Contacts of the strand formed by residues 339 - 350 (chain A) 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 GLY 339 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326A ALA 3.3 8.7 - - - -
327A GLN* 4.4 6.3 - - - +
337A HIS 4.3 0.4 + - - -
338A LEU* 1.4 74.1 - - - +
340A HIS* 1.3 59.5 + - - -
387A TYR* 5.9 0.7 - - - -
92C SER* 4.2 2.9 + - - -
93C SER 5.5 1.2 + - - -
96C GLY 4.4 8.1 + - - +
97C ILE* 4.1 14.6 - - - -
98C GLY 3.0 18.0 + - - +
99C THR* 2.8 19.4 + - - -
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Residues in contact with HIS 340 (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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237A GLN* 3.5 3.8 - - - -
243A ALA* 3.2 24.3 - - + +
325A LEU* 3.7 0.9 - - - -
326A ALA* 2.9 31.3 + - + +
339A GLY* 1.3 74.8 - - - +
341A ALA* 1.3 72.4 + - - +
342A LEU* 3.9 19.3 - - + -
360A ASN* 2.9 25.6 + - - -
361A PRO* 4.6 0.7 - - + -
362A TRP* 3.3 29.5 + + - -
378A LEU* 4.0 17.5 - - + -
384A TYR* 3.6 21.3 - + + -
97C ILE* 3.4 12.9 - - - +
98C GLY 3.9 1.6 - - - +
99C THR* 3.3 21.5 + - - -
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Residues in contact with ALA 341 (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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243A ALA* 3.5 10.9 - - + +
244A ALA* 3.7 37.7 - - + +
247A SER* 3.4 6.6 + - - -
289A MET* 4.2 2.9 - - + -
323A MET* 4.1 9.6 - - - -
324A ILE 3.2 9.9 - - - +
340A HIS* 1.3 82.8 + - - +
342A LEU* 1.3 67.7 + - - +
361A PRO* 3.5 11.8 - - - +
97C ILE* 4.0 10.1 - - + +
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Residues in contact with LEU 342 (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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247A SER* 3.2 10.3 + - - -
323A MET* 3.3 11.3 - - - +
324A ILE* 2.8 57.1 + - + -
326A ALA* 4.1 16.4 - - + -
340A HIS* 3.9 13.7 - - + -
341A ALA* 1.3 84.7 - - - +
343A ALA* 1.3 60.8 + - - +
358A TYR* 3.8 21.3 - - + -
359A TRP 3.5 8.1 - - - +
360A ASN* 3.7 33.9 - - + -
361A PRO* 4.1 0.9 - - - -
376A LEU* 4.5 5.6 - - + -
378A LEU* 4.0 12.8 - - + -
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Residues in contact with ALA 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A PHE* 4.3 9.0 - - + -
247A SER* 3.6 10.0 + - - +
251A LEU* 4.0 26.0 - - + -
322A ILE 3.9 3.4 - - - -
324A ILE* 4.5 1.1 - - - -
342A LEU* 1.3 75.0 - - - +
344A VAL* 1.3 65.4 + - - +
345A VAL* 3.9 0.7 - - - +
358A TYR* 3.2 4.8 - - - +
359A TRP* 2.8 58.5 + - + +
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Residues in contact with VAL 344 (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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228A LEU* 4.5 4.7 - - - +
231A PHE* 4.8 0.3 - - - -
251A LEU* 3.5 20.4 - - - +
307A PRO* 5.5 0.4 - - + -
312A VAL* 4.0 18.8 - - + -
316A THR* 5.2 1.1 - - - +
322A ILE* 2.9 50.2 + - + +
324A ILE* 3.6 23.6 - - + -
342A LEU 4.2 0.2 + - - -
343A ALA* 1.3 74.0 - - - +
345A VAL* 1.3 65.3 + - - +
346A GLY 3.7 19.3 - - - +
356A LEU* 5.5 2.7 - - + -
357A ILE 3.7 8.1 - - - +
358A TYR* 4.3 1.6 - - + +
386A TRP* 3.9 16.8 - - + -
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Residues in contact with VAL 345 (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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227A THR* 3.3 22.5 - - + -
228A LEU* 2.8 36.7 + - - +
231A PHE* 3.7 44.2 - - + -
316A THR* 4.0 1.8 - - - +
343A ALA 3.9 9.0 - - - +
344A VAL* 1.3 77.4 - - - +
346A GLY* 1.3 55.7 + - - +
357A ILE* 2.7 20.7 + - + +
358A TYR 4.1 0.9 - - - -
359A TRP 4.1 5.2 - - - +
366A LEU* 3.7 34.8 - - + -
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Residues in contact with GLY 346 (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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226A ASN 3.1 12.1 - - - -
227A THR* 4.1 0.9 - - - -
312A VAL* 3.7 11.1 - - - +
316A THR* 3.8 15.5 - - - -
344A VAL* 3.7 3.0 - - - +
345A VAL* 1.3 81.8 - - - +
347A ASN* 1.3 65.1 + - - +
356A LEU* 3.5 4.2 - - - +
357A ILE* 2.8 28.4 + - - +
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Residues in contact with ASN 347 (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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224A TYR* 3.7 4.3 - - - -
225A GLU* 3.7 0.3 - - - -
226A ASN* 2.8 55.7 + - - +
309A TYR* 3.4 28.6 + - + -
312A VAL* 3.8 5.2 - - + +
313A ASP* 2.9 43.5 + - - +
346A GLY* 1.3 77.2 - - - +
348A ALA* 1.3 63.2 + - - +
355A LYS 3.2 15.5 - - - +
356A LEU* 3.9 12.3 - - + +
357A ILE* 3.9 7.4 - - - +
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Residues in contact with ALA 348 (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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222A VAL* 5.0 1.3 - - + -
224A TYR* 3.0 15.3 - - - +
225A GLU* 4.2 8.1 - - + -
309A TYR* 3.4 10.8 - - - -
347A ASN* 1.3 78.6 - - - +
349A LYS* 1.3 59.7 + - - +
350A ILE* 3.9 24.2 - - + -
355A LYS* 2.8 38.8 + - + +
357A ILE* 4.0 16.1 - - + +
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Residues in contact with LYS 349 (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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222A VAL 3.7 0.2 - - - -
223A GLN* 2.9 63.3 + - + +
224A TYR* 2.8 23.7 + - + +
309A TYR* 3.7 13.8 + - + +
348A ALA* 1.3 73.6 - - - +
350A ILE* 1.3 63.0 + - - +
352A ASP* 3.0 33.8 + - - +
353A GLN 3.3 15.0 - - - +
354A GLU* 4.6 5.6 - - + +
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Residues in contact with ILE 350 (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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220A ASP* 4.1 17.9 - - + -
221A GLN 3.3 10.5 - - - +
222A VAL* 4.1 19.5 - - + -
348A ALA* 3.9 22.2 - - + -
349A LYS* 1.3 78.7 - - - +
351A ASN* 1.3 89.8 + - - +
352A ASP 3.1 0.4 - - - -
353A GLN* 2.9 26.3 + - - +
355A LYS* 4.0 23.4 - - + -
357A ILE* 6.1 0.7 - - + -
368A ILE* 4.1 26.5 - - + -
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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