Contacts of the helix formed by residues 315 - 323 (chain A) in PDB entry 6PBD
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 315 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305A GLY 4.8 1.1 - - - -
306A SER* 4.7 2.7 - - - +
314A GLY* 1.3 75.6 - - - +
316A ILE* 1.3 65.8 + - - +
317A HIS* 3.5 14.2 + - - +
318A LYS* 3.3 25.4 + - - +
319A ILE* 3.0 22.9 + - - +
158B MET* 3.7 26.4 - - - +
162B GLU* 4.3 10.7 + - - -
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Residues in contact with ILE 316 (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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275A PHE* 3.7 41.1 - - + -
290A LEU* 4.6 1.1 - - + -
305A GLY 4.5 1.8 + - - +
307A ILE* 3.9 22.9 - - + -
315A SER* 1.3 73.3 - - - +
317A HIS* 1.3 85.4 + - + +
320A GLY* 3.1 19.9 + - - -
331A GLY* 3.8 11.3 - - - -
332A TRP* 3.8 33.7 - - + -
335A TRP* 3.2 21.5 + - + -
346A ILE* 4.0 18.8 - - + -
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Residues in contact with HIS 317 (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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315A SER* 3.1 11.4 - - - +
316A ILE* 1.3 97.8 - - + +
318A LYS* 1.3 61.2 + - - +
321A ALA* 3.0 28.9 + - - +
329A CYS* 3.6 23.4 + - - +
330A ASN* 3.8 6.0 - - - -
331A GLY 3.2 23.6 + - - +
332A TRP* 3.6 31.7 + + - -
161B ASP* 4.8 15.1 + - - -
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Residues in contact with LYS 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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314A GLY* 5.1 2.9 - - - -
315A SER* 3.3 21.1 + - - +
317A HIS* 1.3 79.6 - - - +
319A ILE* 1.3 60.5 + - + +
321A ALA* 3.3 6.6 + - - +
322A LEU* 3.0 34.5 + - + +
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Residues in contact with ILE 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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307A ILE* 3.8 22.4 - - + +
309A VAL* 3.7 35.2 - - + +
312A LEU* 4.1 11.7 - - + +
313A SER* 3.7 26.9 - - - +
314A GLY* 3.5 20.2 - - - +
315A SER 3.0 17.4 + - - +
318A LYS* 1.3 72.9 - - + +
320A GLY* 1.3 61.6 + - - +
322A LEU* 3.0 24.4 + - + +
323A VAL* 2.8 27.8 + - + +
335A TRP* 4.3 2.9 - - + -
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Residues in contact with GLY 320 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A ILE 3.1 20.6 + - - -
319A ILE* 1.3 78.5 - - - +
321A ALA* 1.3 60.3 + - - +
323A VAL* 3.3 12.4 - - - +
324A GLN* 3.2 22.0 + - - +
329A CYS* 3.6 13.5 - - - -
334A TYR* 4.4 1.8 - - - -
335A TRP* 3.7 21.2 - - - +
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Residues in contact with ALA 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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317A HIS 3.0 19.8 + - - +
318A LYS* 3.6 7.0 - - - +
320A GLY* 1.3 75.9 - - - +
322A LEU* 1.3 61.9 + - + +
324A GLN 3.5 0.9 + - - -
325A SER* 3.1 6.6 + - - -
326A ALA* 3.1 47.5 + - - +
327A PRO 3.7 13.9 - - - +
328A ALA 4.3 1.1 - - - -
329A CYS* 3.6 16.8 - - + +
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Residues in contact with LEU 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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312A LEU* 4.9 11.7 - - + -
318A LYS* 3.0 21.6 + - + +
319A ILE* 3.0 29.4 + - + +
321A ALA* 1.3 75.0 - - + +
323A VAL* 1.3 62.8 + - - +
324A GLN 3.1 3.3 + - - -
325A SER* 3.3 11.6 + - - +
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Residues in contact with VAL 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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297A HIS* 3.3 49.0 + - + +
309A VAL* 4.6 19.7 - - + -
319A ILE* 2.8 15.0 + - + +
320A GLY* 3.3 16.2 - - - +
322A LEU* 1.3 75.7 - - - +
324A GLN* 1.3 60.3 + - - +
325A SER 3.6 0.2 - - - -
334A TYR* 3.3 33.2 - - + +
335A TRP* 4.1 11.9 - - + -
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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