Contacts of the helix formed by residues 411 - 421 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410D ILE* 1.3 78.9 - - - +
412D PHE* 1.3 66.9 + - - +
413D PHE* 3.2 12.3 - - - -
414D ARG* 3.0 18.2 + - - +
415D HIS* 3.8 8.0 + - - -
495D LEU* 3.7 7.8 - - - +
600D TP9 3.5 24.9 - - - -
603D TAR 5.0 0.2 + - - -
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Residues in contact with PHE 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D TYR* 4.2 15.3 - + + -
274D GLY 6.4 0.4 - - - -
275D ILE* 4.1 20.9 - - + -
411D GLY* 1.3 69.7 - - - +
413D PHE* 1.3 61.4 + - - +
414D ARG 3.0 1.4 + - - -
415D HIS* 3.2 16.7 + + - +
416D TYR* 3.7 34.2 - + - -
494D GLY 4.7 0.7 - - - -
495D LEU* 3.6 36.1 - - + +
498D LEU* 3.9 22.7 - - + -
561D TYR* 3.6 42.4 - + + -
600D TP9 2.9 21.2 + - - +
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Residues in contact with PHE 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384D VAL* 4.0 15.0 - - + +
388D ILE* 4.2 2.1 - - - +
408D SER* 3.3 21.8 - - - -
409D ASP* 3.4 24.9 - - + -
410D ILE 3.5 21.1 - - - -
411D GLY* 3.8 1.1 - - - -
412D PHE* 1.3 78.3 - - - +
414D ARG* 1.3 62.8 + - - +
415D HIS 3.2 0.2 - - - -
416D TYR* 3.1 25.8 + - - +
417D GLY* 3.3 8.1 + - - -
460D ILE* 3.4 32.7 - - + +
461D ALA* 3.5 5.2 - - - -
462D GLY* 3.2 29.6 - - - -
488D VAL* 4.0 12.6 - - + -
561D TYR* 3.8 12.9 + - - +
600D TP9 3.3 27.5 + - - -
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Residues in contact with ARG 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C HIS* 4.6 1.6 - - - -
251D TYR* 3.9 15.1 - - - -
408D SER* 3.4 17.2 + - - +
409D ASP 3.3 27.1 - - - +
410D ILE* 3.5 8.2 - - - +
411D GLY 3.0 19.6 + - - +
413D PHE* 1.3 81.1 - - - +
415D HIS* 1.3 72.6 + - - +
417D GLY* 3.0 4.0 + - - -
418D VAL* 2.8 41.1 + - - +
429D PHE* 4.4 0.7 - - + -
431D THR* 3.1 29.5 + - + +
432D SER 2.8 22.4 + - - -
436D SER* 2.9 27.9 + - - -
603D TAR 3.2 26.3 + - - -
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Residues in contact with HIS 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D TYR* 3.5 18.4 + - - -
269D THR* 3.1 19.9 + - + +
271D TYR* 3.1 45.5 - + + -
275D ILE* 3.9 19.3 - - + -
411D GLY 3.8 10.1 + - - -
412D PHE* 3.2 18.5 + + - +
413D PHE 3.2 0.4 - - - -
414D ARG* 1.3 91.7 + - - +
416D TYR* 1.3 60.2 + - - +
418D VAL* 3.5 5.2 + - - +
419D LEU* 3.1 32.9 + - - +
495D LEU* 4.4 3.9 - - + +
603D TAR 3.4 23.1 + - - -
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Residues in contact with TYR 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D ILE* 3.6 31.0 + - + +
371D PHE* 4.1 3.6 - + - -
384D VAL* 3.6 21.1 - - + -
385D HIS* 3.7 38.0 + - + -
388D ILE* 3.4 16.1 - - + +
412D PHE* 3.7 51.4 - + - -
413D PHE* 3.1 9.3 + - - +
415D HIS* 1.3 76.1 - - - +
417D GLY* 1.3 59.0 + - - +
419D LEU* 5.1 0.7 - - - -
420D PHE* 2.8 58.9 + + + +
561D TYR* 5.0 4.3 - + - -
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Residues in contact with GLY 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254D LYS* 3.9 2.4 - - - -
388D ILE* 3.4 12.7 - - - +
408D SER* 5.2 2.5 - - - -
413D PHE 3.3 5.2 + - - -
414D ARG* 3.0 9.3 + - - -
416D TYR* 1.3 77.7 - - - +
418D VAL* 1.3 64.0 + - - +
421D ALA* 3.0 33.8 + - - +
429D PHE* 3.5 20.1 - - - -
460D ILE* 5.7 2.5 - - - -
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Residues in contact with VAL 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D TYR* 3.6 50.5 - - + -
254D LYS* 3.2 25.8 + - - +
267D ALA* 3.6 22.8 + - + +
268D VAL 4.1 5.4 - - - +
269D THR* 4.1 9.0 - - + -
414D ARG* 2.8 32.4 + - - +
415D HIS* 3.7 10.5 - - - +
416D TYR 3.3 0.2 - - - -
417D GLY* 1.3 76.2 - - - +
419D LEU* 1.3 59.1 + - - +
429D PHE* 3.7 17.5 - - + -
431D THR* 4.6 0.2 - - + -
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Residues in contact with LEU 419 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254D LYS* 4.5 4.3 + - - -
267D ALA 3.6 24.6 + - - +
269D THR* 3.7 12.3 - - + -
272D MET* 3.6 52.3 - - + +
275D ILE* 4.0 25.4 - - + -
276D LEU* 5.1 5.4 - - + -
368D ILE* 5.2 9.8 - - + +
415D HIS 3.1 21.0 + - - +
416D TYR 4.0 2.5 - - - +
418D VAL* 1.3 79.2 - - - +
420D PHE* 1.3 80.5 + - + +
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Residues in contact with PHE 420 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D ILE* 4.1 8.7 - - + -
276D LEU* 3.6 29.8 - - + -
368D ILE* 3.7 33.2 - - + -
371D PHE* 3.7 18.8 - + - -
372D LEU* 3.5 30.3 - - + +
385D HIS* 4.5 7.6 - - + -
388D ILE* 3.7 8.1 - - + -
392D ASN* 2.9 18.9 + - - -
416D TYR* 2.8 59.2 + + + +
419D LEU* 1.3 93.2 - - + +
421D ALA* 1.3 64.0 + - - +
422D ARG* 3.5 0.3 + - - -
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Residues in contact with ALA 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254D LYS* 3.0 24.1 + - - -
388D ILE* 3.7 11.4 - - + +
392D ASN* 3.5 7.6 - - - +
406D ILE* 4.2 13.9 - - + -
417D GLY* 3.0 26.1 + - - +
420D PHE* 1.3 78.6 - - - +
422D ARG* 1.3 63.4 + - - +
423D ALA 3.6 0.7 + - - -
429D PHE* 3.6 25.8 - - + -
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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