Contacts of the helix formed by residues 383 - 399 (chain A) in PDB entry 2IHU
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 ARG 383 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378A TYR* 3.5 49.0 - - + +
380A ASP* 3.0 39.0 + - - -
381A GLY 3.0 26.9 + - - -
382A MET* 1.3 79.1 + - - +
384A VAL* 1.3 66.1 + - - +
385A HIS* 3.3 29.8 - - + +
386A GLN* 2.9 26.0 + - - +
387A VAL* 3.2 12.1 + - - +
559A VAL* 4.9 0.2 - - - -
560A ASN* 3.3 27.0 + - - +
561A TYR 4.8 8.8 + - - -
562A ASP* 5.6 7.3 - - - +
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Residues in contact with VAL 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A MET 4.4 0.2 + - - -
383A ARG* 1.3 72.2 - - - +
385A HIS* 1.3 59.6 + - - +
387A VAL* 2.9 10.4 + - + +
388A ILE* 2.9 35.0 + - + +
413A PHE* 3.9 16.8 - - + -
416A TYR* 3.6 35.1 - - + -
460A ILE* 4.4 9.9 - - + -
488A VAL* 4.9 3.4 - - + -
559A VAL* 4.4 17.3 - - + -
560A ASN 5.2 1.0 + - - +
561A TYR* 3.4 39.7 - - + +
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Residues in contact with HIS 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A PHE* 3.0 58.9 - + + +
372A LEU* 3.9 6.8 - - - +
374A ASP* 3.1 28.2 + - + +
378A TYR* 5.1 0.7 - - - -
383A ARG* 3.3 27.3 - - + +
384A VAL* 1.3 77.0 - - - +
386A GLN* 1.3 66.1 + - + +
388A ILE* 3.6 2.3 + - - +
389A ASP* 3.0 28.4 + - - +
416A TYR* 3.7 18.9 - + + -
420A PHE* 3.9 31.4 - - + -
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Residues in contact with GLN 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ASP* 3.1 20.9 + - - +
376A GLU 2.9 27.3 + - - +
378A TYR* 3.6 22.1 - - - -
382A MET* 3.8 22.6 - - + +
383A ARG* 2.9 27.4 + - - +
385A HIS* 1.3 87.7 - - + +
387A VAL* 1.3 58.5 + - - +
389A ASP* 3.6 2.1 + - - +
390A SER* 2.7 34.6 + - - -
536A ARG* 3.5 33.4 + - - +
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Residues in contact with VAL 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A MET* 4.1 10.1 - - + -
383A ARG 3.2 12.7 + - - +
384A VAL* 2.9 15.1 + - + +
386A GLN* 1.3 76.9 - - - +
388A ILE* 1.3 57.4 + - - +
390A SER* 3.3 4.5 + - - -
391A MET* 3.0 35.0 + - + +
460A ILE* 4.3 9.4 - - + -
486A VAL* 3.8 28.3 - - + -
488A VAL* 4.0 14.8 - - + -
539A LEU* 3.7 17.4 - - + +
557A VAL* 3.9 24.9 - - + -
559A VAL* 4.3 1.8 - - + -
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Residues in contact with ILE 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A VAL* 2.9 23.9 + - + +
385A HIS 4.2 3.6 - - - +
387A VAL* 1.3 73.9 - - - +
389A ASP* 1.3 55.4 + - - +
391A MET* 3.1 11.5 + - + +
392A ASN* 2.8 36.3 + - - +
406A ILE* 6.1 0.2 - - + -
413A PHE 4.3 1.6 - - - +
416A TYR* 3.5 20.4 - - + +
417A GLY* 3.5 31.2 - - - +
420A PHE* 3.6 37.7 - - + +
421A ALA* 3.6 13.7 - - + +
460A ILE* 4.2 20.4 - - + -
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Residues in contact with ASP 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A LEU* 2.9 48.5 - - + +
373A ALA* 5.0 1.1 - - - -
385A HIS 3.0 16.0 + - - +
386A GLN 3.7 6.1 - - - +
388A ILE* 1.3 76.5 - - - +
390A SER* 1.3 61.4 + - - +
392A ASN* 3.3 9.2 + - - +
393A THR* 3.0 32.4 + - - -
536A ARG* 2.7 23.0 + - - +
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Residues in contact with SER 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A GLN 2.7 19.4 + - - -
387A VAL 3.5 7.0 - - - -
389A ASP* 1.3 78.3 + - - +
391A MET* 1.3 63.5 + - - +
393A THR* 3.4 3.4 + - - -
394A VAL* 3.2 28.9 + - - +
536A ARG* 4.2 21.0 + - - +
539A LEU* 3.7 26.2 - - - +
540A LEU* 3.8 20.7 - - - +
543A LEU* 3.6 4.9 - - - -
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Residues in contact with MET 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A VAL* 3.0 23.0 + - + +
388A ILE* 3.1 14.1 + - + +
390A SER* 1.3 77.7 - - - +
392A ASN* 1.3 57.0 + - - +
394A VAL 3.4 0.5 + - - -
395A MET* 2.9 33.0 + - - +
406A ILE* 4.3 17.0 - - + -
458A PHE* 3.6 37.6 - - + -
459A LEU 4.1 17.9 - - - +
460A ILE* 4.0 33.2 - - + +
486A VAL* 4.0 16.6 - - + -
543A LEU* 3.8 21.8 - - + -
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Residues in contact with ASN 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A LEU* 4.3 13.5 - - - +
388A ILE* 2.8 25.0 + - - +
389A ASP* 3.3 11.5 + - - +
391A MET* 1.3 73.1 - - - +
393A THR* 1.3 56.7 + - - +
395A MET* 3.4 3.2 + - - +
396A GLU* 3.0 32.8 + - - +
406A ILE* 3.8 6.7 - - - +
420A PHE 2.8 25.3 + - - -
421A ALA* 3.6 4.3 - - - -
422A ARG* 2.8 41.9 + - + +
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Residues in contact with THR 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ASP* 3.0 21.5 + - - -
390A SER* 3.6 9.1 - - - -
391A MET 3.3 0.4 - - - -
392A ASN* 1.3 77.0 - - - +
394A VAL* 1.3 62.2 + - - +
396A GLU* 3.4 10.4 + - - +
397A GLU* 3.1 40.1 + - + +
540A LEU* 4.0 11.6 - - + +
544A ARG* 3.9 12.8 - - - +
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Residues in contact with VAL 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A SER 3.2 17.4 + - - +
391A MET 4.2 2.0 - - - +
393A THR* 1.3 74.6 - - - +
395A MET* 1.3 54.8 + - - +
397A GLU* 3.2 8.7 + - + +
398A ALA* 2.7 34.1 + - + +
458A PHE* 4.1 10.8 - - + -
540A LEU* 3.8 18.6 - - + +
543A LEU* 3.7 46.9 - - + +
544A ARG* 3.8 28.0 - - + +
547A ALA* 4.2 6.3 - - + -
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Residues in contact with MET 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A MET 2.9 20.3 + - - +
392A ASN 3.7 4.0 - - - +
394A VAL* 1.3 76.4 - - - +
396A GLU* 1.3 57.0 + - - +
398A ALA* 4.4 0.9 - - - +
399A ALA* 2.8 44.3 + - + +
403A GLU 5.2 1.1 - - - +
404A GLY* 3.8 24.0 - - - -
405A THR 3.3 27.6 - - - +
406A ILE* 3.8 18.8 - - + -
422A ARG* 4.1 17.7 - - + +
456A PRO* 3.8 16.6 - - - +
458A PHE* 3.6 38.9 - - + -
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Residues in contact with GLU 396 (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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392A ASN 3.0 18.3 + - - +
393A THR* 3.6 9.9 - - - +
394A VAL 3.3 0.2 - - - -
395A MET* 1.3 75.7 - - - +
397A GLU* 1.3 58.6 + - + +
399A ALA* 3.5 7.2 - - - +
422A ARG* 3.8 41.1 + - - +
602A K 2.9 19.1 - - - -
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Residues in contact with GLU 397 (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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393A THR* 3.1 26.3 + - + +
394A VAL* 3.4 11.3 - - + +
396A GLU* 1.3 77.3 - - + +
398A ALA* 1.3 58.8 + - - +
544A ARG* 2.8 54.2 + - - +
602A K 3.0 16.8 - - - -
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Residues in contact with ALA 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A VAL* 2.7 20.9 + - + +
395A MET* 4.0 3.4 - - - +
397A GLU* 1.3 74.6 - - - +
399A ALA* 1.3 61.1 + - - +
400A GLU* 4.0 2.3 + - - +
456A PRO* 3.7 24.0 - - + +
458A PHE* 4.7 1.3 - - + -
547A ALA* 4.1 26.5 - - + +
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Residues in contact with ALA 399 (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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395A MET* 2.8 28.0 + - + +
396A GLU* 3.5 6.5 - - - +
398A ALA* 1.3 73.6 - - - +
400A GLU* 1.3 64.8 + - - +
401A PRO 3.9 0.2 - - - -
403A GLU 3.3 30.7 - - - +
422A ARG* 6.0 0.9 - - - +
456A PRO* 3.7 20.0 - - + -
602A K 2.8 26.3 - - - -
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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