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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317A GLN* 2.9 46.1 + - - +
318A ASP* 3.9 10.9 + - - +
320A TRP* 1.3 79.0 - - - +
322A LYS* 1.3 67.2 + - + +
323A SER 4.9 1.1 - - - +
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Residues in contact with LYS 322 (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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45A GLU* 4.8 1.6 + - - -
48A TRP* 3.4 19.8 + - - -
318A ASP* 2.9 36.9 + - - +
321A ASP* 1.3 86.6 - - + +
323A SER* 1.3 65.7 + - - +
324A ILE* 4.4 2.9 - - - +
348A ASP* 3.0 28.7 + - - +
350A ARG* 3.5 40.7 - - - +
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Residues in contact with SER 323 (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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48A TRP* 4.4 0.2 - - - -
319A PHE* 2.7 41.3 + - - -
320A TRP* 4.3 6.9 + - - +
321A ASP 3.8 1.4 - - - +
322A LYS* 1.3 82.1 + - - +
324A ILE* 1.3 61.8 + - - +
325A ILE* 4.0 17.7 + - - +
350A ARG* 3.4 5.9 - - - +
351A ILE 3.0 31.5 + - - +
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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