Contacts of the helix formed by residues 43 - 60 (chain H) in PDB entry 3J8B
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 GLY 43 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100F ALA* 5.4 5.8 - - - -
252F ILE* 6.3 3.1 - - - -
42H ASP* 1.3 74.4 - - - +
44H LEU* 1.3 62.5 + - - +
46H VAL* 3.3 4.4 + - - +
47H LEU* 3.1 24.5 + - - +
206H LYS 3.9 8.1 + - - -
207H ASN* 5.7 4.4 - - - +
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Residues in contact with LEU 44 (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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97F VAL* 5.6 1.6 - - - +
100F ALA* 4.9 26.1 - - + +
101F SER* 5.0 7.0 - - - +
104F ASP* 5.0 10.1 - - + -
42H ASP* 3.4 3.2 - - + +
43H GLY* 1.3 75.7 - - - +
45H VAL* 1.3 58.6 + - - +
47H LEU* 4.1 4.9 - - - +
48H LYS* 2.9 31.9 + - - +
79H THR 4.9 7.6 - - - +
80H ASN* 5.4 4.3 - - + -
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Residues in contact with VAL 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H ILE* 4.9 3.4 - - + -
42H ASP* 3.2 20.8 + - - +
43H GLY 3.2 0.4 - - - -
44H LEU* 1.3 80.6 - - - +
46H VAL* 1.3 63.6 + - - +
48H LYS* 3.9 2.5 - - - +
49H ILE* 3.0 24.9 + - - +
78H ILE* 4.1 10.1 - - + +
79H THR 4.3 1.6 + - - -
80H ASN* 4.0 32.3 - - - +
81H CYS* 4.6 10.5 - - + +
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Residues in contact with VAL 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H ILE* 5.0 11.1 - - + +
42H ASP 3.0 17.1 + - - +
43H GLY* 3.9 3.8 - - - +
45H VAL* 1.3 76.8 - - - +
47H LEU* 1.3 62.5 + - - +
49H ILE* 3.2 6.1 + - - +
50H ILE* 3.0 25.4 + - - +
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Residues in contact with LEU 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F VAL* 5.1 17.0 - - + -
245F GLU* 6.3 4.3 - - + -
248F GLY* 6.2 5.8 - - - -
43H GLY 3.1 17.1 + - - +
44H LEU* 4.1 4.7 - - - +
46H VAL* 1.3 76.3 - - - +
48H LYS* 1.3 57.8 + - - +
50H ILE* 3.5 4.7 + - - +
51H LYS* 2.9 30.9 + - - +
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Residues in contact with LYS 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H LEU 2.9 18.7 + - - +
45H VAL* 3.9 4.0 - - - +
47H LEU* 1.3 78.8 - - - +
49H ILE* 1.3 56.9 + - - +
51H LYS* 3.8 5.6 - - - +
52H HIS* 2.8 32.6 + - - +
81H CYS* 5.1 17.3 - - + +
82H PHE* 6.4 0.2 - - - -
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Residues in contact with ILE 49 (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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45H VAL 3.0 18.0 + - - +
46H VAL* 3.7 5.2 - - - +
48H LYS* 1.3 77.0 - - - +
50H ILE* 1.3 57.3 + - - +
52H HIS* 4.0 3.8 - - - +
53H TYR* 2.9 31.7 + - - +
81H CYS* 5.7 0.4 - - - +
120H TYR* 5.3 12.8 - - + -
152H TYR* 5.3 12.9 - - + +
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Residues in contact with ILE 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244F THR* 5.3 11.4 - - - +
248F GLY* 6.0 5.2 - - - -
46H VAL 3.0 16.7 + - - +
47H LEU* 4.0 5.6 - - - +
49H ILE* 1.3 76.6 - - - +
51H LYS* 1.3 62.7 + - - +
53H TYR* 3.9 4.5 - - - +
54H GLN* 3.0 26.7 + - - +
154H PRO* 4.9 2.1 - - - +
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Residues in contact with LYS 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244F THR* 5.2 9.8 - - - -
47H LEU 2.9 19.3 + - - +
48H LYS* 3.8 6.5 - - - +
50H ILE* 1.3 76.7 - - - +
52H HIS* 1.3 58.8 + - - +
54H GLN* 3.8 4.0 - - - +
55H GLU* 2.9 30.8 + - - +
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Residues in contact with HIS 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H LYS 2.8 19.3 + - - +
49H ILE* 4.0 4.7 - - - +
51H LYS* 1.3 75.9 - - - +
53H TYR* 1.3 54.5 + - - +
55H GLU* 3.6 6.1 - - - +
56H GLU* 2.7 37.5 + - - +
63H VAL* 4.1 9.7 - - + +
83H PRO* 4.9 17.9 - - + -
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Residues in contact with TYR 53 (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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49H ILE 2.9 19.2 + - - +
50H ILE* 3.9 4.3 - - - +
52H HIS* 1.3 77.2 - - - +
54H GLN* 1.3 50.2 - - - +
56H GLU* 3.1 9.6 + - - +
57H GLY* 2.7 32.4 + - - -
63H VAL* 4.6 2.9 - - - +
122H SER* 4.0 22.1 - - - -
152H TYR* 5.1 8.7 - - + -
154H PRO* 3.4 26.2 - - + +
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Residues in contact with GLN 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244F THR* 5.0 13.2 - - - -
50H ILE 3.0 18.1 + - - +
51H LYS* 3.9 4.3 - - - +
53H TYR* 1.3 75.3 - - - +
55H GLU* 1.3 61.9 + - - +
57H GLY* 3.0 11.3 + - - +
58H GLN* 3.1 13.9 + - - +
154H PRO* 3.6 14.8 - - + +
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Residues in contact with GLU 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H LYS 2.9 18.1 + - - +
52H HIS* 3.6 7.2 - - - +
54H GLN* 1.3 75.6 - - - +
56H GLU* 1.3 61.6 + - - +
58H GLN* 3.4 9.7 + - - +
59H GLY* 3.2 16.5 + - - -
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Residues in contact with GLU 56 (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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52H HIS 2.7 15.1 + - - +
53H TYR* 3.2 6.7 - - - +
55H GLU* 1.3 74.1 - - - +
57H GLY* 1.3 55.6 + - - +
59H GLY* 3.0 4.4 + - - +
60H THR 2.8 24.4 + - - -
61H GLU 3.3 21.2 + - - +
62H VAL* 5.0 0.4 - - - -
63H VAL* 3.0 39.0 - - + +
122H SER* 5.6 2.0 - - - -
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Residues in contact with GLY 57 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H TYR 2.7 17.2 + - - -
54H GLN* 3.0 6.2 + - - -
56H GLU* 1.3 70.9 - - - +
58H GLN* 1.3 64.3 + - - +
60H THR* 3.1 14.3 + - - -
154H PRO* 5.8 2.7 - - - -
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Residues in contact with GLN 58 (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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54H GLN 3.1 10.3 + - - +
55H GLU* 3.6 11.7 - - - +
56H GLU 3.3 0.2 - - - -
57H GLY* 1.3 76.1 - - - +
59H GLY* 1.3 63.6 + - - +
60H THR* 3.4 2.6 + - - -
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Residues in contact with GLY 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H GLU 3.2 7.7 + - - -
56H GLU* 3.0 8.8 + - - -
58H GLN* 1.3 78.9 - - - +
60H THR* 1.3 67.5 + - - +
61H GLU* 3.2 10.9 + - - +
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Residues in contact with THR 60 (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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56H GLU 2.8 5.8 + - - -
57H GLY* 3.1 14.1 + - - -
58H GLN 4.5 2.0 - - - -
59H GLY* 1.3 81.0 - - - +
61H GLU* 1.3 58.6 + - - +
62H VAL 4.3 0.7 + - - -
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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