Contacts of the helix formed by residues 64 - 76 (chain H) in PDB entry 5U0A
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 ARG 64 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D ASP* 2.2 39.5 + - - +
210D ILE* 3.2 28.3 + - + +
211D PRO* 5.2 0.2 - - - +
212D LYS* 3.5 40.0 - - - +
214D ASN* 6.0 1.6 - - - +
217D GLY* 4.2 16.4 + - - -
62H THR* 3.0 14.0 + - - +
63H ARG* 1.3 93.2 - - + +
65H ILE* 1.3 61.7 + - - +
66H ILE 3.4 2.7 - - - +
67H SER* 3.9 16.8 + - - +
68H GLU* 3.7 17.3 + - - +
110H ALA 5.9 3.6 - - - +
111H PRO 5.4 0.7 - - - -
112H ALA* 4.3 19.0 - - + +
48M T 5.7 4.4 - - - -
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Residues in contact with ILE 65 (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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62H THR* 4.2 15.2 - - + +
63H ARG 3.6 3.4 + - - -
64H ARG* 1.3 74.4 - - - +
66H ILE* 1.3 69.1 + - - +
68H GLU* 3.1 5.0 + - - +
69H ILE* 3.0 30.1 + - + +
90H VAL* 5.9 0.4 - - + -
91H VAL* 4.0 17.7 - - + -
113H THR* 4.0 23.0 - - + +
117H PHE* 4.1 19.5 - - + -
119H LEU* 4.2 21.1 - - + -
124H ILE* 3.9 19.7 - - + -
127H LEU* 4.0 26.9 - - + -
160H LEU* 5.1 1.6 - - + -
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Residues in contact with ILE 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H ARG 3.4 0.6 - - - -
65H ILE* 1.3 79.3 - - + +
67H SER* 1.3 57.2 + - - +
69H ILE* 3.4 2.1 + - - -
70H ALA* 2.9 27.8 + - + +
84H ASP* 4.4 7.9 - - - +
87H ALA* 3.4 30.4 - - + +
88H ARG* 4.3 8.3 - - + +
91H VAL* 3.7 41.7 - - + -
102H LEU* 3.7 22.7 - - + -
110H ALA* 3.8 18.2 - - + -
111H PRO* 3.5 27.4 - - + +
113H THR* 4.6 2.5 - - + -
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Residues in contact with SER 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D ILE* 6.0 2.9 - - - +
212D LYS* 5.9 0.9 + - - -
64H ARG* 3.9 21.3 + - - +
65H ILE 3.3 0.6 - - - -
66H ILE* 1.3 78.2 - - - +
68H GLU* 1.3 58.7 + - - +
70H ALA* 3.1 10.3 + - - +
71H LYS* 3.0 27.8 + - - +
110H ALA* 4.2 20.3 - - - +
111H PRO 5.6 0.2 + - - -
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Residues in contact with GLU 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D ILE* 4.0 35.4 - - + +
64H ARG 3.7 10.5 + - - +
65H ILE 3.1 7.9 + - - +
67H SER* 1.3 75.7 + - - +
69H ILE* 1.3 67.7 + - - +
71H LYS* 3.0 49.6 + - - +
72H ARG* 2.8 53.9 + - - +
124H ILE* 3.5 13.7 - - + -
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Residues in contact with ILE 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65H ILE* 3.0 31.7 + - + +
66H ILE* 3.8 4.5 - - - +
68H GLU* 1.3 75.6 - - - +
70H ALA* 1.3 57.8 + - - +
72H ARG* 3.2 8.0 + - - +
73H LEU* 2.9 36.9 + - + +
87H ALA* 3.9 20.0 - - + +
90H VAL* 3.9 33.4 - - + -
91H VAL* 5.7 0.9 - - + -
124H ILE* 3.9 20.9 - - + +
127H LEU* 4.1 19.5 - - + -
128H ALA* 4.2 21.1 - - - -
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Residues in contact with ALA 70 (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 ILE* 2.9 15.2 + - + +
67H SER* 3.2 16.4 - - - +
68H GLU 3.1 0.2 - - - -
69H ILE* 1.3 78.2 - - - +
71H LYS* 1.3 55.2 + - - +
74H ARG* 2.9 48.4 + - - +
83H ALA* 3.8 26.9 - - - +
84H ASP* 4.7 6.1 - - + +
87H ALA* 4.2 1.7 - - + +
110H ALA* 5.8 2.2 - - + -
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Residues in contact with LYS 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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67H SER* 3.0 11.9 + - - +
68H GLU* 3.1 48.4 + - - +
70H ALA* 1.3 75.2 - - - +
72H ARG* 1.3 60.6 + - + +
74H ARG* 3.3 16.4 + - - +
75H GLU* 2.9 30.8 + - - +
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Residues in contact with ARG 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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68H GLU* 2.8 55.1 + - - +
69H ILE* 3.2 4.5 + - - +
71H LYS* 1.3 80.6 - - + +
73H LEU* 1.3 62.3 + - - +
75H GLU* 3.0 22.3 - - + +
76H ARG* 3.0 26.1 + - - +
121H VAL* 4.3 13.9 - - - +
124H ILE* 3.0 37.6 - - - +
125H ASP* 3.8 34.1 - - - +
128H ALA* 3.7 18.4 - - + -
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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
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69H ILE* 2.9 26.4 + - + +
72H ARG* 1.3 74.8 - - - +
74H ARG* 1.3 62.4 + - - +
76H ARG* 3.1 23.5 + - - -
78H TRP* 3.2 52.6 + - + +
83H ALA* 3.9 34.1 - - + +
86H GLY 4.3 1.8 - - - -
87H ALA 4.2 9.2 - - - +
128H ALA* 3.2 30.5 - - + +
131H ALA* 4.1 19.1 - - + -
132H ASP* 4.2 2.7 - - + +
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Residues in contact with ARG 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70H ALA* 2.9 43.6 + - - +
71H LYS* 3.6 17.4 - - - +
73H LEU* 1.3 77.7 - - - +
75H GLU* 1.3 58.9 + - - +
77H GLY* 3.4 10.2 + - - -
78H TRP 4.0 18.8 - - - +
80H ALA* 3.8 39.8 + - - +
83H ALA* 4.0 5.4 - - + +
84H ASP* 5.3 1.4 - - - +
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Residues in contact with GLU 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 LYS 2.9 17.3 + - - +
72H ARG* 3.0 33.7 - - + +
74H ARG* 1.3 76.3 - - - +
76H ARG* 1.3 70.3 + - - +
77H GLY 3.2 2.3 + - - -
125H ASP* 4.9 4.3 - - - +
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Residues in contact with ARG 76 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72H ARG 3.0 17.9 + - - +
73H LEU* 3.1 19.4 + - - +
75H GLU* 1.3 87.3 + - - +
77H GLY* 1.3 57.9 + - - +
78H TRP* 3.6 11.1 - - + +
125H ASP* 3.4 25.5 + - - -
128H ALA* 4.1 14.5 - - - +
129H ALA* 3.6 30.5 - - - +
132H ASP* 3.5 31.5 + - - +
135H ARG* 5.0 3.5 + - - -
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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