Contacts of the helix formed by residues 121 - 134 (chain G) 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 VAL 121 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58G LYS* 3.1 33.2 + - + +
60G VAL* 3.5 24.7 - - + -
72G ARG* 3.1 46.9 + - - +
120G PRO* 1.3 71.6 - - - +
122G PRO* 1.3 66.1 - - + +
124G ILE* 2.8 25.2 + - + +
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Residues in contact with PRO 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58G LYS 4.6 4.9 - - - +
120G PRO* 3.6 12.3 - - + -
121G VAL* 1.3 93.9 - - + +
123G ALA* 1.3 56.9 + - - +
125G ASP* 3.0 11.3 + - + +
126G GLU* 2.5 42.1 + - - +
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Residues in contact with ALA 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119G LEU* 4.2 11.9 - - + -
120G PRO* 3.1 17.2 + - + +
121G VAL 3.1 0.8 - - - -
122G PRO* 1.3 79.6 - - - +
124G ILE* 1.3 64.3 + - - +
126G GLU* 3.1 12.7 + - - +
127G LEU* 3.0 28.5 + - + +
159G VAL* 3.8 14.6 - - + +
160G LEU* 6.0 0.9 - - + -
162G SER* 3.4 27.1 - - - +
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Residues in contact with ILE 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G VAL* 4.5 24.0 - - + -
62G THR* 5.6 0.2 - - - +
65G ILE* 3.7 21.1 - - + -
68G GLU* 3.0 42.4 - - + +
69G ILE* 4.1 15.6 - - + +
72G ARG* 3.5 14.1 - - - +
119G LEU* 3.3 23.6 - - + -
120G PRO 3.3 1.3 + - - +
121G VAL* 2.8 16.0 + - - +
123G ALA* 1.3 78.6 - - - +
125G ASP* 1.3 62.4 + - - +
127G LEU* 3.1 9.7 + - + +
128G ALA* 3.0 20.4 + - - +
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Residues in contact with ASP 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72G ARG* 3.0 31.8 - - - +
76G ARG* 3.0 22.6 + - - -
121G VAL 3.1 0.2 + - - -
122G PRO* 3.0 15.5 + - + +
124G ILE* 1.3 75.8 - - - +
126G GLU* 1.3 63.3 + - + +
128G ALA* 3.1 6.4 + - - +
129G ALA* 3.0 16.6 + - - +
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Residues in contact with GLU 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G PRO* 2.5 41.9 + - - +
123G ALA* 3.1 15.8 + - - +
125G ASP* 1.3 77.2 - - + +
127G LEU* 1.3 64.5 + - - +
129G ALA* 3.0 9.3 + - + +
130G ILE* 2.9 29.1 + - + +
159G VAL* 4.6 16.0 - - + +
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Residues in contact with LEU 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G ILE* 5.6 4.5 - - + -
69G ILE* 4.2 26.0 - - + -
90G VAL* 4.6 14.1 - - + +
119G LEU* 5.1 6.3 - - + -
123G ALA 3.0 18.4 + - - +
124G ILE* 3.1 11.9 + - - +
126G GLU* 1.3 76.0 - - - +
128G ALA* 1.3 63.6 + - - +
130G ILE* 3.2 7.6 + - + +
131G ALA* 3.0 22.7 + - - +
156G ILE* 3.8 33.4 - - + +
159G VAL* 3.6 24.5 - - + -
160G LEU* 3.8 23.8 - - + -
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Residues in contact with ALA 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G ILE* 4.4 12.5 - - + +
72G ARG* 4.1 20.6 - - + -
73G LEU* 3.2 31.6 - - + +
76G ARG* 3.9 11.7 - - - +
124G ILE 3.0 12.8 + - - +
125G ASP* 3.1 12.1 + - - +
127G LEU* 1.3 76.4 - - - +
129G ALA* 1.3 55.6 + - - +
131G ALA* 3.2 2.4 + - - -
132G ASP* 2.9 22.2 + - - +
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Residues in contact with ALA 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76G ARG* 3.6 21.9 - - - +
125G ASP 3.0 9.3 + - - +
126G GLU* 3.0 12.7 + - + +
128G ALA* 1.3 76.8 - - - +
130G ILE* 1.3 58.3 - - + +
132G ASP* 2.8 21.9 + - - +
133G GLU* 3.0 16.0 + - - +
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Residues in contact with ILE 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126G GLU* 2.9 18.5 + - + +
127G LEU* 3.7 15.5 - - + +
129G ALA* 1.3 75.3 - - + +
131G ALA* 1.3 64.4 + - - +
132G ASP 3.2 0.5 + - - -
133G GLU* 3.4 30.1 - - - +
134G HIS* 3.4 11.2 - - + -
151G LEU* 3.5 13.0 - - + +
152G PRO* 4.8 7.4 - - + -
155G ARG* 4.2 37.5 - - + +
156G ILE* 4.5 15.7 - - + +
159G VAL* 3.6 31.0 - - + -
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Residues in contact with ALA 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G ILE* 5.3 0.2 - - + -
73G LEU* 3.9 18.8 - - + -
78G TRP* 3.6 17.5 - - - -
86G GLY* 4.6 5.4 - - - +
90G VAL* 3.5 31.6 - - + +
127G LEU 3.0 10.3 + - - +
128G ALA* 3.7 7.9 - - - +
130G ILE* 1.3 76.7 - - - +
132G ASP* 1.3 60.5 + - - +
134G HIS* 3.9 10.1 + - - +
138G VAL* 4.6 4.8 - - + +
151G LEU* 4.1 13.0 - - + +
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Residues in contact with ASP 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G LEU* 4.4 1.3 - - + -
76G ARG* 3.9 28.6 + - - +
78G TRP* 2.9 30.7 + - - -
128G ALA 2.9 12.9 + - - +
129G ALA* 2.8 16.2 + - - +
131G ALA* 1.3 75.1 - - - +
133G GLU* 1.3 65.4 + - - +
134G HIS 3.1 3.9 + - - -
135G ARG* 3.2 21.0 + - - +
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Residues in contact with GLU 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129G ALA 3.0 9.3 + - - +
130G ILE* 3.4 19.3 - - - +
132G ASP* 1.3 76.2 - - - +
134G HIS* 1.3 79.3 + - + +
135G ARG 3.4 3.8 + - - -
155G ARG* 2.2 43.9 + - - -
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Residues in contact with HIS 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G ILE* 3.4 13.7 - - + -
131G ALA 3.9 5.7 + - - +
132G ASP 3.1 1.4 + - - -
133G GLU* 1.3 104.6 + - + +
135G ARG* 1.3 62.2 + - - +
136G ASP 3.4 2.4 + - - -
137G ALA* 3.4 16.3 + - + +
138G VAL* 3.2 24.7 + - + +
150G ILE* 5.3 6.6 - - + +
151G LEU* 3.3 37.2 - - + -
152G PRO* 3.9 18.9 - - + +
155G ARG* 4.2 3.3 + - - -
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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
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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