Contacts of the helix formed by residues 440 - 452 (chain C) 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 TYR 440 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58C PHE* 3.9 10.1 - + + -
62C VAL* 3.6 25.8 - - + -
65C ASP* 4.2 2.4 + - - -
66C VAL* 3.5 15.6 - - + +
69C ARG* 4.1 9.9 + - - -
94C THR* 4.0 18.8 - - + -
98C ASP* 4.1 2.6 + - - -
407C VAL* 4.7 0.2 - - + -
408C SER 3.8 16.8 - - - -
409C ASP* 3.3 4.9 + - - +
410C ILE* 4.5 4.0 - - + -
430C LEU* 4.7 6.0 - - - +
431C THR* 3.4 38.6 + - - -
432C SER* 3.7 22.8 - - - -
437C SER* 3.2 18.8 + - - +
438C PHE 3.2 3.2 + - - -
439C GLY* 1.3 75.8 - - - +
441C GLY* 1.3 65.4 + - - +
442C ILE 3.6 0.2 - - - -
443C PRO* 3.4 5.2 - - - +
444C ALA* 3.1 37.5 + - + +
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Residues in contact with GLY 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407C VAL* 3.7 9.2 - - - +
409C ASP* 3.0 23.0 + - - -
440C TYR* 1.3 78.3 - - - +
442C ILE* 1.3 62.2 + - - +
444C ALA* 3.3 1.6 + - - +
445C ALA* 2.9 24.4 + - - +
459C LEU* 3.4 28.5 - - - -
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Residues in contact with ILE 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409C ASP* 4.8 0.6 + - - -
439C GLY 4.0 1.8 + - - +
441C GLY* 1.3 73.9 - - - +
443C PRO* 1.4 66.5 - - + +
445C ALA* 3.1 5.6 + - - +
446C ILE* 2.9 34.8 + - + +
459C LEU* 3.7 8.6 - - + +
466C PHE* 3.7 39.2 - - + -
469C ASN* 3.6 24.2 - - - +
470C SER* 4.1 2.0 - - - +
472C ASP* 3.8 23.1 - - + +
473C LEU* 3.8 25.8 - - + +
476C ILE* 3.7 23.1 - - + +
485C THR* 5.6 0.2 - - - +
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Residues in contact with PRO 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C PHE* 4.4 0.7 - - + -
59C THR* 3.3 41.1 - - + +
62C VAL* 3.6 25.8 - - + -
63C ALA* 3.5 11.8 - - + +
439C GLY 3.3 18.6 - - - +
440C TYR* 3.4 12.3 - - - +
442C ILE* 1.4 95.9 - - + +
444C ALA* 1.3 53.8 + - - +
446C ILE* 3.5 6.0 - - + +
447C GLY* 3.0 23.7 + - - -
469C ASN* 3.5 13.2 - - - +
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Residues in contact with ALA 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C VAL* 3.9 1.0 - - - +
66C VAL* 3.5 26.6 - - + +
407C VAL* 3.6 16.8 - - + -
430C LEU* 4.2 2.9 - - + +
440C TYR* 3.1 46.0 + - + +
443C PRO* 1.3 77.1 - - - +
445C ALA* 1.3 56.4 + - - +
447C GLY 3.4 0.5 + - - -
448C ALA* 2.8 30.3 + - - +
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Residues in contact with ALA 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407C VAL* 4.0 15.4 - - + +
441C GLY 2.9 17.0 + - - +
442C ILE* 3.6 4.9 - - - +
444C ALA* 1.3 71.7 - - - +
446C ILE* 1.3 61.5 + - - +
448C ALA* 3.8 0.5 - - - +
449C GLN* 2.9 32.9 + - - +
457C THR* 3.8 10.8 - - + +
459C LEU* 4.3 11.0 - - + -
476C ILE* 5.6 0.4 - - + -
483C ILE* 3.5 31.2 - - + +
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Residues in contact with ILE 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C PHE* 4.4 4.5 - - + -
52C VAL* 5.6 0.7 - - + -
54C THR* 5.7 1.1 - - + -
59C THR* 4.1 18.4 - - + -
63C ALA* 4.3 13.0 - - + -
442C ILE* 2.9 33.5 + - + +
443C PRO* 3.5 7.2 - - + +
445C ALA* 1.3 76.2 - - - +
447C GLY* 1.3 56.7 + - - +
449C GLN* 3.9 1.0 - - - +
450C MET* 2.9 55.1 + - - +
475C THR* 4.1 25.8 - - + -
476C ILE* 3.9 20.6 - - + -
479C LEU* 4.6 4.7 - - + -
481C LEU* 3.8 18.6 - - + -
483C ILE* 4.0 0.4 - - - -
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Residues in contact with GLY 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C PHE* 5.6 1.1 - - - -
63C ALA* 4.1 19.3 - - - +
66C VAL* 4.1 9.4 - - - -
67C LEU* 4.0 8.7 - - - +
70C ILE* 4.4 0.4 - - - +
443C PRO 3.0 14.9 + - - -
444C ALA 3.7 2.5 - - - -
445C ALA 3.3 0.2 - - - -
446C ILE* 1.3 77.6 - - - +
448C ALA* 1.3 56.9 + - - +
450C MET* 3.5 6.0 + - - +
451C ALA* 2.9 31.6 + - - +
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Residues in contact with ALA 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C VAL* 3.8 1.2 - - - +
70C ILE* 3.7 12.3 - - + -
405C THR* 4.0 13.9 - - + +
407C VAL* 4.4 0.7 - - + -
430C LEU* 3.9 19.1 - - + -
444C ALA 2.8 20.4 + - - +
445C ALA* 3.8 4.7 - - - +
446C ILE 3.3 0.2 - - - -
447C GLY* 1.3 72.9 - - - +
449C GLN* 1.3 57.0 + - - +
451C ALA* 3.3 2.9 + - - +
452C ARG* 2.9 33.8 + - - +
457C THR* 4.0 17.9 - - + -
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Residues in contact with GLN 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445C ALA 2.9 18.1 + - - +
446C ILE 4.0 2.5 - - - +
448C ALA* 1.3 74.0 - - - +
450C MET* 1.3 65.4 + - - +
452C ARG 3.1 19.0 + - - -
453C PRO* 3.2 41.7 + - + +
455C GLN 2.9 25.1 + - - +
456C PRO* 4.9 0.5 - - - +
457C THR* 3.2 24.3 + - - +
481C LEU* 4.0 17.1 - - + +
482C PRO* 3.8 45.3 - - + +
483C ILE* 4.0 10.2 + - + -
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Residues in contact with MET 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C LYS* 3.9 33.4 - - + +
31C PHE* 3.7 37.2 - - + -
52C VAL* 4.4 5.4 - - + -
67C LEU* 4.4 12.7 - - + +
446C ILE* 2.9 31.1 + - - +
447C GLY* 3.9 4.7 - - - +
449C GLN* 1.3 77.9 - - - +
451C ALA* 1.3 61.0 + - - +
452C ARG 3.6 0.2 + - - -
453C PRO* 3.7 11.7 - - - +
479C LEU* 4.6 13.0 - - - -
481C LEU* 4.1 18.4 - - + -
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Residues in contact with ALA 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LEU* 3.8 17.9 - - + +
70C ILE* 3.7 34.7 - - + +
71C THR* 4.7 7.0 - - + +
447C GLY 2.9 18.8 + - - +
448C ALA 3.6 4.7 - - - +
450C MET* 1.3 77.6 - - - +
452C ARG* 1.3 60.8 + - - +
453C PRO* 3.5 6.8 - - - +
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Residues in contact with ARG 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C ILE* 3.6 28.4 - - + +
405C THR* 2.9 29.1 + - - +
425C GLN* 3.5 23.4 + - - +
426C PRO 2.8 26.7 + - - -
427C PHE* 2.8 34.3 + - - +
448C ALA 2.9 15.0 + - - +
449C GLN* 3.1 14.2 + - - -
451C ALA* 1.3 85.7 - - + +
453C PRO* 1.3 64.4 - - - +
454C ASP 3.2 2.9 - - - -
455C GLN* 3.0 48.8 + - + +
457C THR* 4.9 1.7 + - - +
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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