Contacts of the helix formed by residues 70 - 81 (chain H) in PDB entry 6V96
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 ALA 70 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66H THR* 3.7 32.5 - - - +
67H GLN 4.0 8.8 + - - +
68H TYR 3.8 7.9 - - - +
69H LYS* 1.3 74.7 - - - +
71H HIS* 1.3 60.4 + - - +
72H GLU 3.3 2.5 - - - -
73H LEU* 3.1 11.8 + - + -
74H ILE* 2.7 43.5 + - + +
96H PRO* 5.8 0.4 - - + -
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Residues in contact with HIS 71 (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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69H LYS* 3.2 20.0 - - - +
70H ALA* 1.3 77.3 - - - +
72H GLU* 1.3 67.1 + - - +
74H ILE* 3.4 6.5 + - + +
75H ARG* 3.0 47.1 + - + +
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Residues in contact with GLU 72 (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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32H ARG* 4.3 8.7 - - - +
33H ARG* 2.9 51.8 + - + +
37H ALA* 4.7 1.6 - - + -
39H TYR* 3.8 8.2 + - - -
45H ARG* 2.7 39.3 + - - +
69H LYS* 4.5 2.8 + - - +
70H ALA 3.3 0.4 - - - -
71H HIS* 1.3 84.5 + - - +
73H LEU* 1.3 63.0 + - - +
75H ARG* 3.5 5.1 + - - +
76H HIS* 3.1 22.7 + - - +
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Residues in contact with LEU 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H ALA* 3.7 31.2 - - + +
34H ALA* 4.6 9.0 - - + -
36H PRO* 4.5 6.7 - - + -
37H ALA* 3.8 28.1 - - + +
47H ILE* 4.0 33.0 - - + -
66H THR* 3.8 21.8 - - + -
69H LYS 5.2 2.0 + - - +
70H ALA* 3.1 14.4 + - + +
72H GLU* 1.3 77.5 - - - +
74H ILE* 1.3 65.3 + - - +
76H HIS* 3.2 7.5 + - + +
77H LEU* 3.0 37.3 + - + +
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Residues in contact with ILE 74 (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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66H THR* 3.8 9.9 - - + +
70H ALA* 2.7 40.5 + - + +
71H HIS* 3.9 5.4 - - + +
73H LEU* 1.3 71.7 - - - +
75H ARG* 1.3 58.1 + - - +
77H LEU* 3.2 8.1 + - - +
78H GLN* 2.9 54.7 + - + +
94H ILE* 3.9 23.1 - - + -
96H PRO* 3.7 28.7 - - + -
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Residues in contact with ARG 75 (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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71H HIS* 3.0 38.2 + - + +
72H GLU* 4.0 5.8 - - - +
74H ILE* 1.3 76.4 - - - +
76H HIS* 1.3 62.6 + - - +
78H GLN* 3.5 13.6 + - - +
79H ARG* 3.0 73.0 + - + +
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Residues in contact with HIS 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H ARG* 3.2 43.2 + - + +
47H ILE* 4.2 13.9 - - + -
48H ASP* 2.7 41.3 + - - -
72H GLU 3.1 15.3 + - - +
73H LEU* 3.2 9.8 + - + +
75H ARG* 1.3 77.4 - - - +
77H LEU* 1.3 67.0 + - + +
79H ARG* 4.3 5.1 - - - +
80H GLY* 2.8 29.3 + - - -
81H TRP* 4.1 3.5 + + - -
301H THR* 3.5 11.9 - - - -
302H TYR* 3.8 25.2 - - + +
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Residues in contact with LEU 77 (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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47H ILE* 4.1 9.6 - - + -
51H LEU* 3.6 32.3 - - + -
64H VAL* 3.9 27.1 - - + -
66H THR* 4.6 1.1 - - + -
73H LEU* 3.0 33.4 + - + +
74H ILE* 3.6 5.4 - - - +
76H HIS* 1.3 82.2 - - + +
78H GLN* 1.3 60.3 - - - +
81H TRP* 2.9 41.4 + - + +
92H PHE* 4.0 12.4 - - + -
94H ILE* 3.7 34.3 - - + +
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Residues in contact with GLN 78 (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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74H ILE* 2.9 35.4 + - - +
75H ARG* 3.7 19.8 - - - +
77H LEU* 1.3 78.1 - - - +
79H ARG* 1.3 64.6 + - + +
82H ASP* 3.5 18.9 - - - +
94H ILE* 3.8 17.3 - - + +
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Residues in contact with ARG 79 (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 ARG* 6.1 0.8 - - - +
75H ARG* 3.0 71.2 + - + +
76H HIS* 4.3 2.3 - - - +
78H GLN* 1.3 81.1 - - + +
80H GLY* 1.3 61.1 + - - +
82H ASP* 3.7 16.4 - - - +
302H TYR* 3.4 58.4 + - + -
304H GLU* 4.4 5.5 + - - -
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Residues in contact with GLY 80 (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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76H HIS 2.8 17.4 + - - -
79H ARG* 1.3 79.4 - - - +
81H TRP* 1.3 63.6 + - - +
82H ASP* 3.4 10.9 + - - +
83H PHE* 4.0 0.5 - - - -
300H TRP* 2.8 26.7 + - - -
301H THR 4.7 0.2 - - - -
302H TYR* 3.7 26.6 - - - -
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Residues in contact with TRP 81 (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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48H ASP* 2.8 24.9 + - - -
51H LEU* 3.4 46.9 - - + +
52H SER* 3.6 21.8 - - - -
55H LEU* 4.2 9.6 - - + -
62H ILE* 4.9 0.7 - - + -
76H HIS* 4.1 5.6 + - - -
77H LEU* 2.9 29.0 + - + +
78H GLN* 5.6 0.2 - - - -
80H GLY* 1.3 82.6 - - - +
82H ASP* 1.3 55.4 + - - +
83H PHE* 3.6 23.2 + + - -
84H PHE* 3.9 18.6 - + - -
92H PHE* 3.6 52.4 - + + +
300H TRP* 3.5 37.5 + + + -
301H THR* 4.6 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