Contacts of the helix formed by residues 440 - 452 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A PHE* 3.8 9.8 - + + -
62A VAL* 3.6 28.9 - - + -
65A ASP* 4.2 3.7 + - - -
66A VAL* 3.5 18.1 - - + +
69A ARG* 4.2 6.8 + - - -
94A THR* 4.1 14.6 - - + -
98A ASP* 4.1 2.2 + - - -
407A VAL* 4.6 0.4 - - + -
408A SER 3.7 16.8 - - - -
409A ASP* 3.2 2.0 + - - +
410A ILE* 4.5 7.6 - - + -
430A LEU* 4.6 6.3 - - - +
431A THR* 3.6 22.2 + - - -
432A SER* 3.6 41.2 - - - -
437A SER* 3.2 18.8 + - - +
438A PHE 3.2 3.2 + - - -
439A GLY* 1.3 77.8 - - - +
441A GLY* 1.3 64.5 + - - +
442A ILE 3.5 0.2 - - - -
443A PRO* 3.3 5.9 - - - +
444A ALA* 3.1 39.0 + - + +
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Residues in contact with GLY 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A VAL* 3.8 5.6 - - - +
409A ASP* 2.8 27.7 + - - -
439A GLY 3.2 0.2 - - - -
440A TYR* 1.3 74.7 - - - +
442A ILE* 1.3 57.9 + - - +
444A ALA* 3.3 1.2 + - - +
445A ALA* 2.9 31.2 + - - +
459A LEU* 3.4 31.0 - - - +
461A ALA* 5.5 0.2 - - - -
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Residues in contact with ILE 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A THR* 4.8 0.2 - - + -
409A ASP* 4.6 1.0 + - - -
439A GLY 4.1 2.1 + - - +
441A GLY* 1.3 74.5 - - - +
443A PRO* 1.4 65.6 - - + +
445A ALA* 3.3 4.1 + - - +
446A ILE* 2.9 39.8 + - + +
459A LEU* 3.7 9.7 - - + +
466A PHE* 3.6 39.4 - - + -
469A ASN* 3.6 22.9 - - - +
470A SER* 4.0 4.0 - - - -
472A ASP* 3.8 23.8 - - + +
473A LEU* 3.9 23.1 - - + +
476A ILE* 3.8 23.9 - - + +
485A THR* 5.6 0.2 - - - +
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Residues in contact with PRO 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A PHE* 4.3 3.4 - - + -
59A THR* 3.2 41.7 - - + +
62A VAL* 3.5 22.9 - - + -
63A ALA* 3.5 9.9 - - - +
439A GLY 3.3 16.2 - - - +
440A TYR 3.3 15.7 - - - +
442A ILE* 1.4 94.7 - - + +
444A ALA* 1.3 54.8 + - - +
446A ILE* 3.3 7.3 + - + +
447A GLY 2.9 23.7 + - - -
469A ASN* 3.5 14.4 - - - +
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Residues in contact with ALA 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A VAL* 3.8 0.8 - - - +
66A VAL* 3.4 22.7 - - + +
407A VAL* 3.6 16.3 - - + +
430A LEU* 5.2 2.0 - - + -
440A TYR* 3.1 51.4 + - + +
443A PRO* 1.3 73.8 - - - +
445A ALA* 1.3 60.5 + - - +
447A GLY 3.4 0.2 + - - -
448A ALA* 2.8 31.0 + - - +
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Residues in contact with ALA 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A VAL* 4.0 13.2 - - + +
441A GLY 2.9 17.2 + - - +
442A ILE* 3.6 4.9 - - - +
444A ALA* 1.3 72.0 - - - +
446A ILE* 1.3 60.3 + - - +
448A ALA* 3.8 0.5 - - - +
449A GLN* 2.8 33.6 + - - +
457A THR* 3.9 9.0 - - + +
459A LEU* 4.4 14.1 - - + -
476A ILE* 5.7 0.7 - - + -
483A ILE* 3.6 32.8 - - + +
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Residues in contact with ILE 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PHE* 4.6 3.6 - - + -
52A VAL* 5.7 0.4 - - + -
54A THR* 5.8 1.3 - - + -
59A THR* 4.2 17.9 - - + -
63A ALA* 4.3 12.6 - - + -
442A ILE* 2.9 36.6 + - + +
443A PRO* 3.5 7.2 - - + +
445A ALA* 1.3 76.7 - - - +
447A GLY* 1.3 62.9 + - - +
449A GLN* 3.9 1.0 - - - +
450A MET* 3.0 43.4 + - - +
475A THR* 4.3 20.2 - - + -
476A ILE* 3.9 23.1 - - + -
479A LEU* 4.4 6.7 - - + -
481A LEU* 3.8 20.9 - - + -
483A ILE* 4.1 5.2 - - + -
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Residues in contact with GLY 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PHE* 5.6 0.7 - - - -
63A ALA* 3.8 21.3 - - - +
66A VAL* 3.9 9.9 - - - -
67A LEU* 4.0 9.2 - - - +
443A PRO 2.9 15.9 + - - -
444A ALA 3.7 2.7 - - - -
446A ILE* 1.3 77.2 - - - +
448A ALA* 1.3 56.9 + - - +
450A MET* 3.5 6.3 + - - +
451A ALA* 2.9 30.3 + - - +
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Residues in contact with ALA 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL* 3.6 1.6 - - - +
70A ILE* 3.7 13.2 - - + -
405A THR* 4.1 17.0 - - + -
407A VAL* 4.3 1.8 - - + -
430A LEU* 3.9 20.9 - - + -
444A ALA 2.8 21.1 + - - +
445A ALA 3.8 3.4 - - - +
447A GLY* 1.3 70.1 - - - +
449A GLN* 1.3 58.8 - - - +
451A ALA* 3.2 2.1 + - - +
452A ARG* 2.9 34.0 + - - +
457A THR* 4.1 11.7 - - + -
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Residues in contact with GLN 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445A ALA 2.8 20.8 + - - +
446A ILE 4.0 2.9 - - - +
448A ALA* 1.3 73.7 - - - +
450A MET* 1.3 60.6 + - - +
452A ARG 3.0 27.7 + - - -
453A PRO* 3.2 28.1 + - + +
455A GLN 3.0 17.1 + - - +
456A PRO* 4.9 0.5 - - - +
457A THR* 3.1 25.7 + - - +
481A LEU* 3.9 18.0 - - + +
482A PRO* 3.6 45.2 - - + +
483A ILE* 4.0 10.7 + - + -
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Residues in contact with MET 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LYS* 3.9 33.9 - - + +
31A PHE* 3.7 37.9 - - + -
52A VAL* 4.7 3.8 - - + -
67A LEU* 4.3 12.4 - - + +
446A ILE* 3.0 30.2 + - - +
447A GLY* 3.9 4.7 - - - +
449A GLN* 1.3 76.9 - - - +
451A ALA* 1.3 62.2 + - - +
453A PRO* 3.6 13.1 - - - +
479A LEU* 4.8 7.6 - - - -
481A LEU* 4.1 22.2 - - + -
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Residues in contact with ALA 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU* 3.8 19.0 - - + +
70A ILE* 3.6 37.6 - - + +
71A THR* 4.5 7.9 - - + +
447A GLY 2.9 18.1 + - - +
448A ALA 3.2 4.5 + - - +
450A MET* 1.3 77.2 - - - +
452A ARG* 1.3 62.2 + - + +
453A PRO* 3.5 7.2 - - - +
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Residues in contact with ARG 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ILE* 3.6 31.9 - - + +
404A GLY 4.1 0.4 + - - -
405A THR* 2.8 37.9 + - - +
425A GLN* 3.5 24.6 + - - +
426A PRO 3.0 24.5 + - - -
427A PHE* 2.8 33.3 + - - +
448A ALA 2.9 13.1 + - - +
449A GLN* 3.0 17.3 + - - -
451A ALA* 1.3 84.5 - - - +
453A PRO* 1.3 63.9 - - - +
454A ASP 3.1 4.3 + - - -
455A GLN* 3.1 43.5 + - + +
457A THR* 5.6 1.6 - - - +
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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