Contacts of the helix formed by residues 383 - 399 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378B TYR* 3.4 47.5 - - + +
380B ASP* 3.1 30.5 + - - -
381B GLY 2.9 27.5 + - - -
382B MET* 1.3 78.6 + - - +
384B VAL* 1.3 67.8 + - - +
385B HIS* 3.4 29.4 - - + +
386B GLN* 3.0 27.0 + - - +
387B VAL* 3.2 12.7 + - - +
560B ASN* 3.2 31.8 + - - +
561B TYR* 5.1 0.2 - - - +
562B ASP* 4.1 32.3 + - - +
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Residues in contact with VAL 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B ARG* 1.3 72.4 - - - +
385B HIS* 1.3 64.5 + - - +
387B VAL* 3.0 9.1 + - + +
388B ILE* 2.9 32.5 + - + +
413B PHE* 4.0 20.9 - - + -
416B TYR* 3.6 36.0 - - + -
460B ILE* 4.5 7.6 - - + -
488B VAL* 4.7 4.5 - - + -
559B VAL* 4.5 16.4 - - + -
560B ASN 4.9 1.6 + - - -
561B TYR* 3.4 35.8 - - + +
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Residues in contact with HIS 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B PHE* 3.1 65.4 - + + +
372B LEU* 3.9 6.5 - - - +
374B ASP* 2.9 28.3 + - + +
383B ARG* 3.4 27.6 - - + +
384B VAL* 1.3 77.5 + - - +
386B GLN* 1.3 65.8 - - + +
388B ILE* 3.9 2.1 - - - +
389B ASP* 3.0 29.3 + - - +
416B TYR* 3.8 18.5 - + + -
420B PHE* 4.0 21.5 - - + -
603B GOL 4.1 10.8 - - - -
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Residues in contact with GLN 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B ASP* 3.2 19.1 + - - +
376B GLU 2.8 28.1 + - - +
378B TYR* 3.4 23.0 - - - -
382B MET* 3.8 22.5 - - + +
383B ARG* 3.0 28.8 + - - +
385B HIS* 1.3 85.4 - - + +
387B VAL* 1.3 58.8 + - - +
389B ASP* 3.7 1.7 - - - +
390B SER* 2.8 34.0 + - - -
536B ARG* 3.4 32.8 + - - +
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Residues in contact with VAL 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B MET* 4.2 5.4 - - + -
383B ARG 3.2 11.9 + - - +
384B VAL* 3.0 12.4 + - - +
386B GLN* 1.3 77.2 - - - +
388B ILE* 1.3 57.8 + - - +
390B SER* 3.2 4.9 + - - -
391B MET* 2.9 32.9 + - + +
460B ILE* 4.0 11.7 - - + -
486B VAL* 3.9 28.0 - - + -
488B VAL* 4.0 17.7 - - + -
539B LEU* 3.7 17.2 - - + +
557B VAL* 4.1 24.7 - - + -
559B VAL* 4.2 4.3 - - + -
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Residues in contact with ILE 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B VAL* 2.9 24.8 + - + +
385B HIS 4.0 3.4 - - - +
387B VAL* 1.3 71.7 - - - +
389B ASP* 1.3 62.2 + - - +
391B MET* 3.2 11.6 + - + +
392B ASN* 2.8 29.8 + - - +
406B ILE* 6.0 0.4 - - + -
413B PHE 4.3 1.6 - - - +
416B TYR* 3.5 20.4 - - + +
417B GLY* 3.4 31.9 - - - +
420B PHE* 3.6 39.5 - - + +
421B ALA* 3.6 13.0 - - + +
460B ILE* 4.2 20.4 - - + -
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Residues in contact with ASP 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B LEU* 2.9 47.4 - - + +
373B ALA* 5.0 1.3 - - - -
385B HIS 3.0 16.7 + - - +
386B GLN 3.7 5.4 - - - +
387B VAL 3.4 0.2 - - - -
388B ILE* 1.3 75.9 - - - +
390B SER* 1.3 62.5 + - - +
392B ASN* 3.3 9.7 + - - +
393B THR* 3.1 33.4 + - - -
536B ARG* 2.6 23.1 + - - +
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Residues in contact with SER 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B GLN 2.8 19.9 + - - -
387B VAL 3.5 7.6 - - - -
388B ILE 3.2 0.2 - - - -
389B ASP* 1.3 74.3 - - - +
391B MET* 1.3 64.0 + - - +
393B THR* 3.3 4.1 + - - -
394B VAL* 3.2 21.3 + - - +
536B ARG* 4.1 21.2 + - - +
539B LEU* 3.7 26.6 - - - +
540B LEU* 3.9 21.9 - - - +
543B LEU* 3.5 9.4 - - - +
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Residues in contact with MET 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B VAL* 2.9 29.0 + - + +
388B ILE* 3.5 13.5 - - + +
390B SER* 1.3 75.8 - - - +
392B ASN* 1.3 56.9 + - - +
394B VAL 3.6 0.2 + - - -
395B MET* 2.9 32.0 + - - +
406B ILE* 4.2 20.2 - - + -
458B PHE* 3.6 37.3 - - + -
459B LEU 4.0 18.4 - - - +
460B ILE* 3.9 27.8 - - + +
486B VAL* 4.0 15.7 - - + -
539B LEU* 5.7 0.2 - - + -
543B LEU* 3.8 22.4 - - + -
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Residues in contact with ASN 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B LEU* 4.3 10.5 - - - +
388B ILE* 2.8 25.1 + - - +
389B ASP* 3.4 15.2 + - - +
391B MET* 1.3 72.2 - - - +
393B THR* 1.3 57.9 + - - +
395B MET* 3.3 5.1 + - - +
396B GLU* 2.9 33.6 + - - +
406B ILE* 3.7 6.4 - - - +
420B PHE 2.8 24.7 + - - -
421B ALA* 3.6 4.5 - - - -
422B ARG* 2.8 39.6 + - + +
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Residues in contact with THR 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B ASP* 3.1 20.5 + - - -
390B SER* 3.5 8.8 - - - -
392B ASN* 1.3 78.8 - - - +
394B VAL* 1.3 58.7 + - - +
396B GLU* 3.5 8.7 + - - +
397B GLU* 3.0 46.8 + - - +
540B LEU* 4.1 13.0 - - + +
544B ARG* 3.8 13.0 - - - +
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Residues in contact with VAL 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B SER 3.2 15.8 + - - +
393B THR* 1.3 72.4 - - - +
395B MET* 1.3 55.3 + - - +
397B GLU* 3.2 8.6 + - + +
398B ALA* 2.7 33.9 + - + +
458B PHE* 4.0 13.5 - - + -
540B LEU* 3.9 16.8 - - + +
543B LEU* 3.7 29.8 - - + +
544B ARG* 3.8 46.4 - - + +
547B ALA* 4.2 6.5 - - + -
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Residues in contact with MET 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B MET 2.9 20.8 + - - +
392B ASN* 3.6 6.3 - - - +
394B VAL* 1.3 75.9 - - - +
396B GLU* 1.3 57.1 + - - +
398B ALA* 4.6 0.9 - - - -
399B ALA* 2.8 44.5 + - + +
403B GLU 5.1 1.6 - - - +
404B GLY* 3.8 23.3 - - - -
405B THR 3.3 29.8 - - - +
406B ILE* 4.0 13.2 - - + -
422B ARG* 4.1 17.5 - - + +
456B PRO* 3.6 19.3 - - + +
458B PHE* 3.6 36.4 - - + -
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Residues in contact with GLU 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B ASN 2.9 17.9 + - - +
393B THR* 3.7 7.6 - - - +
395B MET* 1.3 75.5 - - - +
397B GLU* 1.3 57.8 + - + +
399B ALA* 3.4 7.8 - - - +
422B ARG* 3.8 41.1 + - - +
602B K 2.9 19.9 - - - -
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Residues in contact with GLU 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B THR* 3.0 25.9 + - + +
394B VAL* 3.2 12.2 + - + +
396B GLU* 1.3 77.1 - - + +
398B ALA* 1.3 59.3 + - - +
544B ARG* 2.7 54.4 + - - +
602B K 3.0 17.2 - - - -
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Residues in contact with ALA 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B VAL* 2.7 21.1 + - + +
395B MET* 4.0 2.2 - - - +
397B GLU* 1.3 74.3 - - - +
399B ALA* 1.3 60.1 + - - +
400B GLU* 4.0 3.6 + - - +
456B PRO* 3.7 23.6 - - + +
458B PHE* 4.9 0.7 - - + -
547B ALA* 4.1 26.7 - - + +
602B K 4.7 0.2 - - - -
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Residues in contact with ALA 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395B MET* 2.8 26.7 + - + +
396B GLU* 3.4 5.8 - - - +
398B ALA* 1.3 73.6 - - - +
400B GLU* 1.3 63.2 + - - +
403B GLU* 3.5 30.7 - - + +
422B ARG* 6.0 1.3 - - - +
456B PRO* 3.6 21.1 - - + -
602B 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