Contacts of the helix formed by residues 134 - 151 (chain C) in PDB entry 3U8Z
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 PRO 134 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C TYR* 3.7 24.4 - - + +
133C CYS* 1.4 88.3 - - - +
135C PRO* 1.4 76.5 - - + +
136C GLU* 3.4 4.3 + - + +
137C ALA* 3.5 11.4 + - + +
138C SER* 3.1 18.8 + - - -
214C LEU* 3.6 21.5 - - + -
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Residues in contact with PRO 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C TYR* 4.6 4.9 - - + +
133C CYS 4.0 1.1 - - - +
134C PRO* 1.4 86.9 - - + +
136C GLU* 1.3 61.9 + - - +
138C SER* 3.2 9.3 + - - -
139C VAL* 3.2 28.0 + - + +
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Residues in contact with GLU 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C PRO* 3.4 2.8 - - + +
135C PRO* 1.3 75.6 - - - +
137C ALA* 1.4 67.2 + - - +
139C VAL* 3.3 16.1 - - + +
140C LEU* 3.3 29.3 + - + +
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Residues in contact with ALA 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C CYS* 3.8 18.4 - - - -
134C PRO* 3.5 18.8 + - + +
136C GLU* 1.4 76.5 - - - +
138C SER* 1.3 52.4 + - - +
140C LEU* 3.2 11.7 + - - +
141C LEU* 2.8 37.8 + - - +
210C ILE* 4.2 18.6 - - + +
214C LEU* 4.7 4.9 - - + -
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Residues in contact with SER 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ILE* 5.6 5.1 - - - +
133C CYS* 3.6 17.4 - - - -
134C PRO 3.1 14.4 + - - -
135C PRO* 3.3 14.8 - - - -
136C GLU 3.2 0.4 - - - -
137C ALA* 1.3 77.2 - - - +
139C VAL* 1.4 58.6 + - - +
141C LEU* 3.6 5.4 + - - +
142C ALA* 3.1 27.5 + - - +
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Residues in contact with VAL 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C PRO* 3.2 12.9 + - + +
136C GLU* 3.3 21.8 - - + +
138C SER* 1.4 74.9 - - - +
140C LEU* 1.4 66.0 + - + +
142C ALA* 3.5 7.1 + - - +
143C SER* 3.2 24.9 + - - -
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Residues in contact with LEU 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C GLU* 3.3 24.0 + - + +
137C ALA* 3.2 13.5 + - - +
139C VAL* 1.4 75.1 - - + +
141C LEU* 1.3 65.2 + - - +
143C SER* 3.2 10.4 + - - -
144C TYR* 3.1 41.7 + - + +
210C ILE* 4.0 22.9 - - + -
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Residues in contact with LEU 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C ILE* 3.9 32.1 - - + -
133C CYS* 3.7 29.2 - - - -
137C ALA 2.8 18.1 + - - +
138C SER* 3.7 5.6 - - - +
140C LEU* 1.3 70.0 - - - +
142C ALA* 1.3 57.0 + - - +
144C TYR* 3.2 4.3 + - - -
145C ALA* 2.9 24.4 + - - +
207C TYR* 3.2 66.9 - - + +
210C ILE* 3.8 23.5 - - + +
211C ALA* 4.2 2.5 - - + +
214C LEU* 4.6 3.8 - - + -
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Residues in contact with ALA 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C LEU* 6.5 1.3 - - + -
138C SER 3.1 18.3 + - - +
139C VAL* 3.7 9.2 - - - +
140C LEU 3.3 0.2 - - - -
141C LEU* 1.3 74.8 - - - +
143C SER* 1.4 56.0 + - - +
145C ALA* 3.4 8.8 + - - +
146C VAL* 3.1 33.3 + - + +
207C TYR* 5.3 0.2 - - - -
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Residues in contact with SER 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C VAL 3.2 12.6 + - - -
140C LEU* 3.2 15.6 + - - -
142C ALA* 1.4 73.5 - - - +
144C TYR* 1.3 65.7 + - - +
146C VAL* 3.4 10.1 + - - +
147C GLN* 3.2 26.3 + - - +
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Residues in contact with TYR 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C LEU* 3.1 36.2 + - + +
141C LEU 3.2 6.0 + - - +
143C SER* 1.3 73.1 - - - +
145C ALA* 1.3 55.4 + - - +
147C GLN* 3.3 7.0 + - + -
148C ALA* 2.8 37.5 + - - +
203C ALA* 3.6 29.3 - - + +
206C GLU* 3.6 40.9 + - + +
207C TYR* 4.2 9.6 - - + -
210C ILE* 3.6 29.6 - - + -
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Residues in contact with ALA 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C PHE* 4.1 13.3 - - + -
123C LYS* 3.9 27.4 - - + -
141C LEU 2.9 13.8 + - - +
142C ALA* 3.5 12.8 - - - +
143C SER 3.4 0.2 - - - -
144C TYR* 1.3 72.8 - - - +
146C VAL* 1.4 64.1 + - - +
148C ALA* 3.3 2.1 + - - +
149C LYS* 3.0 24.1 + - - +
207C TYR* 4.1 5.7 - - + -
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Residues in contact with VAL 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C ALA* 3.1 18.0 + - + +
143C SER* 3.6 10.8 - - - +
144C TYR 3.3 0.2 - - - -
145C ALA* 1.4 74.7 - - - +
147C GLN* 1.3 62.6 + - + +
149C LYS* 3.2 22.0 + - - +
150C TYR* 3.4 11.2 + - + -
157C VAL* 3.5 22.8 - - + +
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Residues in contact with GLN 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C SER 3.2 13.3 + - - +
144C TYR* 3.3 12.3 + - + +
146C VAL* 1.3 78.3 - - + +
148C ALA* 1.4 57.6 + - - +
151C GLY* 2.7 36.5 + - - -
152C ASP 4.0 2.3 + - - -
157C VAL* 3.5 30.6 - - + +
201C ASP* 4.0 1.4 - - - +
203C ALA* 3.9 14.8 - - + +
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Residues in contact with ALA 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ARG* 3.9 7.8 + - - -
119C PHE* 3.7 26.9 - - + -
144C TYR 2.8 20.9 + - - +
145C ALA 3.7 5.2 - - - +
147C GLN* 1.4 69.7 - - - +
149C LYS* 1.3 64.6 + - - +
152C ASP* 4.4 0.7 - - - +
201C ASP* 2.6 31.6 - - - +
203C ALA* 3.6 6.7 - - + +
204C GLU* 3.7 20.3 - - + +
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Residues in contact with LYS 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLU* 2.8 31.5 + - - -
41A TRP* 4.3 9.6 - - + -
52A ARG* 2.9 36.6 + - - +
119C PHE* 5.8 0.2 - - - -
145C ALA 3.0 13.9 + - - +
146C VAL* 3.2 14.1 + - - +
148C ALA* 1.3 77.2 - - - +
150C TYR* 1.4 92.2 + - + +
153C TYR* 4.0 1.2 - - - -
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Residues in contact with TYR 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLU* 3.6 6.2 + - - -
41A TRP* 3.2 35.3 + + - -
146C VAL* 3.4 8.3 + - + -
149C LYS* 1.4 118.2 + - + +
151C GLY* 1.3 60.3 + - - +
152C ASP* 3.2 4.5 - - - -
153C TYR* 3.1 38.2 + + - -
154C ASP* 3.0 29.2 + - + +
157C VAL* 3.9 28.7 - - + -
158C HIS* 3.7 47.1 - + + +
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Residues in contact with GLY 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C GLN* 2.7 29.7 + - - -
150C TYR* 1.3 70.7 - - - +
152C ASP* 1.3 59.6 + - - +
153C TYR 3.2 1.8 + - - -
154C ASP 3.4 19.4 + - - +
155C PRO* 4.5 3.8 - - - +
157C VAL* 4.0 14.1 - - - +
199C ALA* 5.4 2.3 - - - +
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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