Contacts of the helix formed by residues 384 - 394 (chain B) in PDB entry 1IYH
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 ILE 384 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224B TYR* 4.0 20.6 - - + -
340B TRP* 4.4 10.1 - - + -
346B VAL* 4.1 22.2 - - + -
351B PHE* 3.9 26.0 - - + -
380B LYS 3.5 8.7 + - - +
381B VAL* 3.2 22.1 + - - +
383B ALA* 1.3 76.6 - - - +
385B PRO* 1.3 64.8 - - + +
386B ALA* 4.1 6.7 - - + +
387B VAL* 3.0 15.6 + - + -
388B ALA* 2.7 32.4 + - - +
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Residues in contact with PRO 385 (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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383B ALA 3.1 9.1 - - - +
384B ILE* 1.3 88.2 - - + +
386B ALA* 1.3 56.3 + - - +
388B ALA* 3.8 5.2 - - + +
389B ASN* 3.0 30.3 + - - +
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Residues in contact with ALA 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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223B ALA* 3.5 30.2 - - - +
224B TYR* 4.0 15.3 - - + +
384B ILE* 3.4 6.9 - - + +
385B PRO* 1.3 79.4 - - - +
387B VAL* 1.3 62.1 + - - +
389B ASN* 3.6 8.2 + - - +
390B TRP* 3.2 21.0 + - - +
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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
----------------------------------------------------------
220B TYR* 3.9 29.4 - - + +
223B ALA* 5.1 2.0 - - + -
224B TYR* 4.5 9.2 - - + +
351B PHE* 4.1 28.0 - - + -
381B VAL* 3.7 19.5 - - + +
384B ILE* 3.0 25.6 + - + +
386B ALA* 1.3 75.3 - - - +
388B ALA* 1.3 67.2 + - - +
390B TRP* 3.0 7.6 + - + +
391B ILE* 2.8 42.6 + - + +
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Residues in contact with ALA 388 (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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382B GLN 3.2 23.7 + - - +
383B ALA* 4.5 4.0 - - - +
384B ILE 2.7 19.7 + - - +
385B PRO* 3.8 6.3 - - + +
387B VAL* 1.3 72.6 - - - +
389B ASN* 1.3 63.2 + - - +
391B ILE* 3.4 7.4 + - - +
392B LYS* 3.0 25.3 + - - +
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Residues in contact with ASN 389 (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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385B PRO 3.0 18.5 + - - +
386B ALA* 3.7 8.9 + - - +
388B ALA* 1.3 77.6 - - - +
390B TRP* 1.3 62.6 + - - +
392B LYS* 3.4 8.3 + - - +
393B ARG* 3.1 57.3 + - - +
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Residues in contact with TRP 390 (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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216B GLU* 2.8 23.7 + - - -
219B ARG* 3.5 33.8 - - + +
220B TYR* 3.7 26.9 - + - -
223B ALA* 3.9 17.5 - - + -
229B TYR* 4.0 13.0 - + - -
231B ASP* 3.7 21.3 - - - -
233B ARG* 3.8 7.6 - - - -
386B ALA 3.2 11.2 + - - +
387B VAL* 3.0 9.2 + - - +
389B ASN* 1.3 79.0 - - - +
391B ILE* 1.3 64.6 + - - +
393B ARG* 3.1 6.9 + - + -
394B ARG* 2.8 61.1 + - + +
395B PRO* 4.6 2.0 - - + -
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Residues in contact with ILE 391 (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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220B TYR* 3.7 25.8 - - + +
354B GLU* 4.2 3.4 - - - +
382B GLN* 4.0 33.2 - - + +
387B VAL* 2.8 38.6 + - + +
388B ALA* 3.7 7.2 - - - +
390B TRP* 1.3 76.5 - - + +
392B LYS* 1.3 62.6 + - - +
394B ARG* 3.6 40.8 + - - +
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Residues in contact with LYS 392 (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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388B ALA 3.0 17.3 + - - +
389B ASN* 3.8 9.0 - - - +
390B TRP 3.1 0.4 - - - -
391B ILE* 1.3 81.2 - - - +
393B ARG* 1.3 64.5 + - + +
394B ARG 3.7 2.5 - - - +
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Residues in contact with ARG 393 (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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389B ASN* 3.1 42.3 + - - +
390B TRP* 3.1 9.9 + - + +
392B LYS* 1.3 85.5 - - + +
394B ARG* 1.3 66.5 + - - +
395B PRO* 3.7 2.4 - - - +
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Residues in contact with ARG 394 (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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212B ARG* 3.6 30.7 - - - +
216B GLU* 2.9 29.8 + - - -
220B TYR* 3.1 28.5 + - - -
233B ARG* 4.9 0.7 - - - +
354B GLU* 5.3 2.2 + - - -
358B THR* 4.9 10.3 + - - +
390B TRP* 2.8 40.7 + - + +
391B ILE* 3.6 41.0 + - - +
392B LYS 4.6 3.3 - - - +
393B ARG* 1.3 76.7 - - - +
395B PRO* 1.3 86.1 + - + +
396B GLN* 3.3 10.4 + - + +
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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