Contacts of the helix formed by residues 308 - 318 (chain B) in PDB entry 1PXV
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 308 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B VAL 3.5 2.9 + - - -
307B PRO* 1.3 76.4 - - - +
309B TYR* 1.3 64.4 + - - +
310B ASN* 3.5 7.5 + - - +
311B GLN* 3.1 25.7 + - - +
312B VAL* 2.9 23.0 + - - +
371B ALA 5.9 1.3 - - - -
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Residues in contact with TYR 309 (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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224B TYR* 3.3 28.6 - + - -
307B PRO 3.8 0.8 + - - -
308B SER* 1.3 72.3 - - - +
310B ASN* 1.3 72.2 + - - +
312B VAL* 3.3 1.9 + - - +
313B ASP* 3.0 31.8 + - + +
347B ASN* 3.4 25.0 + - + -
348B ALA 3.3 28.3 - - - -
349B LYS* 3.6 6.4 + - - +
354B GLU* 3.4 54.1 - - + +
355B LYS 3.6 17.0 - - - -
356B LEU* 4.2 10.8 - - + +
371B ALA* 4.2 13.6 + - + +
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Residues in contact with ASN 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B SER* 3.2 6.7 + - - +
309B TYR* 1.3 93.8 - - - +
311B GLN* 1.3 60.9 + - - +
313B ASP* 3.6 6.8 - - - +
314B GLN* 3.1 37.2 + - - +
354B GLU* 4.7 4.7 - - - +
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Residues in contact with GLN 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B GLN* 2.8 44.6 + - - +
307B PRO* 3.4 14.2 - - + +
308B SER* 3.1 22.1 + - - +
310B ASN* 1.3 73.9 - - - +
312B VAL* 1.3 62.1 + - - +
314B GLN* 3.4 8.9 + - + +
315B LEU* 2.9 52.4 + - + +
391B ILE* 4.0 3.8 - - - +
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Residues in contact with VAL 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B PRO* 3.7 28.3 - - + -
308B SER 2.9 19.8 + - - +
309B TYR 3.8 3.8 - - - +
311B GLN* 1.3 73.2 - - - +
313B ASP* 1.3 64.3 - - - +
315B LEU* 4.5 4.9 - - - -
316B THR* 2.6 43.1 + - - +
322B ILE* 4.2 9.9 - - + -
344B VAL* 4.0 13.5 - - + -
346B GLY 3.6 24.2 - - - +
347B ASN* 3.8 8.5 - - + +
356B LEU* 3.8 18.2 - - + -
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Residues in contact with ASP 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B TYR* 2.6 27.6 + - - -
226B ASN* 3.2 10.1 + - - -
309B TYR* 3.0 22.3 + - + +
310B ASN* 3.6 10.5 - - - +
311B GLN 3.3 0.2 - - - -
312B VAL* 1.3 76.5 - - - +
314B GLN* 1.3 60.2 + - + +
317B LYS* 2.8 54.1 + - - +
347B ASN* 2.9 29.0 + - - +
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Residues in contact with GLN 314 (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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310B ASN* 3.1 24.4 + - - +
311B GLN* 3.9 7.2 - - + +
313B ASP* 1.3 82.0 - - + +
315B LEU* 1.3 66.0 + - + +
317B LYS* 3.3 7.8 + - - +
318B ASP* 3.0 37.0 + - - +
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Residues in contact with LEU 315 (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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307B PRO* 5.7 0.4 - - + -
311B GLN* 2.9 47.3 + - + +
312B VAL 4.0 2.0 - - - +
314B GLN* 1.3 76.7 - - + +
316B THR* 1.3 60.5 + - - +
318B ASP* 3.2 7.8 + - + +
319B ASN 3.1 4.2 + - - -
320B VAL* 2.9 59.9 + - + +
322B ILE* 3.8 21.5 - - + -
391B ILE* 3.8 27.8 - - + -
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Residues in contact with THR 316 (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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226B ASN* 3.5 26.7 - - - +
227B THR 3.5 8.4 - - - +
228B LEU* 3.5 44.7 - - + +
229B LYS 5.4 0.7 + - - -
312B VAL* 2.6 35.8 + - - +
315B LEU* 1.3 76.9 - - - +
317B LYS* 1.3 57.4 - - - +
319B ASN* 2.9 19.2 + - - +
320B VAL 4.5 2.6 + - - -
322B ILE* 5.3 1.9 - - - +
344B VAL* 5.2 1.6 - - - +
345B VAL 4.0 4.3 + - - +
346B GLY* 3.8 4.5 + - - -
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Residues in contact with LYS 317 (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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224B TYR* 3.0 28.8 + - - -
226B ASN* 3.6 15.0 - - - +
313B ASP* 2.8 38.9 + - - +
314B GLN* 3.3 7.6 + - - +
316B THR* 1.3 75.8 - - - +
318B ASP* 1.3 65.0 + - - +
319B ASN* 3.2 2.6 + - - +
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Residues in contact with ASP 318 (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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314B GLN* 3.0 27.2 + - - +
315B LEU* 3.6 7.9 - - + +
316B THR 3.1 0.2 - - - -
317B LYS* 1.3 80.6 - - - +
319B ASN* 1.3 71.6 + - - +
320B VAL* 3.3 16.2 + - + +
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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