Contacts of the helix formed by residues 319 - 324 (chain A) in PDB entry 2PA5
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 PHE 319 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A PRO* 3.9 25.1 - - + -
317A GLY 4.3 4.9 - - - -
318A THR* 1.3 76.7 - - - +
320A HIS* 1.3 67.7 + - - +
321A CYS 3.3 3.0 + - - -
322A SER* 3.5 7.1 + - - -
323A MET* 3.4 21.9 - - + +
337A PRO* 3.5 26.9 - - + -
338A CYS 3.3 26.5 - - - -
339A LEU* 3.6 27.6 - - + -
340A ASP* 3.7 1.6 - - - -
555A ALA* 3.6 23.8 - - + -
556A PHE* 3.7 26.9 - + - -
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Residues in contact with HIS 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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318A THR* 3.7 26.9 - - + +
319A PHE* 1.3 80.2 - - - +
321A CYS* 1.3 57.3 + - - +
323A MET* 3.3 5.4 + - - +
324A SER* 2.7 33.6 + - - +
340A ASP* 3.0 20.3 + - - +
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Residues in contact with CYS 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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320A HIS* 1.3 78.6 - - - +
322A SER* 1.3 61.7 + - - +
323A MET 3.2 0.9 + - - -
324A SER* 3.2 12.3 + - - -
327A ASN* 2.9 38.9 + - - -
340A ASP* 2.9 18.5 + - - +
343A ARG* 3.3 48.5 - - - +
356A ASP* 4.5 2.9 - - - -
357A TYR* 3.9 4.9 - - + -
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Residues in contact with SER 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 PHE 3.5 7.0 + - - -
321A CYS* 1.3 78.4 - - - +
323A MET* 1.3 60.8 + - - +
327A ASN* 3.8 13.2 - - - +
328A LEU* 3.8 0.9 + - - -
331A ASN* 3.0 23.6 + - - -
337A PRO* 3.4 26.5 - - - -
338A CYS* 2.9 27.6 + - - -
340A ASP* 4.5 0.6 + - - -
357A TYR* 2.7 31.7 + - - -
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Residues in contact with MET 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 PHE* 3.4 20.6 - - + +
320A HIS* 3.3 6.5 + - - +
321A CYS 3.1 0.4 - - - -
322A SER* 1.3 81.8 - - - +
324A SER* 1.3 62.3 + - - +
325A PRO* 4.7 0.5 - - - +
328A LEU* 3.9 35.2 - - + +
331A ASN* 4.8 2.5 - - - -
334A GLY* 4.1 20.2 - - - +
337A PRO* 4.1 22.7 - - + -
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Residues in contact with SER 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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320A HIS* 2.7 23.7 + - - +
321A CYS* 3.2 15.0 + - - -
323A MET* 1.3 77.9 - - - +
325A PRO* 1.4 73.9 - - - +
327A ASN* 2.9 27.6 + - - +
328A LEU* 3.3 11.7 + - - +
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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