Contacts of the helix formed by residues 338 - 353 (chain A) in PDB entry 2IAG
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 THR 338 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A GLU* 3.3 17.3 - - - +
313A LEU* 3.8 19.3 - - + -
316A ILE* 3.8 7.4 - - + -
334A VAL* 2.8 34.9 + - - +
336A ASP 3.8 1.6 + - - -
337A SER* 1.3 79.5 - - - +
339A PRO* 1.4 59.8 - - - +
340A VAL 3.3 2.9 - - - -
341A LEU* 3.3 7.7 + - + -
342A ASP* 2.9 31.5 + - - -
452A LYS* 2.7 34.2 + - - +
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Residues in contact with PRO 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLU* 3.3 10.8 - - + +
337A SER* 3.3 10.8 - - - +
338A THR* 1.4 90.0 - - - +
340A VAL* 1.3 61.8 + - + +
342A ASP* 3.3 12.3 + - + +
343A SER 3.1 17.3 + - - -
410A LEU* 3.5 14.4 - - + +
414A GLY 3.7 23.3 - - - +
415A SER* 5.4 0.4 - - - -
416A GLU* 5.3 7.7 - - + +
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Residues in contact with VAL 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ALA* 4.0 40.4 - - + +
309A VAL* 4.0 12.3 - - + -
312A GLU* 2.8 29.4 + - + +
339A PRO* 1.3 71.9 - - + +
341A LEU* 1.3 65.1 + - - +
343A SER* 3.2 5.2 + - - -
344A VAL* 2.9 20.4 + - - +
406A TYR* 4.1 16.8 - - + -
410A LEU* 4.2 19.5 - - + -
414A GLY* 5.8 2.0 - - - +
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Residues in contact with LEU 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LEU* 4.6 18.2 - - + -
309A VAL* 4.5 13.2 - - + +
312A GLU* 2.9 18.6 + - - +
313A LEU* 4.2 23.1 - - + -
334A VAL* 5.0 0.9 - - + +
338A THR* 3.7 10.1 - - + +
340A VAL* 1.3 78.4 - - - +
342A ASP* 1.3 56.3 + - - +
344A VAL* 3.3 11.8 + - + -
345A LEU* 3.0 29.7 + - + +
451A ILE* 6.1 1.1 - - + -
452A LYS* 3.8 45.1 - - + +
455A VAL* 4.3 25.6 - - + -
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Residues in contact with ASP 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ASP 5.7 1.4 - - - +
338A THR 2.9 23.5 + - - +
339A PRO* 3.5 12.7 - - + +
340A VAL 3.2 0.4 - - - -
341A LEU* 1.3 75.0 - - - +
343A SER* 1.3 57.9 + - - +
345A LEU* 3.5 6.0 + - - +
346A SER* 3.0 33.9 + - - +
416A GLU* 5.1 13.9 - - + +
448A VAL* 4.9 3.3 - - - +
452A LYS* 2.6 36.0 + - - +
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Residues in contact with SER 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A PRO 3.1 4.9 + - - -
340A VAL 3.5 8.1 - - - -
342A ASP* 1.3 76.9 - - - +
344A VAL* 1.3 58.3 + - - +
346A SER* 3.7 1.6 - - - -
347A GLU* 2.9 31.4 + - - +
406A TYR 2.5 24.9 + - - -
407A ASN* 3.6 3.1 - - - -
409A PHE* 3.3 36.3 + - - -
410A LEU* 3.6 24.0 - - - -
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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
----------------------------------------------------------
295A LEU* 3.7 27.8 - - + -
299A LEU* 3.7 22.2 - - + -
309A VAL* 3.6 22.2 - - + -
340A VAL 2.9 17.0 + - - +
341A LEU* 3.3 11.4 + - + +
343A SER* 1.3 75.5 - - - +
345A LEU* 1.3 56.9 + - - +
347A GLU* 3.4 3.9 + - - +
348A SER* 2.9 31.0 + - - -
404A PHE* 4.0 9.8 - - + -
406A TYR* 3.9 32.5 - - + +
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Residues in contact with LEU 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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291A ALA* 5.2 3.1 - - + +
295A LEU* 3.8 24.7 - - + +
341A LEU* 3.0 18.8 + - + +
342A ASP* 3.8 5.4 - - - +
344A VAL* 1.3 73.6 - - - +
346A SER* 1.3 66.1 + - - +
348A SER* 3.4 3.5 + - - -
349A LEU* 2.9 55.8 + - + +
434A TRP* 5.3 0.4 - - + -
448A VAL* 3.8 44.6 - - + +
451A ILE* 4.0 28.9 - - + -
452A LYS* 5.2 6.5 - - + -
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Residues in contact with SER 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ASP* 3.0 21.5 + - - +
343A SER* 3.7 1.5 - - - -
345A LEU* 1.3 75.3 - - - +
347A GLU* 1.3 56.1 + - - +
349A LEU* 3.8 5.1 - - - -
350A ARG* 2.9 24.8 + - - +
409A PHE* 3.5 30.5 - - - +
431A ASN* 3.0 23.2 + - - +
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Residues in contact with GLU 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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343A SER 2.9 18.8 + - - +
344A VAL* 3.8 4.0 - - - +
346A SER* 1.3 73.2 - - - +
348A SER* 1.3 66.1 + - - +
350A ARG* 2.8 42.7 + - - +
351A LEU* 3.2 24.0 + - + +
403A VAL 3.1 1.7 - - - +
404A PHE* 3.3 25.4 - - + -
405A LYS 2.8 40.0 + - - +
406A TYR 4.8 0.7 - - - +
408A ARG* 2.8 28.2 + - - -
409A PHE* 3.5 8.8 - - + -
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Residues in contact with SER 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ALA 4.2 2.3 + - - -
294A TRP* 3.6 3.5 - - - +
295A LEU* 3.1 43.0 + - - +
298A PHE* 3.4 20.3 - - - -
344A VAL 2.9 18.6 + - - -
345A LEU* 3.6 7.4 - - - -
347A GLU* 1.3 78.0 - - - +
349A LEU* 1.3 56.2 - - - -
351A LEU* 3.4 1.7 + - - +
352A THR* 2.7 35.8 + - - +
404A PHE* 4.0 1.5 - - - -
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Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ALA* 4.0 27.6 - - + -
345A LEU* 2.9 41.3 + - + +
346A SER* 3.9 6.5 - - - +
348A SER* 1.3 74.0 - - - +
350A ARG* 1.3 67.1 + - - +
351A LEU 3.1 2.0 - - - -
352A THR* 4.1 2.5 - - - -
353A ALA* 3.0 28.1 + - + +
392A GLN* 3.6 3.4 + - - -
431A ASN* 4.5 1.1 - - - -
433A PRO* 3.9 21.7 - - + +
434A TRP* 3.8 29.4 - - + +
485A LEU* 4.1 22.4 - - + -
600A HEM 4.1 9.6 - - + -
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Residues in contact with ARG 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 SER 2.9 15.3 + - - +
347A GLU* 2.8 48.5 + - - +
349A LEU* 1.3 77.1 - - - +
351A LEU* 1.3 70.7 + - - +
388A PHE* 4.5 3.8 - - - -
392A GLN* 2.8 68.6 + - + +
393A ARG* 4.4 4.0 - - - +
398A TYR* 3.7 26.9 - - + -
401A PRO* 2.8 38.9 + - - +
403A VAL 3.0 12.3 + - - -
408A ARG* 3.3 13.5 - - - +
409A PHE* 4.0 5.4 - - + -
431A ASN* 3.4 22.6 + - - +
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Residues in contact with LEU 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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298A PHE* 3.8 17.5 - - + -
347A GLU* 3.2 15.6 + - - +
348A SER 3.7 4.7 - - - +
349A LEU 3.1 0.8 - - - -
350A ARG* 1.3 94.0 - - - +
352A THR* 1.3 61.5 - - + +
353A ALA 4.0 0.2 - - - -
388A PHE* 3.4 8.9 - - - -
393A ARG* 2.8 42.5 + - - +
401A PRO 3.3 26.9 - - - +
402A GLU 3.9 12.8 - - - +
404A PHE* 3.8 39.9 - - + +
476A PHE* 3.4 10.7 - - - -
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Residues in contact with THR 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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291A ALA* 5.3 0.5 - - - -
294A TRP* 3.4 51.4 - - + +
298A PHE* 4.0 13.5 - - + -
348A SER 2.7 23.2 + - - +
349A LEU* 4.1 0.7 - - - +
351A LEU* 1.3 85.1 - - + +
353A ALA* 1.3 60.5 + - - +
354A ALA 3.9 0.2 - - - -
388A PHE* 4.6 1.1 - - - -
476A PHE* 4.0 14.6 - - + -
485A LEU* 3.4 15.8 - - - +
486A MET* 2.8 36.8 + - - +
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Residues in contact with ALA 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 LEU* 3.0 19.1 + - + +
352A THR* 1.3 78.2 + - - +
354A ALA* 1.3 57.5 + - - +
355A PRO* 3.4 9.8 - - + +
388A PHE* 3.5 6.3 + - - +
392A GLN* 3.1 22.2 + - - -
433A PRO* 3.6 30.3 - - + +
484A GLY 3.9 3.8 - - - -
485A LEU* 3.9 22.0 - - + -
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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