Contacts of the helix formed by residues 136 - 143 (chain B) in PDB entry 1CP3
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 LEU 136 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B LEU* 3.5 32.8 - - + -
125B GLY* 2.9 29.8 + - - +
126B ILE 4.3 3.4 - - - +
127B ILE* 3.9 31.2 - - + -
134B VAL 3.6 0.6 + - - -
135B ASP* 1.3 73.8 + - - +
137B LYS* 1.3 59.9 + - - +
139B ILE* 3.1 11.9 + - + +
140B THR* 2.9 42.3 + - + +
160B ILE* 4.4 25.8 - - + -
197B TYR* 4.8 12.3 - - + +
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Residues in contact with LYS 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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201A PRO* 5.3 10.3 - - - -
203A TYR* 5.9 2.9 - - - -
135B ASP* 2.9 18.2 + - - +
136B LEU* 1.3 77.6 - - - +
138B LYS* 1.3 62.3 + - - +
140B THR* 3.3 11.6 + - - +
141B ASN* 3.0 55.8 + - - +
190B ASP* 3.4 30.1 + - - -
195B TYR* 4.4 7.8 + - - -
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Residues in contact with LYS 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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93B ARG* 4.9 17.5 - - - +
97B VAL* 4.2 35.1 - - + +
134B VAL* 4.8 7.9 - - + +
135B ASP* 3.2 23.8 + - + +
137B LYS* 1.3 80.9 - - - +
139B ILE* 1.3 59.7 + - - +
141B ASN* 3.9 10.4 + - - +
142B PHE* 3.3 24.0 - - + -
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Residues in contact with ILE 139 (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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96B ILE* 3.9 20.4 - - + -
97B VAL* 5.4 4.3 - - + -
100B MET* 3.7 27.7 - - + +
118B LEU* 4.5 13.7 - - + -
127B ILE* 3.6 31.2 - - + -
134B VAL* 4.1 13.9 - - + -
135B ASP 3.6 11.0 - - - +
136B LEU* 3.1 19.7 + - + +
138B LYS* 1.3 76.8 - - - +
140B THR* 1.3 64.0 + - + +
142B PHE* 3.6 18.3 - - - -
143B PHE* 3.7 13.0 - - - -
158B PHE* 4.5 12.6 - - + -
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Residues in contact with THR 140 (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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136B LEU* 2.9 24.1 + - + +
137B LYS* 3.3 23.0 + - - +
139B ILE* 1.3 75.5 - - + +
141B ASN* 1.3 66.4 + - - +
142B PHE 3.1 2.9 - - - -
143B PHE* 2.9 20.4 + - - +
144B ARG* 3.9 3.5 + - - -
158B PHE* 3.8 29.2 - - + -
193B PHE* 3.9 10.8 - - - -
195B TYR* 3.8 34.4 + - + -
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Residues in contact with ASN 141 (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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137B LYS* 3.0 53.4 + - - +
138B LYS* 4.2 8.2 - - - +
139B ILE 3.4 0.6 - - - -
140B THR* 1.3 77.3 + - - +
142B PHE* 1.3 60.6 + - + +
143B PHE 3.2 0.7 + - - -
144B ARG* 3.3 48.0 + - - +
147B ARG* 3.3 25.7 + - - +
190B ASP* 4.8 0.4 + - - -
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Residues in contact with PHE 142 (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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97B VAL* 3.6 37.7 - - + -
100B MET* 4.0 11.7 - - + +
101B ARG* 3.5 51.4 - - + -
104B SER* 3.6 31.5 + - - -
138B LYS* 3.3 29.8 - - + -
139B ILE* 3.6 10.1 - - - -
140B THR 3.0 1.0 + - - -
141B ASN* 1.3 77.9 - - + +
143B PHE* 1.3 68.0 + - + +
144B ARG 3.5 0.2 - - - -
147B ARG* 3.5 21.2 - - - +
148B CYS* 3.6 4.5 - - - +
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Residues in contact with PHE 143 (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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100B MET* 3.8 35.9 - - + -
103B VAL* 4.0 4.5 - - + -
104B SER* 3.6 27.6 - - - -
108B HIS* 5.2 0.2 - - - -
114B PHE* 3.6 32.5 - + - -
139B ILE 3.7 20.6 - - - -
140B THR 2.9 7.1 + - - +
142B PHE* 1.3 81.1 - - + +
144B ARG* 1.3 67.5 + - - +
145B GLY* 4.3 0.3 - - - -
148B CYS* 4.1 9.8 - - - +
151B LEU* 4.0 20.6 - - + +
156B LYS* 3.0 36.2 + - + +
158B PHE* 3.6 25.4 - + + -
193B PHE* 3.7 8.7 - - + -
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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