Contacts of the helix formed by residues 343 - 363 (chain A) in PDB entry 5IG3
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 HIS 343 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A GLY 3.6 0.8 - - - -
342A PRO* 1.3 99.8 - - + +
344A MET* 1.3 64.7 + - - +
345A VAL* 3.3 2.9 - - - +
346A ARG* 4.8 6.1 - - + +
347A LYS* 3.2 31.9 + - + +
421A LEU* 3.6 29.8 - - + +
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Residues in contact with MET 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A PHE* 3.1 48.9 - - + +
340A GLN* 5.7 0.9 - - - -
341A GLY 4.5 7.4 - - - +
342A PRO 3.5 5.8 + - - +
343A HIS* 1.3 74.7 - - - +
345A VAL* 1.3 67.9 + - + +
347A LYS* 3.3 6.4 + - - +
348A GLN* 2.9 57.5 + - - +
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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
----------------------------------------------------------
343A HIS* 3.3 1.0 - - - +
344A MET* 1.3 78.7 - - + +
346A ARG* 1.3 58.6 + - - +
348A GLN* 3.1 13.2 + - + +
349A GLU* 2.9 32.7 + - - +
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Residues in contact with ARG 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A HIS* 3.9 6.9 + - + +
344A MET 3.4 0.4 - - - -
345A VAL* 1.3 76.2 - - - +
347A LYS* 1.3 66.9 + - - +
349A GLU* 3.0 19.3 + - + +
350A ILE* 2.9 28.3 + - + +
421A LEU* 3.6 37.9 - - + -
423A GLY 3.8 5.1 + - - -
424A ASP* 2.3 60.0 + - - +
426A SER 5.4 0.2 - - - -
457A ARG* 2.9 29.5 - - - +
462A TRP* 4.0 16.1 - - + -
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Residues in contact with LYS 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A LEU* 2.7 47.2 + - + +
339A PHE* 4.4 15.0 - - + +
340A GLN 3.9 11.3 + - - -
341A GLY* 4.5 8.0 - - - -
342A PRO* 5.2 3.6 - - - +
343A HIS* 3.2 28.1 + - - +
344A MET* 3.3 4.8 + - - +
346A ARG* 1.3 78.2 - - - +
348A GLN* 1.3 56.7 + - - +
350A ILE 3.2 1.7 + - - -
351A ILE* 2.9 34.7 + - - +
419A ILE* 3.4 39.9 - - + +
421A LEU* 4.8 8.7 - - + +
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Residues in contact with GLN 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A PHE* 3.5 31.1 - - + -
344A MET* 2.9 52.1 + - - +
345A VAL* 3.1 11.7 + - - +
347A LYS* 1.3 74.9 - - - +
349A GLU* 1.3 56.8 + - - +
351A ILE* 3.5 3.2 + - - +
352A LYS* 2.9 30.0 + - - +
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Residues in contact with GLU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A VAL* 2.9 18.5 + - - +
346A ARG* 3.0 27.8 + - + +
348A GLN* 1.3 77.2 - - - +
350A ILE* 1.3 59.0 + - + +
352A LYS* 3.1 13.0 + - + +
353A VAL* 3.0 33.1 + - + +
457A ARG* 4.4 9.9 + - - -
462A TRP* 3.2 34.6 + - + +
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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
----------------------------------------------------------
346A ARG* 2.9 22.6 + - + +
347A LYS 3.8 5.6 - - - +
349A GLU* 1.3 75.7 - - - +
351A ILE* 1.3 54.6 + - - +
353A VAL* 3.2 4.1 - - + +
354A THR* 2.7 38.0 + - - +
419A ILE* 4.1 11.4 - - + -
421A LEU* 4.7 3.4 - - + -
427A ALA* 3.6 32.3 - - + -
429A ILE* 4.0 21.5 - - + +
455A TRP* 3.8 27.1 - - + -
462A TRP* 3.8 39.5 - - + +
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Residues in contact with ILE 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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333A SER* 5.1 0.4 - - - +
335A LEU* 3.6 28.0 - - + -
338A LEU* 3.6 24.2 - - + -
339A PHE* 3.4 32.1 - - + -
347A LYS 2.9 16.5 + - - +
348A GLN* 3.9 4.7 - - - +
350A ILE* 1.3 75.5 - - - +
352A LYS* 1.3 57.9 + - - +
354A THR* 3.7 6.4 - - - -
355A GLU* 2.9 52.5 + - + +
414A ILE* 6.1 1.1 - - + -
417A PRO* 5.0 1.3 - - + -
419A ILE* 3.6 10.8 - - + -
429A ILE* 4.3 9.6 - - + -
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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
----------------------------------------------------------
348A GLN 2.9 19.4 + - - +
349A GLU* 3.1 12.5 + - + +
351A ILE* 1.3 78.9 - - - +
353A VAL* 1.3 62.8 + - + +
355A GLU* 3.3 8.3 + - - +
356A GLN* 2.9 59.0 + - + +
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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
----------------------------------------------------------
349A GLU* 3.0 17.5 + - + +
350A ILE* 3.2 22.4 - - + +
352A LYS* 1.3 79.6 - - + +
354A THR* 1.3 57.8 + - - +
356A GLN* 3.4 19.2 + - - +
357A LEU* 2.9 21.8 + - - +
372A MET* 4.1 4.8 - - + +
455A TRP* 3.4 43.6 - - + -
461A LYS* 6.1 3.1 - - + +
462A TRP* 4.3 26.5 - - + +
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Residues in contact with THR 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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350A ILE 2.7 22.7 + - - -
351A ILE* 3.7 7.4 - - - -
353A VAL* 1.3 78.1 - - - +
355A GLU* 1.3 57.5 + - - +
357A LEU* 3.0 5.9 + - + +
358A ILE* 2.9 32.9 + - + +
414A ILE* 4.9 6.7 - - + -
429A ILE* 3.6 15.3 - - + +
431A TYR* 3.9 36.6 - - + +
453A ARG* 4.9 4.0 - - + -
455A TRP* 3.1 26.2 + - + -
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Residues in contact with GLU 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A HIS* 3.5 37.0 + - + +
333A SER* 3.0 24.3 + - - -
335A LEU* 4.8 2.9 - - - +
351A ILE* 2.9 37.4 + - + +
352A LYS* 3.8 6.4 - - - +
354A THR* 1.3 76.0 - - - +
356A GLN* 1.3 58.2 + - + +
358A ILE* 3.9 5.3 - - - +
359A GLU* 2.9 29.9 + - - +
414A ILE* 3.9 15.0 - - + -
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Residues in contact with GLN 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A LYS* 2.9 55.9 + - + +
353A VAL* 3.6 18.6 - - - +
355A GLU* 1.3 75.3 - - + +
357A LEU* 1.3 59.3 + - - +
359A GLU* 3.4 17.2 + - - +
360A ALA* 2.9 28.1 + - - +
372A MET* 3.6 16.3 - - - +
461A LYS* 5.5 4.3 + - - -
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Residues in contact with LEU 357 (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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353A VAL 2.9 14.9 + - - +
354A THR* 3.0 9.8 + - + +
356A GLN* 1.3 76.2 - - - +
358A ILE* 1.3 64.0 + - + +
360A ALA* 3.0 5.4 + - - +
361A ILE* 2.9 28.8 + - + +
369A TYR* 3.5 33.9 - - + -
372A MET* 3.6 30.0 - - + -
373A CYS* 4.4 6.3 - - - -
431A TYR* 5.6 0.4 - - - +
453A ARG* 3.5 45.8 - - + +
455A TRP* 4.2 4.0 - - + -
464A ILE* 3.9 19.1 - - + -
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Residues in contact with ILE 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A HIS* 4.9 9.4 - - + +
354A THR* 2.9 19.4 + - + +
355A GLU* 4.1 4.9 - - - +
357A LEU* 1.3 76.7 - - + +
359A GLU* 1.3 57.7 + - - +
361A ILE* 3.2 10.8 + - + +
362A SER* 2.9 32.0 + - - +
412A THR* 3.7 31.6 - - + +
414A ILE* 3.6 34.1 - - + -
431A TYR* 3.7 30.3 - - + +
433A ARG* 4.4 16.8 - - - +
451A GLU* 4.6 3.8 - - - +
453A ARG* 5.5 1.3 - - - +
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Residues in contact with GLU 359 (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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329A HIS* 5.7 5.4 - - + +
331A HIS* 4.0 18.7 - - + -
355A GLU 2.9 19.3 + - - +
356A GLN* 3.7 18.6 - - - +
357A LEU 3.2 0.2 - - - -
358A ILE* 1.3 78.1 - - - +
360A ALA* 1.3 59.7 + - - +
362A SER* 3.5 4.8 + - - -
363A ASN* 3.0 48.5 + - - +
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Residues in contact with ALA 360 (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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356A GLN 2.9 14.4 + - - +
357A LEU 3.0 8.3 + - - +
359A GLU* 1.3 77.1 - - - +
361A ILE* 1.3 60.6 + - - +
363A ASN* 3.7 0.6 + - - +
364A GLY 3.2 2.3 + - - -
365A ASP* 2.9 47.9 + - - +
368A SER* 4.0 8.7 - - - -
369A TYR* 4.0 10.1 - - + +
372A MET* 3.7 18.4 - - + -
399A PHE* 3.6 4.5 - - - -
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Residues in contact with ILE 361 (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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357A LEU* 2.9 20.5 + - + +
358A ILE* 3.7 9.9 - - - +
360A ALA* 1.3 75.7 - - - +
362A SER* 1.3 65.8 + - - +
364A GLY* 3.2 10.2 + - - -
369A TYR* 3.7 32.8 - - + +
399A PHE* 4.1 9.8 - - + -
403A TRP* 3.4 46.8 - - + -
433A ARG* 3.8 26.7 - - - +
453A ARG* 3.9 23.3 - - - +
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Residues in contact with SER 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A HIS* 3.7 40.8 + - - -
330A HIS 5.4 1.6 + - - -
331A HIS* 5.9 0.7 + - - -
358A ILE* 2.9 22.0 + - - +
359A GLU* 4.0 6.7 - - - -
360A ALA 3.4 0.2 - - - -
361A ILE* 1.3 77.1 - - - +
363A ASN* 1.3 60.1 + - - +
364A GLY 3.8 0.2 + - - -
403A TRP* 4.5 13.9 - - - +
406A ASN* 4.3 5.2 - - - +
410A VAL* 4.9 9.2 + - - +
412A THR* 3.7 19.8 + - - -
433A ARG* 4.7 4.6 + - - +
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Residues in contact with ASN 363 (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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329A HIS* 3.4 34.9 + - - +
359A GLU* 3.0 38.6 + - - +
360A ALA* 4.4 1.0 - - - +
361A ILE 3.2 0.6 - - - -
362A SER* 1.3 78.5 - - - +
364A GLY* 1.3 62.9 + - - +
365A ASP* 3.3 12.0 + - + +
403A TRP 4.3 5.8 - - - +
404A SER* 5.3 1.7 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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