Contacts of the helix formed by residues 411 - 421 (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 GLY 411 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410B ILE* 1.3 81.5 - - - +
412B PHE* 1.3 66.4 + - - +
413B PHE* 3.2 10.4 - - - -
414B ARG* 3.1 18.1 + - - +
415B HIS* 3.7 9.4 + - - -
495B LEU* 4.0 7.7 - - - +
600B TP9 3.5 25.8 - - - -
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Residues in contact with PHE 412 (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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271B TYR* 4.4 10.8 - + - -
275B ILE* 4.0 26.9 - - + -
411B GLY* 1.3 70.7 - - - +
413B PHE* 1.3 61.4 + - - +
414B ARG 3.1 1.4 + - - -
415B HIS* 3.2 15.5 + + - +
416B TYR* 3.7 33.9 - + - -
494B GLY 4.7 0.9 - - - -
495B LEU* 3.6 35.9 - - + +
498B LEU* 3.9 22.2 - - + -
561B TYR* 3.6 40.8 - + + -
562B ASP 5.7 4.3 - - - -
600B TP9 2.9 20.7 + - - +
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Residues in contact with PHE 413 (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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384B VAL* 4.0 19.3 - - + +
388B ILE* 4.3 1.4 - - - +
408B SER* 3.3 22.7 - - - -
409B ASP* 3.3 25.1 - - + -
410B ILE 3.3 22.4 - - - -
411B GLY* 3.8 1.6 - - - -
412B PHE* 1.3 77.9 - - - +
414B ARG* 1.3 62.1 + - - +
416B TYR* 3.1 17.1 + - - +
417B GLY* 3.1 16.1 + - - -
460B ILE* 3.5 32.7 - - + +
461B ALA* 3.6 5.6 - - - -
462B GLY* 3.2 29.2 - - - -
488B VAL* 4.0 11.0 - - + -
561B TYR* 3.9 13.1 + - - +
600B TP9 3.3 25.1 + - - -
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Residues in contact with ARG 414 (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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120A HIS* 4.5 6.5 + - - -
251B TYR* 4.1 14.6 - - - -
408B SER* 3.4 17.7 - - - +
409B ASP 3.2 26.5 - - - +
410B ILE* 3.5 16.0 - - - +
411B GLY 3.1 17.0 + - - +
413B PHE* 1.3 80.1 - - - +
415B HIS* 1.3 79.9 + - - +
417B GLY* 3.1 3.0 + - - +
418B VAL* 2.9 39.1 + - - +
429B PHE* 4.4 1.3 - - + -
431B THR* 3.0 32.0 + - - +
432B SER 2.8 24.4 + - - -
436B SER* 2.9 26.3 + - - -
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Residues in contact with HIS 415 (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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251B TYR* 3.3 26.2 + + - -
269B THR* 2.8 24.3 + - + +
271B TYR* 3.3 40.5 + + + -
275B ILE* 3.7 22.0 - - + -
411B GLY 3.7 17.2 + - - -
412B PHE* 3.2 11.6 + + + +
414B ARG* 1.3 100.2 + - - +
416B TYR* 1.3 63.7 + - - +
418B VAL* 3.5 6.5 + - - +
419B LEU* 3.2 28.9 + - - +
495B LEU* 4.9 6.3 - - + +
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Residues in contact with TYR 416 (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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275B ILE* 3.7 32.5 + - + +
371B PHE* 4.6 3.9 - + - -
384B VAL* 3.6 13.2 - - + -
385B HIS* 3.8 35.9 + - - -
388B ILE* 3.5 14.8 - - + -
412B PHE* 3.7 49.7 - + - -
413B PHE* 3.1 14.5 + - - +
415B HIS* 1.3 74.1 - - - +
417B GLY* 1.3 58.8 - - - +
419B LEU 3.3 0.2 + - - -
420B PHE* 2.8 58.7 + + + +
561B TYR* 4.9 5.8 - + - -
562B ASP 5.5 6.1 + - - -
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Residues in contact with GLY 417 (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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254B LYS* 3.9 2.1 + - - -
388B ILE* 3.4 13.6 - - - +
408B SER* 5.3 2.0 - - - -
413B PHE 3.1 11.4 + - - -
414B ARG* 3.1 6.6 + - - -
416B TYR* 1.3 76.5 - - - +
418B VAL* 1.3 57.5 + - - +
421B ALA* 2.9 34.9 + - - +
429B PHE* 3.6 21.1 - - - -
460B ILE* 5.8 3.6 - - - -
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Residues in contact with VAL 418 (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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251B TYR* 3.7 48.5 - - + -
254B LYS* 2.7 28.7 + - - +
267B ALA* 3.8 24.2 + - + +
268B VAL 4.0 3.1 - - - +
269B THR* 3.9 18.8 - - + -
414B ARG* 2.9 29.7 + - - +
415B HIS* 3.6 11.7 - - - +
416B TYR 3.3 0.6 - - - -
417B GLY* 1.3 74.1 - - - +
419B LEU* 1.3 57.6 + - - +
429B PHE* 3.8 12.8 - - + -
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Residues in contact with LEU 419 (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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254B LYS* 4.4 3.3 + - - -
267B ALA 4.2 9.9 - - - +
269B THR* 3.8 11.4 - - + -
272B MET* 3.6 55.2 - - + -
275B ILE* 4.1 26.2 - - + -
276B LEU* 4.3 15.5 - - + -
368B ILE* 4.5 19.8 - - + +
415B HIS 3.2 18.6 + - - +
416B TYR 3.9 2.9 - - - +
418B VAL* 1.3 78.0 - - - +
420B PHE* 1.3 77.1 + - + +
421B ALA 3.9 0.2 - - - -
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Residues in contact with PHE 420 (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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254B LYS* 4.8 0.2 - - - -
275B ILE* 4.5 1.1 - - + -
276B LEU* 3.7 27.4 - - + -
368B ILE* 3.9 22.4 - - + -
371B PHE* 3.7 30.5 - + + -
372B LEU* 3.7 32.5 - - + +
385B HIS* 4.0 9.6 - - + -
388B ILE* 3.6 15.3 - - + -
392B ASN* 2.8 23.7 + - - -
416B TYR* 2.8 61.8 + + + +
419B LEU* 1.3 89.3 - - + +
421B ALA* 1.3 62.7 + - - +
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Residues in contact with ALA 421 (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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254B LYS* 3.0 24.1 + - - -
388B ILE* 3.6 10.8 - - + +
392B ASN* 3.6 5.2 - - - -
406B ILE* 4.4 14.8 - - + -
417B GLY* 2.9 24.7 + - - +
420B PHE* 1.3 78.1 - - - +
422B ARG* 1.3 62.6 + - - +
423B ALA 3.7 0.9 + - - -
429B PHE* 3.5 27.4 - - + -
460B ILE* 6.6 0.2 - - + -
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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