Contacts of the helix formed by residues 337 - 353 (chain A) in PDB entry 1X8B
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 337 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A PRO* 3.9 1.2 - - - +
334A LEU* 2.4 40.7 + - - -
335A ALA 3.2 1.4 + - - -
336A GLY* 1.3 79.1 - - - +
338A VAL* 1.3 65.3 + - - +
339A ASP* 3.5 9.2 + - - +
340A GLU* 2.9 26.4 + - - +
341A GLN* 3.0 18.0 + - - +
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Residues in contact with VAL 338 (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 SER* 1.3 72.9 - - - +
339A ASP* 1.3 72.1 + - - +
341A GLN* 3.2 21.5 + - - +
342A ASN* 2.9 24.6 + - + +
345A ARG* 5.3 2.2 + - - +
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Residues in contact with ASP 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A PRO* 3.9 15.2 - - + +
337A SER* 3.1 10.0 + - - +
338A VAL* 1.3 87.8 - - - +
340A GLU* 1.3 56.1 + - - +
342A ASN* 3.3 8.2 + - - +
343A ALA* 2.9 26.7 + - - +
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Residues in contact with GLU 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LYS* 5.9 2.9 - - + +
333A PRO* 3.6 22.1 - - + +
334A LEU 3.6 3.4 - - - +
335A ALA* 2.6 15.9 - - - +
336A GLY* 2.2 39.0 + - - -
337A SER* 2.9 21.6 + - - +
339A ASP* 1.3 73.6 - - - +
341A GLN* 1.3 62.6 + - + +
343A ALA* 3.1 2.4 + - + +
344A LEU* 2.8 52.1 + - + +
372A MET* 5.6 1.6 - - + -
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Residues in contact with GLN 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A GLY* 4.4 13.6 + - - +
337A SER 3.0 14.5 + - - +
338A VAL* 3.5 23.8 - - - +
340A GLU* 1.3 77.1 - - + +
342A ASN* 1.3 61.3 + - - +
344A LEU* 3.4 8.2 + - - +
345A ARG* 3.0 39.9 + - - +
348A TYR* 5.7 0.3 - - - -
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Residues in contact with ASN 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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338A VAL* 2.9 17.0 + - + +
339A ASP* 3.7 8.9 + - - +
341A GLN* 1.3 74.8 - - - +
343A ALA* 1.3 66.1 + - - +
345A ARG* 3.0 33.8 + - - +
346A GLU* 3.6 2.3 + - - +
465A GLY 3.7 7.8 + - - +
466A HIS* 5.4 0.7 - - - -
476A GLU* 5.4 17.0 + - - +
602A MG 2.4 44.1 - - - -
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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
----------------------------------------------------------
333A PRO* 3.9 9.0 - - + -
339A ASP 2.9 17.0 + - - +
340A GLU* 3.1 4.9 + - - +
342A ASN* 1.3 78.2 - - - +
344A LEU* 1.3 64.4 + - - +
346A GLU* 3.3 23.1 + - - +
347A VAL* 3.7 9.4 + - - +
372A MET* 3.5 32.3 - - + +
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Residues in contact with LEU 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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340A GLU* 2.8 46.1 + - + +
341A GLN* 3.9 6.5 - - - +
343A ALA* 1.3 76.3 - - + +
345A ARG* 1.3 65.8 + - - +
347A VAL* 3.1 13.3 + - + +
348A TYR* 2.9 57.2 + - + +
372A MET* 4.4 18.8 - - - -
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Residues in contact with ARG 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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338A VAL* 5.3 2.8 + - - +
341A GLN* 3.0 29.7 + - - +
342A ASN* 3.0 47.7 + - - +
344A LEU* 1.3 75.4 - - - +
346A GLU* 1.3 58.1 + - - +
348A TYR* 3.8 12.8 - - + +
349A ALA* 2.8 33.4 + - - +
464A LEU 5.1 0.7 - - - -
467A VAL* 3.9 23.7 + - + +
468A THR* 4.3 17.9 + - - +
469A ARG 5.7 0.4 - - - +
476A GLU* 6.0 2.8 - - - +
602A MG 3.8 4.7 - - - -
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Residues in contact with GLU 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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328A LYS* 2.7 40.6 + - - -
342A ASN 3.6 4.2 + - - +
343A ALA* 3.3 16.7 + - - +
344A LEU 3.1 0.8 - - - -
345A ARG* 1.3 80.6 - - - +
347A VAL* 1.3 59.7 + - + +
349A ALA* 3.7 2.4 - - - +
350A HIS* 2.9 43.3 + - + +
374A ILE* 4.8 5.9 - - + +
463A ASP* 4.4 1.4 - - - +
464A LEU* 3.9 27.6 + - - +
465A GLY* 4.1 20.2 + - - -
602A MG 4.1 0.8 - - - -
901A 824 3.5 16.5 - - - -
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Residues in contact with VAL 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ALA 3.8 13.0 - - - +
344A LEU* 3.1 16.8 + - + +
346A GLU* 1.3 78.4 - - + +
348A TYR* 1.3 62.9 + - + +
350A HIS* 3.2 7.7 + - - +
351A ALA* 2.7 35.8 + - + +
362A TYR* 4.3 11.5 - - + +
365A ALA* 4.2 29.6 - - + -
372A MET* 4.6 14.6 - - - -
374A ILE* 4.7 10.1 - - + -
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Residues in contact with TYR 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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341A GLN 5.7 0.4 - - - -
344A LEU* 2.9 55.2 + - + +
345A ARG* 3.8 12.3 - - + +
347A VAL* 1.3 87.0 - - + +
349A ALA* 1.3 62.0 + - - +
351A ALA* 3.3 15.9 + - + +
352A VAL* 3.3 20.4 + - - +
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Residues in contact with ALA 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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345A ARG 2.8 22.5 + - - +
346A GLU 3.7 3.8 - - - +
348A TYR* 1.3 67.9 - - - +
350A HIS* 1.3 67.6 + - - +
352A VAL* 3.1 12.4 + - - +
353A LEU* 3.0 26.7 + - + +
422A LEU* 5.2 2.9 - - + -
464A LEU* 3.9 15.3 - - + -
467A VAL* 3.5 36.8 - - + -
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Residues in contact with HIS 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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346A GLU* 2.9 34.4 + - + +
347A VAL 3.5 7.4 - - - +
349A ALA* 1.3 77.7 - - - +
351A ALA* 1.3 60.3 + - - +
352A VAL 3.1 1.4 + - - -
353A LEU* 3.3 17.8 + - - +
354A GLY* 3.8 2.1 + - - -
359A VAL* 5.5 0.4 - - + -
360A VAL* 3.9 23.6 + - + -
362A TYR* 3.6 44.0 - + + +
374A ILE* 3.8 18.4 - - + -
376A ASN* 3.3 28.1 + - - -
462A GLY* 5.9 0.7 - - - -
463A ASP 5.4 3.8 + - - -
464A LEU* 3.5 33.0 + - + +
901A 824 5.4 1.0 - - - -
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Residues in contact with ALA 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 VAL* 2.7 22.4 + - + +
348A TYR* 3.6 11.4 - - + +
349A ALA 3.3 0.8 - - - -
350A HIS* 1.3 71.9 - - - +
352A VAL* 1.3 62.6 + - + +
354A GLY* 4.9 1.9 + - - -
355A GLN* 5.6 0.2 - - - +
362A TYR* 4.0 22.8 - - + +
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Residues in contact with VAL 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 TYR 3.3 13.6 + - - +
349A ALA* 3.3 13.5 - - - +
350A HIS 3.1 0.2 - - - -
351A ALA* 1.3 85.2 - - + +
353A LEU* 1.3 60.1 + - + +
354A GLY 3.4 2.7 - - - -
355A GLN* 3.6 7.3 + - - +
416A TYR* 3.4 9.5 + - - -
420A MET* 3.4 29.2 - - + +
422A LEU* 4.0 26.0 - - + -
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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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349A ALA* 3.0 25.9 + - + +
350A HIS* 3.3 7.6 + - - +
352A VAL* 1.3 87.4 - - + +
354A GLY* 1.3 56.8 + - - +
355A GLN 3.6 0.4 + - - -
356A HIS 4.8 0.5 + - - -
359A VAL* 3.9 24.9 - - + +
360A VAL 4.3 5.7 - - - +
361A ARG* 5.1 0.2 - - - -
416A TYR* 3.3 31.5 - - + -
417A ILE* 3.9 37.2 - - + -
420A MET* 3.8 24.0 - - + -
422A LEU* 4.3 13.9 - - + -
464A LEU* 3.9 19.3 - - + -
467A VAL* 4.9 4.5 - - + -
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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