Contacts of the helix formed by residues 126 - 138 (chain B) in PDB entry 2C5L
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 GLU 126 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123B ARG* 3.8 29.6 - - - +
124B THR* 4.9 3.1 - - - +
125B VAL* 1.3 76.9 - - - +
127B SER* 1.3 68.1 + - - +
128B ARG* 4.1 12.6 - - + +
129B GLN* 3.0 36.0 + - + +
130B ALA* 3.2 8.3 + - - +
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Residues in contact with SER 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ASP* 2.7 29.4 + - - +
48A GLY 5.0 1.6 - - - -
49A GLU* 3.9 14.7 + - - -
123B ARG* 3.5 10.1 - - - +
126B GLU* 1.3 72.6 + - - +
128B ARG* 1.3 59.2 + - - +
130B ALA* 3.1 4.9 + - - +
131B GLN* 2.8 54.1 + - - +
141B TYR* 3.7 13.5 - - - -
143B GLU* 3.7 13.5 - - - -
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Residues in contact with ARG 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLU* 3.7 16.2 + - - +
126B GLU* 3.1 9.5 - - + +
127B SER* 1.3 80.4 - - - +
129B GLN* 1.3 65.7 + - + +
131B GLN* 3.4 14.7 + - - +
132B ASP* 3.0 44.4 + - - +
135B ARG* 6.1 0.2 - - - +
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Residues in contact with GLN 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B PHE* 3.8 25.6 - - + -
124B THR 4.1 5.5 + - - -
125B VAL* 3.7 13.7 - - + +
126B GLU* 3.0 40.1 + - + +
128B ARG* 1.3 81.0 - - + +
130B ALA* 1.3 63.1 + - - +
132B ASP* 3.2 11.2 + - - +
133B LEU* 3.1 17.7 + - - +
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PHE* 3.7 16.8 - - + -
90B PHE* 3.6 13.6 - - + -
113B LEU* 3.5 9.6 - - + +
125B VAL* 4.6 0.9 - - + +
126B GLU 3.2 5.2 + - - +
127B SER 3.1 5.0 + - - +
129B GLN* 1.3 79.0 - - - +
131B GLN* 1.3 57.8 + - - +
133B LEU 3.3 1.0 + - - -
134B ALA* 2.9 25.6 + - - +
141B TYR* 3.3 42.6 - - + +
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Residues in contact with GLN 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLU* 2.8 30.6 + - - +
164A ARG* 3.3 44.3 - - - +
165A GLN* 3.1 29.3 - - - +
127B SER* 2.8 37.8 + - - +
128B ARG* 3.6 15.2 - - - +
129B GLN 3.3 0.2 - - - -
130B ALA* 1.3 72.3 - - - +
132B ASP* 1.3 56.7 + - - +
134B ALA* 3.3 3.4 + - - -
135B ARG* 2.8 37.0 + - - +
141B TYR* 4.0 6.9 - - + -
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Residues in contact with ASP 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ARG* 3.0 38.6 + - - +
129B GLN* 3.2 11.4 + - - +
131B GLN* 1.3 71.9 - - - +
133B LEU* 1.3 63.3 + - - +
135B ARG* 2.7 35.0 + - - +
136B SER* 3.0 24.4 + - - -
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B PHE* 3.5 35.2 - - + +
93B ILE* 4.2 23.8 - - + -
113B LEU* 4.1 11.7 - - + -
129B GLN 3.1 13.1 + - - +
130B ALA 3.5 8.1 - - - +
132B ASP* 1.3 76.3 - - - +
134B ALA* 1.3 62.5 + - - +
136B SER* 2.7 24.5 + - - +
137B TYR* 3.1 37.0 + - + +
1169B GOL 3.3 39.3 - - - +
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Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A GLN* 3.9 4.3 - - - +
113B LEU* 4.1 9.6 - - + +
130B ALA 2.9 17.0 + - - +
131B GLN 3.7 4.0 - - - +
133B LEU* 1.3 76.2 - - - +
135B ARG* 1.3 58.2 + - - +
137B TYR* 3.2 3.8 + - - -
138B GLY 2.9 23.4 + - - -
139B ILE* 3.0 41.4 + - + +
140B PRO 4.3 0.2 - - - -
141B TYR* 3.8 23.1 - - + +
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Residues in contact with ARG 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ARG* 3.0 23.6 + - - +
165A GLN* 3.6 45.6 + - - +
166A HIS* 4.0 11.7 + - - -
128B ARG* 6.1 0.2 - - - +
131B GLN* 2.8 26.7 + - - +
132B ASP* 2.7 43.7 + - - +
134B ALA* 1.3 77.5 - - - +
136B SER* 1.3 61.2 + - - +
138B GLY* 3.2 13.3 + - - +
139B ILE 5.1 0.2 - - - -
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Residues in contact with SER 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ASP 3.0 13.4 + - - -
133B LEU* 2.7 25.5 + - - +
135B ARG* 1.3 76.9 - - - +
137B TYR* 1.3 72.9 + - - +
138B GLY 3.5 0.2 - - - -
1169B GOL 5.0 2.6 + - - -
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Residues in contact with TYR 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ILE* 3.9 17.4 - - + +
94B HIS* 3.2 43.7 + + - -
97B ARG* 3.3 63.2 + - + +
98B GLU* 5.7 0.4 - - - -
107B ASP 4.9 2.8 - - - +
111B MET* 5.4 0.2 - - - -
113B LEU* 5.7 1.6 - - + -
133B LEU* 3.1 44.9 + - + +
134B ALA* 3.7 6.3 - - - +
135B ARG 3.2 0.4 - - - -
136B SER* 1.3 88.5 - - - +
138B GLY* 1.3 60.9 + - - +
139B ILE* 3.6 28.6 + - + +
1169B GOL 3.3 6.4 + - - -
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Residues in contact with GLY 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ALA 2.9 4.9 + - - -
135B ARG* 3.2 12.3 + - - -
137B TYR* 1.3 78.0 - - - +
139B ILE* 1.4 62.3 + - - +
140B PRO* 4.8 0.5 - - - +
162B GLU* 5.5 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