Contacts of the helix formed by residues 319 - 328 (chain A) in PDB entry 2A1X
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 ASN 319 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320A LEU* 1.3 63.6 + - - +
321A LYS* 3.2 27.8 + - - +
322A ASP* 2.9 42.1 + - - +
323A ILE* 3.4 19.9 - - - +
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Residues in contact with LEU 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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182A PRO* 3.9 15.7 - - + -
292A VAL* 4.5 11.4 - - + -
300A ILE* 3.8 37.2 - - + +
301A GLU* 4.4 21.8 - - + +
319A ASN* 1.3 75.1 - - - +
321A LYS* 1.3 63.7 + - - +
322A ASP 3.1 1.0 + - - -
323A ILE* 3.3 18.7 + - + +
324A TRP* 3.2 53.9 + - + +
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Residues in contact with LYS 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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182A PRO* 5.8 1.1 - - - +
289A TYR* 3.8 44.3 - - + -
319A ASN* 3.2 17.4 + - - +
320A LEU* 1.3 78.0 - - - +
322A ASP* 1.3 73.9 + - - +
324A TRP* 3.6 2.4 + - - +
325A MET* 2.8 49.0 + - - +
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Residues in contact with ASP 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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319A ASN* 2.9 40.6 + - - +
321A LYS* 1.3 97.1 + - - +
323A ILE* 1.3 57.4 + - + +
325A MET* 3.5 10.0 - - - +
326A PHE* 2.6 56.5 + - + -
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Residues in contact with ILE 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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319A ASN* 3.4 30.5 + - - +
320A LEU* 3.3 18.1 + - + +
322A ASP* 1.3 76.5 - - + +
324A TRP* 1.3 62.8 + - + +
326A PHE* 4.0 7.5 - - + +
327A ARG* 3.1 52.2 + - - +
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Residues in contact with TRP 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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154A MET* 3.6 35.2 - - + +
155A HIS* 3.8 13.9 - + + -
180A TYR* 3.4 22.5 + + + -
181A PHE* 3.6 23.8 - + - -
182A PRO* 3.5 28.7 - - + +
183A PHE* 3.7 21.8 - + - -
289A TYR* 3.7 23.6 + + + +
300A ILE* 5.6 0.4 - - - +
320A LEU* 3.2 39.3 + - + +
323A ILE* 1.3 79.5 - - + +
325A MET* 1.3 59.3 + - - +
327A ARG* 3.4 35.9 - - - +
328A ALA* 2.9 30.1 + - - +
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Residues in contact with MET 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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289A TYR* 3.3 26.5 - - + +
321A LYS* 2.8 53.0 + - - +
322A ASP* 3.5 11.7 - - - +
324A TRP* 1.3 75.9 - - - +
326A PHE* 1.3 62.8 + - + +
327A ARG 3.3 0.5 + - - -
328A ALA* 3.4 11.8 + - - +
335A ARG* 3.8 26.0 + - - +
337A ASN 5.3 3.1 - - - +
338A LEU 3.8 14.1 - - - +
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Residues in contact with PHE 326 (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 ASP* 2.6 43.8 + - + +
323A ILE* 4.0 7.6 - - + +
325A MET* 1.3 73.6 - - + +
327A ARG* 1.3 56.6 + - - +
329A ARG* 2.9 22.7 + - - -
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Residues in contact with ARG 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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122A GLN* 6.2 0.2 - - - +
123A ASP* 2.9 39.4 + - - +
125A GLN* 4.1 22.7 - - - +
153A ALA 4.4 2.9 - - - +
154A MET 3.3 25.6 - - - +
155A HIS* 4.4 10.7 + - - +
156A THR 6.1 0.2 - - - +
323A ILE* 3.1 37.6 + - - +
324A TRP* 3.4 51.2 - - - +
326A PHE* 1.3 76.3 - - - +
328A ALA* 1.3 61.2 + - - +
329A ARG* 2.9 20.9 + - - +
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Residues in contact with ALA 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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152A MET* 3.6 13.7 - - + -
153A ALA 4.0 7.2 - - - -
154A MET* 3.5 28.3 - - + +
289A TYR* 4.5 4.0 - - - +
324A TRP 2.9 17.4 + - - +
325A MET 3.4 7.3 + - - +
327A ARG* 1.3 78.1 - - - +
329A ARG* 1.3 71.2 + - - +
335A ARG* 3.9 23.3 + - - +
338A LEU 4.9 0.4 - - - +
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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