Contacts of the helix formed by residues 344 - 356 (chain A) in PDB entry 2D7I
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 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A LEU* 4.3 1.6 - - - -
343A GLY* 1.3 69.5 - - - -
345A GLU* 1.3 64.0 + - - -
346A GLN* 3.0 18.9 + - - +
347A TYR* 3.1 11.2 + - - +
348A GLU 3.0 17.3 + - - -
386A LEU* 4.3 0.6 - - - +
389A ASN* 4.8 2.0 - - - -
390A LEU* 4.0 23.6 - - - +
393A VAL* 3.6 16.0 - - - +
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Residues in contact with GLU 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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217A LEU* 3.9 4.9 - - + -
218A ILE* 3.1 30.7 - - + -
221A ARG* 2.7 27.9 + - - +
319A GLY 4.3 1.0 - - - +
335A TYR* 3.1 31.1 + - + -
339A LEU* 3.7 15.7 - - + +
343A GLY 3.3 7.6 + - - -
344A GLY* 1.3 73.2 + - - +
346A GLN* 1.3 69.0 + - - +
348A GLU* 3.8 1.3 - - - +
349A ILE* 2.9 28.6 + - - +
702A NGA 2.5 42.6 + - - -
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Residues in contact with GLN 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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294A TYR* 4.5 11.0 - - + +
317A MET* 3.6 17.5 - - - +
318A ALA 3.6 19.1 + - - +
319A GLY* 3.6 15.7 - - - -
335A TYR* 5.4 0.2 - - - -
342A TRP* 5.8 3.6 - - - -
343A GLY* 5.4 0.8 - - - -
344A GLY* 3.0 26.8 + - - +
345A GLU* 1.3 85.6 + - - +
347A TYR* 1.3 92.9 + - + +
349A ILE* 3.5 7.4 - - - +
350A SER* 2.7 36.6 + - - -
702A NGA 4.0 19.3 + - - +
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Residues in contact with TYR 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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287A ALA 4.8 1.6 - - - -
288A PHE* 3.6 23.0 - + + +
292A MET* 2.6 56.0 + - + -
293A TYR 3.3 1.9 - - - -
294A TYR* 2.9 27.2 + - + +
316A VAL* 3.7 26.0 - - + -
344A GLY* 3.1 14.4 + - - +
346A GLN* 1.3 101.8 + - + +
348A GLU* 1.3 65.3 + - - +
350A SER* 4.5 2.0 - - - -
351A PHE* 2.9 48.8 + + + -
390A LEU* 4.5 10.1 - - + -
393A VAL* 4.1 8.5 - - + -
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Residues in contact with GLU 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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335A TYR* 3.3 13.0 - - - +
336A ASP* 2.8 44.9 + - - +
339A LEU* 3.7 7.7 - - + +
344A GLY 3.0 12.8 + - - +
345A GLU* 3.8 5.8 - - - +
347A TYR* 1.3 77.9 - - - +
349A ILE* 1.3 62.6 + - - +
351A PHE* 3.9 3.0 - - - +
352A LYS* 2.8 64.2 + - - +
393A VAL* 3.8 21.9 - - + +
397A TRP* 4.0 15.1 + - + +
423A GLN* 3.8 5.7 - - - +
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Residues in contact with ILE 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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261A ILE* 4.2 18.4 - - + -
317A MET* 4.0 27.6 - - + -
322A PHE* 5.1 3.4 - - + -
329A PHE* 4.2 23.3 - - + -
332A LEU* 4.6 16.2 - - + -
334A GLY* 3.8 22.7 - - - +
335A TYR* 4.1 16.2 - - + +
345A GLU 2.9 21.0 + - - +
346A GLN* 3.5 7.6 - - - +
348A GLU* 1.3 77.4 - - - +
350A SER* 1.3 64.3 + - - +
352A LYS* 3.2 12.1 + - + +
353A VAL* 2.8 30.5 + - - +
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Residues in contact with SER 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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315A PRO 3.6 10.5 - - - -
316A VAL* 3.5 8.2 - - - -
317A MET* 3.0 28.4 + - - +
346A GLN 2.7 22.0 + - - -
347A TYR* 3.9 2.9 - - - -
349A ILE* 1.3 81.4 - - - +
351A PHE* 1.3 66.5 + - - +
353A VAL* 3.5 7.3 + - - +
354A TRP* 3.5 27.9 + - - -
360A MET* 3.1 17.0 - - - +
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Residues in contact with PHE 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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288A PHE* 3.7 28.0 - + - -
292A MET* 4.3 4.0 - - + -
316A VAL* 4.5 7.4 - - + -
347A TYR* 2.9 42.5 + + + +
348A GLU* 3.9 3.1 - - - +
350A SER* 1.3 77.6 - - - +
352A LYS* 1.3 58.0 + - - +
354A TRP* 4.2 0.2 - - - -
355A MET* 3.0 50.5 + - - +
393A VAL* 4.2 10.1 - - + -
397A TRP* 4.3 18.4 - - + -
398A MET* 3.9 18.8 - - + -
435A PHE* 3.8 25.4 - + - -
438A PHE* 3.6 38.6 - + - -
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Residues in contact with LYS 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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332A LEU* 3.6 39.5 + - + +
333A GLY 4.2 3.2 + - - -
334A GLY 2.8 28.9 + - - +
335A TYR* 4.1 1.0 - - - +
336A ASP 4.3 0.4 - - - +
348A GLU* 2.8 56.2 + - + +
349A ILE* 3.2 14.8 + - + +
351A PHE* 1.3 74.7 - - - +
353A VAL* 1.3 60.8 + - - +
356A CYS* 2.9 41.5 + - - +
397A TRP* 3.3 34.7 - - + -
423A GLN* 4.7 0.8 + - - -
426A LEU* 4.2 8.2 - - - +
430A LEU* 5.9 0.7 - - + -
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Residues in contact with VAL 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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259A LYS 3.8 8.5 - - - +
261A ILE* 3.5 36.1 - - + -
328A TRP* 3.9 9.6 - - - +
332A LEU* 4.6 7.8 - - + +
349A ILE* 2.8 22.1 + - + +
350A SER* 3.7 11.2 - - - +
352A LYS* 1.3 74.4 - - - +
354A TRP* 1.3 58.6 + - - +
357A GLY 3.9 0.2 + - - -
358A GLY* 2.6 36.4 + - - +
359A ARG 3.2 32.8 - - - +
360A MET* 4.7 10.5 - - + -
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Residues in contact with TRP 354 (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 GLU* 3.9 28.7 - - + -
314A SER 3.0 23.0 + - - -
315A PRO* 3.6 14.9 + - - +
350A SER 3.5 21.3 + - - +
352A LYS 3.3 0.4 - - - -
353A VAL* 1.3 82.1 - - + +
355A MET* 1.3 63.1 + - - +
356A CYS 3.3 1.4 + - - -
357A GLY* 3.6 7.1 + - - -
358A GLY 3.7 11.7 - - - +
359A ARG* 3.6 38.8 - - + -
360A MET* 3.2 37.1 - - + +
433A LYS* 5.2 0.7 - - - +
437A TRP* 3.5 22.8 - + + -
438A PHE* 3.8 23.6 - + + -
442A ILE* 3.7 36.1 - - + -
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Residues in contact with MET 355 (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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351A PHE* 3.0 29.5 + - - +
354A TRP* 1.3 75.3 - - - +
356A CYS* 1.3 60.5 + - - +
357A GLY 3.6 1.3 + - - -
397A TRP* 3.9 16.8 - - + +
427A ARG* 3.7 24.9 - - - +
431A ASN 4.5 0.3 - - - +
432A CYS* 3.1 6.3 - - + -
433A LYS* 2.8 58.7 + - - +
434A SER 3.8 12.8 - - - +
435A PHE* 3.8 28.3 - - - +
437A TRP* 3.9 9.2 - - + -
438A PHE* 4.0 20.9 - - + -
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Residues in contact with CYS 356 (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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259A LYS* 5.4 1.2 + - - -
328A TRP* 3.5 17.9 - - - -
332A LEU* 4.5 9.9 - - + -
352A LYS* 2.9 22.5 + - - +
353A VAL 4.2 0.7 - - - -
355A MET* 1.3 78.1 - - - +
357A GLY* 1.3 57.1 + - - +
358A GLY 3.5 2.2 - - - -
397A TRP* 3.6 21.3 - - - -
430A LEU* 4.2 20.5 - - + +
431A ASN 4.7 4.3 - - - -
432A CYS* 2.0 48.0 - - - +
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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