Contacts of the helix formed by residues 472 - 480 (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 ASP 472 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54B THR* 3.4 6.8 - - - -
55B ARG* 2.8 21.6 + - - +
56B HIS* 3.5 14.7 + - - +
59B THR* 2.7 33.7 + - + +
442B ILE* 3.8 24.3 - - + +
469B ASN* 3.8 10.6 + - - +
470B SER 3.1 1.4 + - - -
471B SER* 1.3 74.2 - - - +
473B LEU* 1.3 63.4 + - - +
474B GLU 3.1 1.1 - - - -
475B THR* 2.6 37.3 + - - +
476B ILE* 3.2 15.8 + - - +
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Residues in contact with LEU 473 (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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442B ILE* 3.9 9.2 - - + +
466B PHE* 3.9 35.2 - - + -
470B SER 3.0 19.7 + - - +
472B ASP* 1.3 77.5 - - - +
474B GLU* 1.3 56.8 + - - +
476B ILE* 3.3 17.5 + - + +
477B ALA 3.0 22.3 + - - -
485B THR* 5.3 4.3 - - - +
519B PHE 5.6 0.2 - - - +
522B LEU* 4.3 9.4 - - + -
523B ALA* 4.0 24.2 - - + -
526B ASN* 3.7 24.0 - - + +
528B VAL* 3.6 26.7 - - + +
554B LEU* 4.1 11.9 - - + -
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Residues in contact with GLU 474 (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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514A PHE* 3.8 0.5 - - - -
515A GLY* 2.8 31.7 + - - +
516A GLY 4.3 9.6 - - - +
517A VAL* 3.6 25.4 - - + -
55B ARG* 3.0 25.0 + - + +
471B SER 3.3 9.4 + - - +
472B ASP 3.1 0.8 - - - -
473B LEU* 1.3 75.7 - - - +
475B THR* 1.3 55.0 + - - +
477B ALA* 3.3 2.4 + - + +
478B ARG* 2.8 67.7 + - - +
526B ASN* 3.4 28.3 + - - +
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Residues in contact with THR 475 (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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52B VAL* 5.1 1.6 - - + -
53B LEU 3.6 18.8 - - - +
54B THR* 3.8 7.6 - - + -
55B ARG* 3.8 6.1 + - - +
446B ILE* 4.3 13.2 - - + -
472B ASP* 2.6 36.2 + - - +
474B GLU* 1.3 75.7 + - - +
476B ILE* 1.3 58.9 + - - +
478B ARG* 3.3 19.1 + - - +
479B LEU* 2.9 58.4 + - + +
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Residues in contact with ILE 476 (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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442B ILE* 3.9 35.2 - - + +
445B ALA* 5.4 0.9 - - + -
446B ILE* 3.8 20.6 - - + -
459B LEU* 5.8 0.2 - - + -
472B ASP 3.2 7.5 + - - +
473B LEU* 3.5 17.9 - - + +
475B THR* 1.3 76.6 - - - +
477B ALA* 1.3 56.9 + - - +
479B LEU 3.6 0.3 + - - -
480B ASN* 3.0 23.4 + - - -
481B LEU* 3.1 28.7 + - - +
483B ILE* 4.1 26.0 - - + -
485B THR* 5.0 5.2 - - - +
528B VAL* 4.8 3.6 - - + -
552B PRO* 3.3 30.1 - - + +
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Residues in contact with ALA 477 (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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473B LEU 3.0 10.8 + - - +
474B GLU* 3.5 6.5 - - + +
476B ILE* 1.3 75.6 - - - +
478B ARG* 1.3 62.5 + - - +
480B ASN* 3.0 18.5 + - - +
526B ASN 3.5 25.4 - - - +
527B GLY* 3.9 10.5 - - - +
528B VAL* 3.9 9.9 - - + -
552B PRO* 4.2 11.0 - - - +
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Residues in contact with ARG 478 (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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513A LYS 3.7 17.8 + - - -
514A PHE* 3.8 19.6 - - - +
515A GLY* 4.0 10.8 - - - +
53B LEU* 2.7 41.8 + - - +
55B ARG* 3.9 4.0 - - - +
474B GLU* 2.8 54.6 + - - +
475B THR* 3.3 23.0 + - - +
477B ALA* 1.3 73.1 - - - +
479B LEU* 1.3 71.1 + - + +
480B ASN* 3.2 2.1 + - - +
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Residues in contact with LEU 479 (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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52B VAL* 3.8 30.5 - - + -
446B ILE* 4.5 7.0 - - + -
450B MET* 4.7 6.1 - - - -
475B THR* 2.9 37.3 + - + +
478B ARG* 1.3 90.5 - - + +
480B ASN* 1.3 69.2 + - - +
481B LEU* 3.4 35.8 + - + +
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Residues in contact with ASN 480 (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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476B ILE 3.0 9.5 + - - -
477B ALA 3.0 12.9 + - - +
478B ARG 3.2 1.9 - - - +
479B LEU* 1.3 79.9 - - - +
481B LEU* 1.3 61.3 + - - +
482B PRO* 3.5 8.7 - - - +
550B GLY 3.6 17.4 + - - -
551B ARG* 3.7 15.9 - - - +
552B PRO* 3.4 19.7 - - - +
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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