Contacts of the helix formed by residues 64 - 76 (chain F) in PDB entry 5U07
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62F THR* 3.4 4.2 - - - -
63F ARG* 1.3 79.4 - - - +
65F ILE* 1.3 65.3 + - - +
66F ILE 3.4 2.6 + - - +
67F SER* 3.8 16.8 + - - +
68F GLU 3.7 10.9 + - - -
110F ALA 5.8 2.2 - - - +
111F PRO 5.1 1.8 - - - +
112F ALA* 4.6 13.8 - - + +
113F THR 4.9 0.2 - - - +
208G ASP* 3.0 33.7 + - - +
210G ILE* 2.7 61.6 + - + +
211G PRO 5.2 1.3 - - - -
212G LYS* 3.4 25.5 - - - +
215G ASP* 3.1 27.8 + - - +
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Residues in contact with ILE 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F THR* 3.4 23.8 - - - +
63F ARG 3.6 1.0 + - - -
64F ARG* 1.3 74.2 - - - +
66F ILE* 1.3 84.4 + - + +
68F GLU* 2.9 8.2 + - - +
69F ILE* 2.9 40.1 + - + +
90F VAL* 5.6 1.6 - - + -
91F VAL* 3.4 31.0 - - + -
113F THR* 3.9 8.2 - - + +
117F PHE* 3.8 44.4 - - + -
119F LEU* 5.1 3.4 - - + -
124F ILE* 4.5 21.5 - - + -
127F LEU* 5.7 2.9 - - + -
210G ILE* 5.5 0.2 - - - -
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Residues in contact with ILE 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F ARG 3.4 0.6 - - - -
65F ILE* 1.3 80.9 - - + +
67F SER* 1.3 57.7 + - - +
69F ILE* 4.7 0.4 - - - -
70F ALA* 2.9 28.9 + - + +
84F ASP* 4.6 6.7 - - - +
87F ALA* 3.6 27.7 - - + +
88F ARG* 4.5 6.1 - - + +
91F VAL* 3.5 44.6 - - + -
102F LEU* 3.8 19.5 - - + -
110F ALA* 3.8 17.3 - - + -
111F PRO* 3.7 34.5 - - + +
113F THR* 4.2 4.7 - - + -
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Residues in contact with SER 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F ARG* 3.8 24.7 + - - +
65F ILE 3.2 0.8 - - - -
66F ILE* 1.3 80.0 - - - +
68F GLU* 1.3 57.0 + - - +
70F ALA* 3.3 6.4 + - - +
71F LYS* 2.9 26.7 + - - +
110F ALA* 3.9 25.3 + - - +
111F PRO 5.2 0.6 + - - -
210G ILE* 6.1 1.8 - - - +
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Residues in contact with GLU 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F ARG 3.7 1.9 + - - +
65F ILE* 2.9 10.9 + - - +
67F SER* 1.3 76.9 - - - +
69F ILE* 1.3 64.2 + - - +
71F LYS* 2.9 36.1 + - - +
72F ARG* 2.4 61.1 + - - +
124F ILE* 3.0 20.2 - - + +
210G ILE* 3.5 33.8 - - + +
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Residues in contact with ILE 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F ILE* 2.9 34.5 + - + +
66F ILE 3.9 3.6 - - - +
68F GLU* 1.3 79.3 - - - +
70F ALA* 1.3 57.6 + - - +
72F ARG* 3.2 4.6 + - - +
73F LEU* 2.9 40.9 + - + +
87F ALA* 3.9 19.5 - - + +
90F VAL* 4.2 16.8 - - + -
124F ILE* 3.9 23.3 - - + +
127F LEU* 4.0 33.4 - - + -
128F ALA* 4.4 14.4 - - - -
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Residues in contact with ALA 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F ILE* 2.9 19.8 + - + +
67F SER* 3.4 9.4 - - - +
69F ILE* 1.3 76.5 - - - +
71F LYS* 1.3 57.2 + - - +
73F LEU* 3.5 0.6 + - - -
74F ARG* 2.9 42.8 + - - +
83F ALA* 3.5 33.1 - - + +
84F ASP* 4.6 6.3 - - + +
87F ALA* 4.1 2.4 - - + +
110F ALA* 5.4 3.8 - - + -
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Residues in contact with LYS 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F SER 2.9 12.6 + - - +
68F GLU* 2.9 36.9 + - - +
70F ALA* 1.3 77.9 - - - +
72F ARG* 1.3 66.1 + - - +
74F ARG* 3.3 18.8 + - - +
75F GLU* 3.0 23.8 + - + +
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Residues in contact with ARG 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F VAL* 6.3 0.2 - - - +
68F GLU* 2.4 51.7 + - - +
69F ILE* 3.2 5.6 + - - +
71F LYS* 1.3 82.1 - - - +
73F LEU* 1.3 57.8 + - - +
75F GLU* 2.9 11.5 + - - +
76F ARG* 2.8 34.3 + - + +
121F VAL* 3.1 38.3 + - - +
124F ILE* 3.2 18.0 - - - +
125F ASP* 2.9 45.0 - - - +
128F ALA* 4.4 12.8 - - + -
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Residues in contact with LEU 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F ILE* 2.9 32.2 + - + +
70F ALA 4.0 3.4 - - - +
72F ARG* 1.3 75.5 - - - +
74F ARG* 1.3 62.5 + - - +
76F ARG* 3.0 20.8 + - + +
77F GLY 3.4 0.3 + - - -
78F TRP* 3.2 42.9 + - + +
83F ALA* 4.0 30.1 - - + +
86F GLY* 4.6 5.2 - - - -
87F ALA 4.4 4.7 - - - +
128F ALA* 3.5 34.3 - - + +
131F ALA* 4.4 15.3 - - + -
132F ASP* 4.6 10.8 - - + +
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Residues in contact with ARG 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F ALA* 2.9 33.6 + - - +
71F LYS* 3.6 26.1 - - - +
73F LEU* 1.3 76.3 - - - +
75F GLU* 1.3 60.4 + - - +
77F GLY* 3.4 10.4 + - - -
78F TRP 3.8 19.4 - - - +
80F ALA* 3.8 37.6 + - - +
83F ALA* 4.1 4.6 - - + +
84F ASP* 5.6 0.8 - - - +
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Residues in contact with GLU 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F LYS* 3.0 14.4 + - + +
72F ARG* 2.9 12.3 + - - +
74F ARG* 1.3 76.1 - - - +
76F ARG* 1.3 79.2 + - - +
77F GLY* 3.2 1.8 + - - -
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Residues in contact with ARG 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F ARG* 2.8 21.1 + - + +
73F LEU* 3.0 20.1 + - + +
75F GLU* 1.3 90.1 - - - +
77F GLY* 1.3 55.6 + - - +
78F TRP* 3.6 14.0 + - + +
125F ASP* 4.1 17.6 + - - -
128F ALA* 5.0 4.5 - - + +
129F ALA* 4.7 19.4 - - - +
132F ASP* 3.1 28.9 + - - +
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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