Contacts of the helix formed by residues 44 - 56 (chain H) in PDB entry 3HR4
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 THR 44 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563G CYS 3.4 21.3 - - - +
564G ALA* 4.6 5.8 - - + -
686G VAL* 5.1 3.0 - - + +
687G ARG* 5.2 5.8 + - - +
692G ILE* 3.1 35.0 - - + -
37H ARG* 4.0 5.8 - - - +
42H ASN 3.7 1.3 + - - +
43H PRO* 1.3 75.2 - - - +
45H GLU* 1.3 65.1 + - - +
46H ALA* 3.9 5.6 + - - +
47H GLU* 2.7 42.1 + - - +
48H LEU* 3.1 22.2 + - - +
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Residues in contact with GLU 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688G GLY* 6.3 2.7 - - - -
691G HIS* 5.6 13.0 - - + +
692G ILE* 5.4 1.0 - - - +
29H THR* 5.4 4.9 + - - -
37H ARG* 3.0 27.0 + - - +
44H THR* 1.3 73.8 - - - +
46H ALA* 1.3 61.8 + - - +
48H LEU* 3.4 13.0 + - - +
49H GLN* 2.9 27.6 + - - +
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Residues in contact with ALA 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687G ARG* 3.3 52.6 + - + +
44H THR* 3.4 4.7 + - - +
45H GLU* 1.3 76.5 - - - +
47H GLU* 1.3 54.5 + - + +
49H GLN* 3.1 9.0 + - - +
50H ASP* 2.4 44.6 + - - +
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Residues in contact with GLU 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529G MET* 4.6 0.2 - - - +
532G THR* 3.3 36.8 + - + +
536G ARG* 3.2 34.2 + - - +
564G ALA* 4.9 1.5 - - - -
687G ARG* 5.5 5.2 - - - +
43H PRO* 3.9 10.5 - - + +
44H THR* 2.7 48.8 + - - +
45H GLU 3.2 0.2 - - - -
46H ALA* 1.3 75.5 - - + +
48H LEU* 1.3 65.7 + - - +
50H ASP* 3.0 12.0 + - - +
51H MET* 2.9 28.4 + - - +
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Residues in contact with LEU 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H THR* 4.1 15.0 - - - +
30H LYS* 5.9 0.7 - - - -
32H LEU* 3.7 11.9 - - + +
33H GLY* 3.3 42.2 - - - +
36H MET* 4.2 5.6 - - + -
37H ARG* 3.5 25.6 - - + +
43H PRO* 4.2 10.5 - - + +
44H THR 3.1 13.7 + - - +
45H GLU* 3.6 15.7 - - - +
47H GLU* 1.3 73.6 - - - +
49H GLN* 1.3 56.5 + - - +
51H MET* 2.7 60.8 + - + +
52H ILE* 3.0 16.8 + - - +
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Residues in contact with GLN 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H THR* 3.3 28.8 - - + +
45H GLU 2.9 19.5 + - - +
46H ALA* 3.3 9.9 - - - +
48H LEU* 1.3 76.6 - - - +
50H ASP* 1.3 54.4 + - - +
52H ILE* 4.0 4.7 - - - +
53H ASN* 2.3 54.7 + - - +
61H GLY 5.3 1.6 - - - +
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Residues in contact with ASP 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532G THR* 4.8 6.3 - - + -
687G ARG* 2.9 35.2 + - - -
46H ALA* 2.4 36.6 + - - +
47H GLU* 3.3 10.7 + - - +
48H LEU 3.0 0.4 - - - -
49H GLN* 1.3 75.7 - - - +
51H MET* 1.3 55.1 + - - +
53H ASN* 3.7 11.7 + - - +
54H GLU* 2.7 39.0 + - - +
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Residues in contact with MET 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528G LEU* 3.3 45.2 - - + +
532G THR* 3.8 16.2 - - + -
32H LEU* 3.4 12.1 - - + -
36H MET* 3.4 21.8 - - + +
43H PRO* 4.5 5.4 - - + -
47H GLU 2.9 12.5 + - - +
48H LEU* 2.7 56.8 + - + +
50H ASP* 1.3 71.0 - - - +
52H ILE* 1.3 68.3 + - - +
54H GLU* 2.8 31.5 + - - +
55H VAL* 3.3 11.5 + - - +
63H ILE* 5.6 0.2 - - - -
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Residues in contact with ILE 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H ILE 3.2 26.9 - - - +
29H THR* 3.3 32.3 - - + +
32H LEU* 4.0 15.7 - - + -
48H LEU 3.0 11.0 + - - +
49H GLN* 3.9 11.7 - - - +
51H MET* 1.3 74.2 - - - +
53H ASN* 1.3 59.8 + - - +
54H GLU 2.7 12.6 + - - -
55H VAL* 2.8 13.9 + - - +
56H ASP* 2.8 27.7 + - + +
61H GLY 3.9 22.4 - - - +
62H THR* 4.3 0.4 - - - -
63H ILE* 3.3 26.2 - - + -
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Residues in contact with ASN 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H GLN* 2.3 47.3 + - - +
50H ASP* 3.7 14.5 + - - +
52H ILE* 1.3 83.0 - - - +
54H GLU* 1.3 60.1 + - + +
56H ASP* 4.1 19.9 + - - +
57H ALA* 5.5 0.7 - - - -
61H GLY* 6.0 1.2 - - - -
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Residues in contact with GLU 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528G LEU* 5.3 6.6 - - + +
531G LYS* 2.7 43.2 + - - +
532G THR* 3.7 15.9 - - - +
50H ASP* 2.7 30.6 - - - +
51H MET* 2.8 25.2 - - - +
52H ILE 2.7 5.5 + - - -
53H ASN* 1.3 76.0 - - + +
55H VAL* 1.3 62.3 + - + +
57H ALA* 4.8 2.9 + - - -
71H MET* 5.8 0.9 - - + -
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Residues in contact with VAL 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524G PHE* 4.6 7.4 - - + -
528G LEU* 4.1 12.8 - - + -
51H MET 3.7 12.1 - - - +
52H ILE 2.8 10.4 + - - +
54H GLU* 1.3 72.8 - - + +
56H ASP* 1.3 50.2 + - - +
57H ALA* 2.5 23.9 + - - +
63H ILE* 3.8 28.9 - - + -
67H GLU* 3.5 34.2 - - - +
68H PHE* 4.3 4.9 - - - +
71H MET* 3.2 37.7 - - + -
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Residues in contact with ASP 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H ILE* 2.8 26.7 + - + +
53H ASN* 4.4 15.3 - - - +
54H GLU 3.6 0.2 - - - -
55H VAL* 1.3 71.9 - - - +
57H ALA* 1.3 53.1 + - - +
58H ASP* 2.7 11.7 - - - +
59H GLY* 2.6 35.5 + - - -
60H ASN 2.9 6.1 + - - -
61H GLY* 2.7 26.1 + - - -
62H THR 2.7 17.7 - - - +
63H ILE* 4.5 2.6 - - + +
67H GLU* 3.4 9.9 - - - -
202H CA 2.3 30.3 - - - -
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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
------------------------------------------------------------
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