Contacts of the helix formed by residues 317 - 321 (chain A) in PDB entry 2F24
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 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312A ASN* 2.9 23.0 + - - -
314A ARG* 3.3 19.9 + - + +
315A PRO 3.4 0.2 - - - -
316A PRO* 1.3 74.9 - - - +
318A PRO* 1.3 71.6 - - - +
319A GLU* 3.6 20.4 - - - +
320A ALA* 3.1 13.8 + - + +
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Residues in contact with PRO 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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245A GLN* 3.6 17.9 - - - +
259A GLN* 4.6 19.3 - - + -
260A LEU 4.7 4.0 - - - +
261A VAL* 3.9 27.5 - - + +
263A LYS* 4.1 7.1 - - - +
316A PRO 3.0 5.6 - - - +
317A ALA* 1.3 83.1 - - - +
319A GLU* 1.3 74.3 + - + +
321A TRP* 3.4 29.2 + - + +
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Residues in contact with GLU 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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263A LYS* 2.8 36.3 + - - +
314A ARG* 5.0 3.6 + - - -
317A ALA* 3.6 17.4 - - - +
318A PRO* 1.3 105.4 - - + +
320A ALA* 1.3 59.6 + - - +
321A TRP 3.3 0.2 - - - -
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Residues in contact with ALA 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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312A ASN* 3.3 21.1 - - - +
313A PRO* 3.4 21.1 - - - +
314A ARG* 3.8 46.5 + - + +
317A ALA* 3.1 14.8 + - + +
319A GLU* 1.3 77.0 + - - +
321A TRP* 1.3 63.5 + - - +
322A SER* 3.4 1.0 + - - -
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Residues in contact with TRP 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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235A ASN* 4.5 7.2 - - - -
245A GLN* 3.5 21.3 + - - -
261A VAL* 3.6 15.3 - - + -
263A LYS* 3.4 29.8 + - + +
264A LEU* 3.9 30.1 - - + +
276A VAL* 4.4 3.4 - - + -
293A LEU* 3.7 39.5 - - + -
295A TYR* 3.6 25.1 - + + -
310A TYR* 3.6 33.4 - - + -
311A LEU 3.6 12.1 - - - -
312A ASN* 3.3 34.7 - - + +
317A ALA 4.3 0.2 + - - -
318A PRO* 3.4 25.3 + - + +
319A GLU 3.3 2.0 - - - -
320A ALA* 1.3 78.2 - - - +
322A SER* 1.3 63.6 + - - +
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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