Contacts of the helix formed by residues 396 - 401 (chain B) in PDB entry 2PO5
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 396 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225B ASP* 2.6 37.9 + - - -
226B ARG* 3.4 19.5 + - - -
393B GLU* 3.6 7.3 + - - -
395B CYS* 1.3 88.2 - - - +
397B LYS* 1.3 66.1 + - - +
398B GLN* 3.3 6.3 + - - -
399B LEU* 3.1 16.8 + - - +
400B THR* 3.9 1.7 + - - +
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Residues in contact with LYS 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A SER* 5.4 8.8 + - - +
293A TYR* 3.5 30.7 - - + +
294A CYS* 3.6 17.8 + - - +
295A ASN 3.5 2.7 - - - +
296A PRO* 3.5 37.1 - - + +
395B CYS 3.9 0.6 + - - -
396B SER* 1.3 73.6 - - - +
398B GLN* 1.3 62.6 + - + +
400B THR* 2.4 43.4 + - + +
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Residues in contact with GLN 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A TYR* 5.4 8.0 - - + -
295A ASN 4.2 1.0 + - - -
296A PRO* 3.1 16.7 - - - +
297A TYR* 2.7 81.7 + - + +
298A ARG* 4.1 9.7 + - - +
226B ARG* 3.3 39.8 + - - +
275B PRO* 5.1 4.2 - - - +
279B GLU* 4.8 1.9 - - - +
396B SER* 3.1 6.8 + - - +
397B LYS* 1.3 80.4 - - + +
399B LEU* 1.3 61.5 + - - +
401B LEU* 3.1 23.2 + - - +
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Residues in contact with LEU 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B TYR* 3.7 37.0 - - + +
203B LEU* 4.2 14.6 - - + -
223B THR* 4.0 15.0 - - + -
225B ASP* 3.6 12.8 - - - +
226B ARG* 3.9 4.3 - - - +
395B CYS* 3.6 27.8 - - + -
396B SER* 3.1 16.9 + - - +
398B GLN* 1.3 77.1 - - - +
400B THR* 1.3 57.1 + - - +
401B LEU 3.1 7.3 + - - +
402B SER* 5.2 0.9 + - - -
414B THR* 5.9 1.8 - - + -
415B LYS* 3.1 31.2 - - + +
418B PHE* 4.6 12.8 - - + -
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Residues in contact with THR 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A PRO* 4.0 8.5 - - - +
327A ARG* 2.9 21.6 + - - -
395B CYS* 4.3 3.1 - - - -
396B SER 4.0 9.4 - - - +
397B LYS* 2.4 45.8 + - + +
399B LEU* 1.3 75.9 - - - +
401B LEU* 1.3 56.9 + - - +
415B LYS* 3.3 23.3 - - - +
419B THR* 4.1 22.9 - - + -
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Residues in contact with LEU 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A VAL* 3.9 16.4 - - + -
258A ILE 5.6 0.4 - - - +
259A LEU* 6.0 1.6 - - + -
296A PRO* 3.4 22.4 - - + -
297A TYR* 3.7 30.3 - - - +
298A ARG* 3.0 39.7 + - + +
322A LEU* 3.8 24.9 - - + -
327A ARG* 3.9 17.3 - - + +
398B GLN 3.1 9.4 + - - +
399B LEU 3.1 5.2 - - - +
400B THR* 1.3 78.8 + - - +
402B SER* 1.3 78.3 + - - +
404B PRO* 5.8 0.7 - - + -
999B FES 5.4 0.2 - - - -
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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