Contacts of the helix formed by residues 342 - 353 (chain A) in PDB entry 1XV9
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 VAL 342 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264A PRO* 6.2 2.0 - - + -
265A VAL* 4.9 7.4 - - + +
268A ILE* 6.2 1.1 - - + -
337A ALA* 3.5 18.8 + - + +
340A ALA* 3.2 14.8 - - + +
341A GLY* 1.3 75.8 - - - +
343A GLY* 1.3 64.5 + - - +
344A ALA* 3.6 2.0 - - - -
345A ILE* 3.3 25.1 - - + +
346A PHE* 3.6 7.1 - - + +
435A HIS* 3.8 20.6 - - + -
439A PHE* 4.2 17.0 - - + -
1003A F15 4.3 20.4 - - + -
438C PHE* 4.0 11.0 - - + -
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Residues in contact with GLY 343 (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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337A ALA* 4.1 2.7 - - - -
338A HIS* 3.7 45.9 - - - +
341A GLY 3.3 7.3 + - - -
342A VAL* 1.3 75.7 - - - +
344A ALA* 1.3 64.6 + - - +
346A PHE* 2.8 21.5 + - - +
347A ASP* 3.0 7.6 + - - +
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Residues in contact with ALA 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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338A HIS* 4.5 4.1 + - - -
341A GLY 5.0 0.4 + - - -
342A VAL 3.6 0.8 - - - -
343A GLY* 1.3 73.1 - - - +
345A ILE* 1.3 56.7 + - - +
347A ASP* 3.5 8.5 + - - +
348A ARG* 3.2 22.9 + - - +
258C PRO* 5.5 12.5 - - + +
443C GLY* 5.3 14.4 - - - -
444C ASP 5.5 3.4 - - - +
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Residues in contact with ILE 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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342A VAL 3.3 17.0 - - - +
344A ALA* 1.3 74.2 - - - +
346A PHE* 1.3 68.2 + - - +
348A ARG* 3.2 13.5 + - + +
349A VAL* 3.0 24.4 + - + +
428A ILE* 4.3 13.5 - - + +
431A LYS* 3.9 28.9 - - + -
432A CYS* 4.0 20.0 - - - -
435A HIS* 3.5 34.3 - - + +
1003A F15 3.6 29.4 - - + -
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Residues in contact with PHE 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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322A ASP 4.4 0.9 - - - -
323A GLY* 4.2 5.2 - - - -
324A ILE* 4.2 19.5 - - + -
332A VAL* 3.4 35.7 - - + -
333A HIS 3.8 7.9 - - - -
334A ARG* 3.6 23.3 - - + -
337A ALA* 3.4 17.7 - - + -
342A VAL* 3.6 11.2 - - + +
343A GLY 2.8 11.2 + - - +
345A ILE* 1.3 78.9 - - - +
347A ASP* 1.3 72.4 + - - +
349A VAL* 3.0 6.5 + - - +
350A LEU* 2.9 52.2 + - + +
1003A F15 4.1 27.1 - - + -
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Residues in contact with ASP 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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334A ARG* 3.4 35.8 + - - -
338A HIS* 3.1 31.7 + - - -
343A GLY 3.0 6.2 + - - +
344A ALA* 3.7 10.8 - - - +
346A PHE* 1.3 86.5 - - - +
348A ARG* 1.3 56.3 + - - +
350A LEU* 3.7 7.8 - - - +
351A THR* 3.0 35.8 + - - +
256C LEU 4.5 1.9 - - - +
258C PRO* 6.0 1.4 - - - +
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Residues in contact with ARG 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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344A ALA 3.2 13.3 + - - +
345A ILE* 3.2 21.4 + - + +
346A PHE 3.1 1.0 - - - -
347A ASP* 1.3 74.1 - - - +
349A VAL* 1.3 61.7 + - - +
351A THR* 4.9 1.1 - - - -
352A GLU* 2.8 50.2 + - + +
427A SER* 3.5 31.3 + - - -
428A ILE* 4.3 17.3 - - + +
431A LYS* 4.4 20.4 - - - +
271B ASP* 3.0 43.5 + - - +
272B ARG* 4.2 3.6 - - - +
273B PRO* 4.1 24.2 - - - +
320B ARG* 4.3 2.6 - - - +
444C ASP* 5.1 2.6 + - - -
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Residues in contact with VAL 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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313A PHE* 3.9 29.4 - - + -
314A SER* 4.0 12.6 - - - +
324A ILE* 4.5 8.3 - - + -
345A ILE* 3.0 25.7 + - + +
346A PHE* 3.0 7.4 + - + +
348A ARG* 1.3 76.1 - - - +
350A LEU* 1.3 66.0 + - + +
353A LEU* 2.8 26.7 + - + -
354A VAL* 3.4 16.1 + - + -
428A ILE* 4.2 28.7 - - + -
432A CYS* 5.2 2.7 - - - -
1003A F15 4.4 15.0 - - + -
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Residues in contact with LEU 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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322A ASP* 3.7 30.7 - - - +
323A GLY 4.1 21.3 - - - +
324A ILE* 4.7 8.1 - - + -
334A ARG* 4.5 11.2 - - - +
346A PHE* 2.9 51.0 + - + +
347A ASP* 3.7 11.4 - - - +
349A VAL* 1.3 77.8 - - + +
351A THR* 1.3 62.0 + - - +
352A GLU 3.3 0.2 + - - -
354A VAL* 4.2 18.2 - - + -
355A SER* 2.7 34.5 + - - -
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Residues in contact with THR 351 (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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347A ASP* 3.0 19.3 + - - +
348A ARG* 4.5 0.9 - - - -
350A LEU* 1.3 77.9 - - - +
352A GLU* 1.3 76.5 + - - +
355A SER* 3.9 14.0 + - - +
356A LYS* 4.0 7.4 - - - +
278B ARG* 3.5 31.4 + - - +
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Residues in contact with GLU 352 (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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348A ARG* 2.8 39.9 + - + +
351A THR* 1.3 88.8 - - - +
353A LEU* 1.3 63.2 + - + +
356A LYS* 3.3 7.0 - - - +
421A ARG* 3.3 34.7 + - - -
424A ALA* 4.5 6.2 - - + +
428A ILE* 3.6 15.0 - - + -
271B ASP* 3.4 34.0 + - + +
278B ARG* 2.7 50.3 + - - -
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Residues in contact with LEU 353 (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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310A ILE* 3.5 24.0 - - + -
311A ALA* 4.6 3.1 - - - -
314A SER* 3.0 32.3 - - - +
349A VAL* 2.8 18.9 + - + +
352A GLU* 1.3 79.4 - - + +
354A VAL* 1.3 57.9 + - - +
356A LYS* 3.0 5.5 + - - +
357A MET* 2.7 49.5 + - + +
421A ARG* 4.5 14.4 - - + +
424A ALA* 4.7 1.6 - - + -
425A LEU* 3.8 27.8 - - + +
428A ILE* 3.6 27.8 - - + -
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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