Contacts of the helix formed by residues 121 - 134 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58H LYS* 3.2 27.8 + - + +
60H VAL* 3.5 26.5 - - + -
72H ARG* 3.1 40.1 + - - +
120H PRO* 1.3 68.4 - - - +
122H PRO* 1.3 68.1 - - + +
124H ILE* 2.8 24.6 + - + +
125H ASP 3.1 8.5 + - - -
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Residues in contact with PRO 122 (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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58H LYS 4.7 3.4 - - - +
120H PRO* 3.6 13.5 - - + -
121H VAL* 1.3 93.4 - - + +
123H ALA* 1.3 56.5 + - - +
125H ASP* 3.2 10.5 + - + +
126H GLU* 2.9 39.4 + - + +
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Residues in contact with ALA 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119H LEU* 4.1 12.1 - - + -
120H PRO* 3.1 20.1 + - + +
121H VAL 3.0 0.8 - - - -
122H PRO* 1.3 79.8 - - - +
124H ILE* 1.3 61.9 + - - +
126H GLU* 3.2 6.7 + - - +
127H LEU* 2.9 26.9 + - + +
159H VAL* 4.0 20.2 - - + +
160H LEU* 5.9 2.0 - - + -
162H SER* 3.5 24.7 - - - +
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Residues in contact with ILE 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D ILE* 5.8 0.9 - - + -
60H VAL* 4.6 22.2 - - + -
62H THR* 5.3 0.9 - - + -
65H ILE* 3.7 20.2 - - + -
68H GLU* 2.9 44.9 - - + +
69H ILE* 3.9 16.8 - - + +
72H ARG* 3.6 9.6 - - - +
119H LEU* 3.3 24.2 - - + -
120H PRO 3.4 0.9 + - - +
121H VAL* 2.8 18.8 + - + +
123H ALA* 1.3 77.7 - - - +
125H ASP* 1.3 62.4 + - - +
127H LEU* 3.1 10.6 + - - +
128H ALA* 3.0 19.6 + - - +
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Residues in contact with ASP 125 (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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72H ARG* 3.1 33.7 - - - +
76H ARG* 2.8 33.1 + - - -
121H VAL 3.1 2.5 + - - +
122H PRO* 3.6 12.6 - - + +
124H ILE* 1.3 76.0 - - - +
126H GLU* 1.3 57.7 + - + +
128H ALA* 3.1 5.5 + - - +
129H ALA* 3.0 22.0 + - - +
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Residues in contact with GLU 126 (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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122H PRO* 2.9 23.4 + - + +
123H ALA* 3.2 10.2 + - - +
125H ASP* 1.3 74.1 - - + +
127H LEU* 1.3 64.7 + - - +
129H ALA* 3.1 9.0 + - - +
130H ILE* 2.9 31.7 + - + +
159H VAL* 3.2 26.5 - - + +
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Residues in contact with LEU 127 (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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65H ILE* 4.9 10.5 - - + -
69H ILE* 3.7 28.5 - - + -
90H VAL* 4.0 16.8 - - + +
119H LEU* 5.2 3.4 - - + -
123H ALA 2.9 18.3 + - - +
124H ILE* 3.1 11.2 + - - +
126H GLU* 1.3 74.8 - - - +
128H ALA* 1.3 64.1 + - - +
130H ILE* 3.3 6.7 + - + +
131H ALA* 3.0 23.8 + - - +
156H ILE* 3.6 27.4 - - + -
159H VAL* 3.4 27.6 - - + -
160H LEU* 4.2 17.7 - - + -
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Residues in contact with ALA 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H ILE* 4.1 14.7 - - + +
72H ARG* 4.3 16.2 - - + -
73H LEU* 3.2 35.6 - - + +
76H ARG* 3.9 10.1 - - - +
124H ILE 3.0 12.2 + - - +
125H ASP* 3.1 11.4 + - - +
127H LEU* 1.3 75.7 - - - +
129H ALA* 1.3 56.6 + - - +
131H ALA* 3.3 2.6 + - - +
132H ASP* 2.9 22.3 + - - +
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Residues in contact with ALA 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H ARG* 3.7 22.1 - - - +
125H ASP 3.0 9.0 + - - +
126H GLU* 3.1 11.8 + - + +
128H ALA* 1.3 73.2 - - - +
130H ILE* 1.3 62.0 + - + +
132H ASP* 2.8 22.9 + - - +
133H GLU* 3.0 15.5 + - - +
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Residues in contact with ILE 130 (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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126H GLU* 2.9 25.6 + - + +
127H LEU* 3.8 5.8 - - + +
129H ALA* 1.3 76.9 - - + +
131H ALA* 1.3 62.1 + - - +
132H ASP 3.2 0.5 + - - -
133H GLU* 3.5 18.3 - - - +
134H HIS* 3.3 20.4 - - - -
151H LEU* 3.3 13.6 - - + +
152H PRO* 4.5 14.8 - - + -
155H ARG* 4.3 45.8 - - + +
156H ILE* 4.4 20.6 - - + -
159H VAL* 4.8 10.8 - - + -
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Residues in contact with ALA 131 (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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73H LEU* 4.1 15.5 - - + -
78H TRP* 3.5 17.1 - - - -
86H GLY* 4.2 7.6 - - - +
90H VAL* 3.4 32.5 - - + -
127H LEU 3.0 11.7 + - - +
128H ALA* 3.7 4.5 - - - +
130H ILE* 1.3 77.6 - - - +
132H ASP* 1.3 60.2 + - - +
134H HIS* 3.8 11.5 + - - +
138H VAL* 4.6 4.0 - - + +
151H LEU* 3.7 14.3 - - + +
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Residues in contact with ASP 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H LEU* 4.4 3.6 - - + -
76H ARG* 4.1 22.2 + - - +
78H TRP* 2.7 36.7 + - - +
128H ALA 2.9 12.6 + - - +
129H ALA* 2.8 16.2 + - - +
131H ALA* 1.3 74.9 - - - +
133H GLU* 1.3 63.7 + - - +
134H HIS 3.1 3.4 + - - -
135H ARG* 3.2 21.8 + - - +
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Residues in contact with GLU 133 (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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129H ALA 3.0 11.9 + - - +
130H ILE* 3.5 17.3 - - - +
132H ASP* 1.3 76.4 - - - +
134H HIS* 1.3 74.4 + - + +
135H ARG* 3.3 3.6 + - - +
136H ASP* 4.8 2.3 - - - +
155H ARG* 2.3 44.2 + - - -
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Residues in contact with HIS 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H ILE* 3.3 23.8 - - + +
131H ALA 3.8 5.3 + - - +
132H ASP 3.1 1.4 - - - -
133H GLU* 1.3 100.4 + - + +
135H ARG* 1.3 62.3 + - - +
136H ASP* 3.3 8.9 + - - -
137H ALA* 3.4 11.8 + - + +
138H VAL* 3.2 25.0 + - + +
150H ILE* 5.3 9.3 - - + +
151H LEU* 3.4 27.1 - - + -
152H PRO* 3.6 23.1 - - + +
155H ARG* 4.4 2.1 + - - -
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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