Contacts of the helix formed by residues 440 - 452 (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 TYR 440 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58D PHE* 3.8 10.2 - + + -
62D VAL* 3.6 26.7 - - + -
65D ASP* 4.1 2.0 + - - -
66D VAL* 3.6 15.1 - - + +
69D ARG* 4.0 10.6 + - - -
94D THR* 3.9 19.7 - - + -
98D ASP* 4.1 1.5 + - - -
407D VAL* 4.8 0.4 - - + -
408D SER 3.8 16.2 - - - -
409D ASP* 3.2 2.4 + - - +
410D ILE* 4.5 6.5 - - + -
430D LEU* 4.8 5.0 - - - +
431D THR* 3.5 21.7 + - - -
432D SER* 3.5 40.1 - - - -
437D SER* 3.1 18.8 + - - +
438D PHE 3.2 2.8 + - - -
439D GLY* 1.3 77.6 - - - +
441D GLY* 1.3 63.8 + - - +
443D PRO* 3.1 16.0 - - - +
444D ALA* 3.2 27.9 + - + +
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Residues in contact with GLY 441 (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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407D VAL* 3.8 7.9 - - - +
409D ASP* 2.8 28.1 + - - -
440D TYR* 1.3 74.0 - - - +
442D ILE* 1.3 62.8 + - - +
445D ALA* 3.0 24.8 + - - +
459D LEU* 3.4 30.1 - - - +
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Residues in contact with ILE 442 (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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409D ASP* 4.6 0.6 + - - -
439D GLY 4.0 2.2 + - - +
441D GLY* 1.3 74.3 - - - +
443D PRO* 1.4 71.7 - - + +
445D ALA* 3.2 5.8 + - - +
446D ILE* 3.0 29.6 + - + +
459D LEU* 3.8 9.8 - - + +
466D PHE* 3.6 40.1 - - + +
469D ASN* 3.7 22.0 - - - +
470D SER* 4.1 2.0 - - - +
472D ASP* 3.8 25.1 - - + +
473D LEU* 4.0 24.9 - - + +
476D ILE* 3.8 21.9 - - + +
485D THR* 5.4 0.4 - - - +
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Residues in contact with PRO 443 (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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58D PHE* 4.4 2.2 - - + -
59D THR* 3.2 40.8 - - + +
62D VAL* 3.7 22.0 - - + -
63D ALA* 3.5 10.6 - - - +
439D GLY 3.3 14.4 - - - +
440D TYR* 3.1 19.1 - - - +
442D ILE* 1.4 93.3 - - + +
444D ALA* 1.3 55.1 + - - +
446D ILE* 3.3 7.2 + - + +
447D GLY 2.9 24.6 + - - -
469D ASN* 3.5 14.1 - - - +
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Residues in contact with ALA 444 (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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62D VAL* 4.0 1.2 - - + +
66D VAL* 3.5 27.5 - - + +
407D VAL* 3.6 17.3 - - + -
430D LEU* 4.3 2.6 - - + +
440D TYR* 3.2 42.9 + - + +
443D PRO* 1.3 78.2 - - - +
445D ALA* 1.3 56.8 + - - +
447D GLY 3.5 0.2 + - - -
448D ALA* 2.8 30.3 + - - +
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Residues in contact with ALA 445 (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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407D VAL* 4.0 12.4 - - + +
441D GLY 3.0 18.7 + - - +
442D ILE* 3.5 6.1 - - - +
444D ALA* 1.3 73.5 - - - +
446D ILE* 1.3 59.5 + - - +
448D ALA* 3.7 0.9 - - - +
449D GLN* 2.8 33.3 + - - +
457D THR* 3.8 8.5 - - + +
459D LEU* 4.4 12.8 - - + -
476D ILE* 5.5 0.7 - - + -
483D ILE* 3.6 31.5 - - + +
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Residues in contact with ILE 446 (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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31D PHE* 4.3 4.7 - - + -
52D VAL* 5.6 0.4 - - + -
54D THR* 5.6 1.1 - - + -
59D THR* 4.1 17.9 - - + -
63D ALA* 4.3 12.1 - - + -
442D ILE* 3.0 35.1 + - + +
443D PRO* 3.4 6.7 - - + +
445D ALA* 1.3 75.2 - - - +
447D GLY* 1.3 63.8 + - - +
449D GLN* 3.8 1.2 - - - +
450D MET* 3.0 44.4 + - - +
475D THR* 4.2 21.3 - - + -
476D ILE* 3.8 22.2 - - + -
479D LEU* 4.5 6.3 - - + -
481D LEU* 3.9 23.7 - - + +
483D ILE* 3.8 1.1 - - + +
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Residues in contact with GLY 447 (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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31D PHE* 5.5 0.7 - - - -
63D ALA* 3.8 21.7 - - - +
66D VAL* 4.1 7.9 - - - -
67D LEU* 3.9 12.8 - - - +
443D PRO 2.9 17.8 + - - -
444D ALA 3.7 2.9 - - - -
446D ILE* 1.3 75.0 - - - +
448D ALA* 1.3 55.2 + - - +
450D MET* 3.9 5.5 - - - +
451D ALA* 3.0 29.3 + - - +
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Residues in contact with ALA 448 (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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66D VAL* 3.9 1.0 - - - +
70D ILE* 3.8 13.9 - - + -
405D THR* 4.0 15.2 + - + +
407D VAL* 4.4 0.2 - - + -
430D LEU* 3.7 23.1 - - + -
444D ALA 2.8 21.7 + - - +
445D ALA* 3.8 4.5 - - - +
447D GLY* 1.3 70.2 - - - +
449D GLN* 1.3 60.8 + - - +
451D ALA* 3.3 2.4 + - - +
452D ARG* 3.0 33.4 + - - +
457D THR* 4.2 12.1 + - + -
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Residues in contact with GLN 449 (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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445D ALA 2.8 21.4 + - - +
446D ILE 3.9 2.7 - - - +
448D ALA* 1.3 73.2 - - - +
450D MET* 1.3 61.8 + - - +
452D ARG 3.0 20.4 + - - -
453D PRO* 3.1 41.2 + - + +
455D GLN 3.0 24.9 + - - +
456D PRO* 4.9 0.3 - - - +
457D THR* 3.1 24.7 + - - +
481D LEU* 4.0 28.4 - - + +
482D PRO* 3.8 34.1 - - + +
483D ILE* 4.0 10.5 - - + -
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Residues in contact with MET 450 (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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29D LYS* 3.7 44.2 - - + -
31D PHE* 3.7 31.2 - - + -
52D VAL* 4.4 5.4 - - + -
67D LEU* 4.4 12.6 - - + +
446D ILE* 3.0 28.5 + - - +
447D GLY* 3.9 4.9 - - - +
449D GLN* 1.3 76.0 - - - +
451D ALA* 1.3 60.9 - - - +
452D ARG 3.5 0.3 + - - -
453D PRO* 3.7 12.6 - - - +
479D LEU* 4.7 11.4 - - + -
481D LEU* 4.1 19.1 - - + -
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Residues in contact with ALA 451 (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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67D LEU* 3.8 18.6 - - + +
70D ILE* 3.7 34.8 - - + +
71D THR* 4.5 7.7 - - + +
447D GLY 3.0 18.8 + - - +
448D ALA 3.7 4.9 - - - +
449D GLN 3.3 0.2 - - - -
450D MET* 1.3 76.1 - - - +
452D ARG* 1.3 62.1 + - - +
453D PRO* 3.5 6.1 - - - +
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Residues in contact with ARG 452 (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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70D ILE* 3.7 29.0 - - + +
404D GLY 4.1 0.4 + - - -
405D THR* 2.9 30.9 + - - +
425D GLN* 3.4 26.8 + - - +
426D PRO 2.9 26.1 + - - -
427D PHE* 2.8 30.3 + - - +
448D ALA 3.0 13.1 + - - +
449D GLN* 3.0 17.9 + - - -
451D ALA* 1.3 86.2 - - + +
453D PRO* 1.4 64.8 - - - +
454D ASP 3.2 2.5 - - - -
455D GLN* 3.0 43.8 + - + +
457D THR* 4.8 1.1 + - - +
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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