Contacts of the helix formed by residues 440 - 452 (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 TYR 440 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58B PHE* 3.9 9.6 - + + -
62B VAL* 3.6 27.1 - - + -
65B ASP* 4.5 0.4 - - - -
66B VAL* 3.4 18.6 - - + +
69B ARG* 4.0 10.4 + - - -
94B THR* 4.0 18.6 - - + -
98B ASP* 4.2 2.1 + - - -
407B VAL* 4.8 0.2 - - + -
408B SER 3.7 17.5 - - - -
409B ASP* 3.2 4.2 + - - +
410B ILE* 4.5 4.9 - - + -
430B LEU* 4.6 4.8 - - - +
431B THR* 3.5 21.4 + - - -
432B SER* 3.5 39.9 - - - -
437B SER* 3.1 19.9 + - - +
438B PHE 3.2 2.8 + - - -
439B GLY* 1.3 76.7 - - - +
441B GLY* 1.3 65.3 + - - +
443B PRO* 3.3 5.6 - - - +
444B ALA* 3.1 38.7 + - + +
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Residues in contact with GLY 441 (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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407B VAL* 4.2 6.7 - - - -
409B ASP* 2.8 27.7 + - - +
440B TYR* 1.3 72.3 - - - +
442B ILE* 1.3 57.5 + - - +
444B ALA* 3.2 2.1 + - - +
445B ALA* 2.8 31.4 + - - +
459B LEU* 3.3 29.9 - - - +
466B PHE* 6.4 0.2 - - - -
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Residues in contact with ILE 442 (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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409B ASP* 4.6 0.8 + - - -
439B GLY 3.9 1.4 + - - +
441B GLY* 1.3 74.3 - - - +
443B PRO* 1.4 68.0 - - + +
445B ALA* 3.2 3.8 + - - +
446B ILE* 2.9 40.3 + - + +
459B LEU* 3.8 9.0 - - + +
466B PHE* 3.6 39.8 - - + -
469B ASN* 3.7 22.0 - - - +
470B SER* 4.1 2.7 - - - -
472B ASP* 3.8 24.0 - - + +
473B LEU* 3.9 25.8 - - + +
476B ILE* 3.9 17.0 - - + +
485B THR* 5.5 0.7 - - - +
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Residues in contact with PRO 443 (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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58B PHE* 4.3 2.5 - - + -
59B THR* 3.3 41.5 - - + +
62B VAL* 3.6 23.8 - - + -
63B ALA* 3.6 9.6 - - + +
439B GLY 3.2 18.8 - - - +
440B TYR* 3.3 12.8 - - - +
442B ILE* 1.4 94.1 - - + +
444B ALA* 1.3 54.1 + - - +
446B ILE* 3.3 6.3 + - + +
447B GLY 2.9 23.7 + - - -
469B ASN* 3.5 13.7 - - - +
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Residues in contact with ALA 444 (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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62B VAL* 4.0 0.4 - - - +
66B VAL* 3.5 24.6 - - + +
407B VAL* 3.6 17.5 - - + -
430B LEU* 4.9 2.0 - - + -
440B TYR* 3.1 46.1 + - + +
443B PRO* 1.3 74.1 - - - +
445B ALA* 1.3 60.3 - - - +
447B GLY 3.3 0.3 + - - -
448B ALA* 2.8 31.8 + - - +
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Residues in contact with ALA 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B VAL* 4.1 11.5 - - + +
441B GLY 2.8 16.7 + - - +
442B ILE* 3.6 5.4 - - - +
444B ALA* 1.3 73.6 - - - +
446B ILE* 1.3 60.1 + - - +
448B ALA* 3.8 0.2 - - - +
449B GLN* 2.8 33.6 + - - +
457B THR* 3.9 8.2 - - + +
459B LEU* 4.3 14.6 - - + -
476B ILE* 5.4 0.7 - - + -
483B ILE* 3.6 32.0 - - + +
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Residues in contact with ILE 446 (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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31B PHE* 4.5 4.3 - - + -
52B VAL* 5.7 0.7 - - + -
54B THR* 5.6 1.8 - - + -
59B THR* 4.1 19.3 - - + -
63B ALA* 4.3 12.6 - - + -
442B ILE* 2.9 35.7 + - + +
443B PRO* 3.5 6.7 - - + +
445B ALA* 1.3 76.3 - - - +
447B GLY* 1.3 63.8 + - - +
449B GLN* 3.9 0.9 - - - +
450B MET* 3.1 40.1 + - - +
475B THR* 4.3 20.9 - - + -
476B ILE* 3.8 24.0 - - + -
479B LEU* 4.5 5.6 - - + -
481B LEU* 3.8 23.5 - - + +
483B ILE* 3.8 1.1 - - + +
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Residues in contact with GLY 447 (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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31B PHE* 5.6 0.9 - - - -
63B ALA* 3.9 21.1 - - - +
66B VAL* 3.9 9.4 - - - -
67B LEU* 4.0 9.0 - - - +
443B PRO 2.9 17.8 + - - -
444B ALA 3.3 2.7 + - - -
446B ILE* 1.3 75.7 - - - +
448B ALA* 1.3 56.5 + - - +
450B MET* 3.5 5.8 + - - +
451B ALA* 2.9 30.4 + - - +
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Residues in contact with ALA 448 (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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66B VAL* 3.6 1.8 - - - +
70B ILE* 3.8 14.4 - - + -
405B THR* 4.1 17.3 - - + +
407B VAL* 4.4 0.4 - - + -
430B LEU* 3.7 22.2 - - + -
444B ALA 2.8 22.2 + - - +
445B ALA* 3.8 3.4 - - - +
447B GLY* 1.3 73.0 - - - +
449B GLN* 1.3 56.2 + - - +
451B ALA* 3.3 2.6 + - - +
452B ARG* 2.9 33.5 + - - +
457B THR* 4.2 10.8 - - + -
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Residues in contact with GLN 449 (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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445B ALA 2.8 21.2 + - - +
446B ILE 4.0 2.2 - - - +
448B ALA* 1.3 72.9 - - - +
450B MET* 1.3 57.6 + - - +
452B ARG 3.0 44.1 + - - +
453B PRO* 3.1 20.6 + - + +
455B GLN 2.9 25.5 + - - +
456B PRO* 4.9 0.3 - - - +
457B THR* 3.0 27.0 + - - +
481B LEU* 3.9 15.9 - - + -
482B PRO* 3.8 44.3 - - + +
483B ILE* 3.9 10.3 + - + -
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Residues in contact with MET 450 (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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29B LYS* 3.9 33.9 - - + -
31B PHE* 3.6 39.3 - - + -
52B VAL* 4.5 4.3 - - + -
67B LEU* 4.4 11.4 - - + +
446B ILE* 3.1 30.5 + - - +
447B GLY* 3.8 4.3 - - - +
449B GLN* 1.3 74.1 - - - +
451B ALA* 1.3 62.9 + - - +
453B PRO* 3.7 12.8 - - - +
479B LEU* 4.7 11.7 - - - -
481B LEU* 4.0 18.2 - - + -
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Residues in contact with ALA 451 (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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67B LEU* 3.7 19.2 - - + +
70B ILE* 3.7 35.8 - - + +
71B THR* 4.6 6.9 - - + +
447B GLY 2.9 17.9 + - - +
448B ALA 3.3 4.7 + - - +
450B MET* 1.3 77.0 - - - +
452B ARG* 1.3 61.9 + - - +
453B PRO* 3.4 7.2 - - - +
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Residues in contact with ARG 452 (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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70B ILE* 3.8 29.4 - - + +
404B GLY 4.1 0.2 + - - -
405B THR* 2.9 32.1 + - - +
425B GLN* 3.4 25.8 + - - +
426B PRO 3.0 25.5 + - - -
427B PHE* 3.0 28.1 + - - +
448B ALA 2.9 14.9 + - - +
449B GLN* 3.0 18.0 + - - -
451B ALA* 1.3 83.8 - - + +
453B PRO* 1.3 65.0 - - - +
454B ASP 3.1 4.0 + - - -
455B GLN* 3.1 42.7 + - + +
457B 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