Contacts of the helix formed by residues 135 - 143 (chain C) in PDB entry 2UZ3
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 135 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98C VAL 3.8 14.4 - - - +
99C GLN* 3.6 9.4 - - - +
101C PHE 3.2 25.4 - - - +
102C ASP* 3.7 25.8 - - - +
103C ASP* 3.9 17.0 - - - +
105C ILE* 3.9 14.8 - - + -
106C CYS* 4.2 4.8 - - - -
133C PHE 3.5 3.1 - - - +
134C GLY* 1.3 82.2 - - - +
136C ILE* 1.3 66.5 + - + +
137C ALA* 3.0 5.8 + - - -
138C LYS* 3.3 17.2 + - + +
139C LEU* 3.7 6.9 + - + +
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Residues in contact with ILE 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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141A THR* 3.5 10.8 - - + +
16C PHE* 4.1 17.9 - - + -
98C VAL* 4.4 9.4 - - + -
99C GLN* 4.0 19.7 - - + +
124C LEU 3.3 20.6 - - - +
125C ASP* 3.2 30.3 - - - +
132C PRO* 4.4 1.3 - - + -
133C PHE 3.2 24.0 + - - +
134C GLY 3.3 0.6 - - - -
135C PRO* 1.3 77.6 - - + +
137C ALA* 1.3 68.6 + - - +
139C LEU* 3.0 24.3 + - + +
140C PHE* 3.3 36.0 + - + -
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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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137A ALA* 3.6 39.2 - - + +
138A LYS* 4.4 9.0 - - - +
141A THR* 4.2 1.3 - - - +
132C PRO* 4.1 23.3 - - + -
134C GLY 4.6 2.8 + - - +
135C PRO 3.0 2.0 + - - -
136C ILE* 1.3 88.6 - - - +
138C LYS* 1.3 63.4 + - + +
140C PHE* 3.3 18.9 + - - +
141C THR 3.9 1.4 + - - -
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Residues in contact with LYS 138 (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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132A PRO* 4.1 22.4 - - + -
137A ALA* 4.3 7.8 - - + +
103C ASP* 2.9 34.3 + - + +
106C CYS* 3.6 24.0 - - + -
135C PRO* 3.3 5.8 + - + +
137C ALA* 1.3 78.4 - - + +
139C LEU* 1.3 58.3 + - - +
141C THR* 2.9 29.1 + - - -
142C TYR* 3.2 23.4 - - + +
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Residues in contact with LEU 139 (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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14C ILE* 5.5 2.7 - - + +
16C PHE* 4.4 15.3 - - + -
98C VAL* 4.0 40.2 - - + -
105C ILE* 4.4 12.6 - - + +
106C CYS* 3.4 37.7 - - + +
109C ALA* 5.0 4.0 - - + -
121C ILE* 4.3 22.7 - - + -
135C PRO* 3.7 1.7 + - + +
136C ILE* 3.0 25.6 + - + +
138C LYS* 1.3 78.1 - - - +
140C PHE* 1.3 60.8 + - - +
142C TYR* 3.8 7.7 - - + +
143C ALA* 2.9 27.8 + - - +
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Residues in contact with PHE 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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140A PHE* 3.3 44.7 - + + -
141A THR* 3.7 10.8 - - - -
146A ILE* 3.8 18.4 - - + -
148A LYS* 2.8 28.6 + - - -
16C PHE* 3.7 13.2 - + - -
18C THR* 3.6 31.9 - - + -
125C ASP* 3.9 9.4 - - + -
136C ILE* 3.3 46.5 + - + -
137C ALA 3.5 6.5 - - - +
138C LYS 3.2 0.6 - - - -
139C LEU* 1.3 79.3 - - - +
141C THR* 1.3 51.3 + - - +
143C ALA* 3.7 2.5 + - - -
146C ILE* 3.4 34.7 - - + +
148C LYS* 4.1 4.0 - - - -
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Residues in contact with THR 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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125A ASP* 3.7 22.8 - - - +
126A LYS* 3.1 37.1 + - + -
131A GLU 4.3 0.2 - - - -
132A PRO* 3.7 32.1 - - + +
136A ILE* 3.6 19.2 - - - +
137A ALA* 4.1 8.7 - - - +
140A PHE* 4.1 6.6 - - - -
148A LYS* 3.2 9.9 + - - +
137C ALA 4.1 0.3 + - - -
138C LYS 2.9 14.0 + - - -
140C PHE* 1.3 80.7 - - - +
142C TYR* 1.3 61.1 + - + +
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Residues in contact with TYR 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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126A LYS* 4.9 6.7 + - - +
130A GLY 3.7 23.8 - - - -
131A GLU* 4.2 11.2 - - + +
132A PRO* 3.5 25.0 - - + +
192A ARG* 3.4 24.0 + - - +
14C ILE* 3.7 10.9 - - + +
106C CYS* 3.6 30.1 - - + +
110C ASN* 3.4 36.6 - - - +
138C LYS* 3.2 38.0 - - + +
139C LEU* 3.1 10.3 + - + +
141C THR* 1.3 80.5 - - + +
143C ALA* 1.3 64.4 + - - +
144C ASP 3.5 2.6 + - - -
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Residues in contact with ALA 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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126A LYS* 5.2 1.2 + - - -
148A LYS* 2.6 31.9 + - - +
14C ILE* 3.7 17.9 - - + +
16C PHE* 3.7 28.7 - - + -
139C LEU 2.9 16.7 + - - +
140C PHE* 4.0 6.1 - - - +
141C THR 3.4 0.6 - - - +
142C TYR* 1.3 75.6 - - - +
144C ASP* 1.3 60.5 + - - +
145C LYS 3.8 9.6 - - - +
146C ILE* 4.2 4.9 - - + +
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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