Contacts of the helix formed by residues 320 - 324 (chain A) in PDB entry 1Y2C
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 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A TRP* 3.8 25.6 - - - -
167A ASP* 4.4 5.0 + - - -
171A SER* 3.6 13.3 + - - -
316A CYS 3.4 9.2 - - - -
317A ALA* 2.6 26.3 + - - -
318A ASP 3.4 0.8 - - - -
319A LEU* 1.3 76.4 - - - +
321A ASN* 1.3 67.5 + - - +
322A PRO* 3.3 3.1 - - - -
323A THR* 2.8 24.7 + - - -
324A LYS* 3.4 13.4 + - - +
381A TRP* 4.0 4.5 - - - +
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Residues in contact with ASN 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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159A TYR* 2.5 39.7 + - - -
164A HIS* 5.1 1.8 + - - -
167A ASP* 3.4 24.2 + - - -
317A ALA 5.4 0.6 + - - -
318A ASP 4.9 4.8 + - - -
319A LEU 3.5 0.4 - - - -
320A SER* 1.3 77.4 + - - +
322A PRO* 1.3 69.4 - - + +
323A THR 3.1 1.6 + - - -
324A LYS* 3.2 19.0 + - - +
329A TYR* 3.3 18.9 - - + +
332A TRP* 3.5 35.5 - - + +
1003A 3DE 3.5 15.1 - - + +
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Residues in contact with PRO 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 LEU 3.8 13.2 - - - +
320A SER 3.5 4.3 - - - -
321A ASN* 1.3 93.0 - - + +
323A THR* 1.3 54.3 - - - +
324A LYS 3.4 0.4 - - - -
329A TYR* 3.5 38.8 - - + +
372A PHE* 4.0 25.8 - - + -
373A ILE* 4.1 5.2 - - + -
377A VAL* 4.1 8.1 - - + -
399A LEU* 3.5 31.1 - - + +
402A ASN* 2.9 23.8 + - - +
1003A 3DE 5.2 0.2 - - - -
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Residues in contact with THR 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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102A TRP* 3.1 35.0 + - - -
319A LEU 4.5 1.6 - - - +
320A SER* 2.8 17.8 + - - +
322A PRO* 1.3 78.0 - - - +
324A LYS* 1.3 58.6 + - - +
377A VAL* 4.6 0.7 - - + -
381A TRP* 3.6 38.6 - - + +
395A ILE* 3.5 20.8 - - + +
398A THR* 3.3 19.8 - - - +
399A LEU* 4.2 22.4 - - + +
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Residues in contact with LYS 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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102A TRP* 3.4 46.7 - - + +
103A GLY* 4.0 17.2 - - - +
167A ASP* 3.0 20.6 + - - -
170A GLN* 4.7 5.6 + - - -
171A SER* 2.9 24.6 + - - -
320A SER* 3.4 19.2 + - - +
321A ASN* 3.2 14.9 + - - +
323A THR* 1.3 78.1 - - - +
325A PRO* 1.3 80.5 - - + +
326A LEU* 4.1 0.2 - - - -
328A LEU* 4.2 15.7 - - + -
329A TYR* 4.1 2.3 - - - +
332A TRP* 5.4 5.2 - - + +
398A THR* 3.6 2.6 - - - +
402A ASN* 2.8 21.1 + - - -
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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