Contacts of the helix formed by residues 134 - 145 (chain A) in PDB entry 1CIP
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 SER 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A GLY* 3.3 18.4 - - - -
97A ASP* 5.7 0.8 + - - -
132A LYS 3.6 3.2 + - - -
133A ASP* 1.3 74.0 + - - +
135A GLY* 1.3 59.0 + - - +
137A GLN* 3.4 7.4 + - - +
138A ALA* 2.9 27.7 + - - +
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Residues in contact with GLY 135 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A MET* 3.9 6.9 - - - +
93A ILE* 3.6 12.6 - - - +
94A ASP 3.4 21.3 - - - -
96A GLY* 3.6 2.8 - - - +
133A ASP* 2.9 10.1 + - - -
134A SER* 1.3 79.6 + - - +
136A VAL* 1.3 66.3 + - - +
138A ALA* 3.2 6.7 + - - +
139A CYS* 3.0 19.8 + - - +
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Residues in contact with VAL 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ILE* 4.2 14.8 - - + -
84A ILE* 3.7 17.5 - - + +
85A ILE* 5.1 3.4 - - + -
88A MET* 3.8 14.1 - - - +
95A PHE* 3.8 29.8 - - + -
130A LEU* 3.2 35.9 - - + +
131A TRP* 4.3 14.4 - - + +
133A ASP* 3.2 12.0 + - + +
135A GLY* 1.3 74.8 - - - +
137A GLN* 1.3 58.7 + - - +
139A CYS* 3.2 4.0 + - - +
140A PHE* 2.8 27.3 + - - +
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Residues in contact with GLN 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A TRP* 2.8 62.3 + - - +
132A LYS* 4.7 4.3 - - - +
133A ASP 2.9 21.0 + - - +
134A SER* 3.7 8.1 - - - +
136A VAL* 1.3 73.8 - - - +
138A ALA* 1.3 66.0 + - - +
140A PHE* 3.2 18.2 + - - +
141A ASN* 2.9 40.0 + - - +
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Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ILE* 4.7 10.1 - - + -
134A SER 2.9 17.6 + - - +
135A GLY* 3.2 9.4 + - - +
137A GLN* 1.3 77.4 - - - +
139A CYS* 1.3 61.6 + - - +
141A ASN* 3.4 13.2 + - - +
142A ARG* 3.5 23.1 - - - +
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Residues in contact with CYS 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ILE* 3.6 13.7 - - + -
87A ALA* 3.5 33.4 - - - -
88A MET* 3.7 22.0 - - + -
91A LEU* 4.4 2.5 - - - -
93A ILE* 3.7 19.2 - - + +
135A GLY 3.0 12.7 + - - +
136A VAL 3.6 7.6 - - - +
138A ALA* 1.3 75.6 - - - +
140A PHE* 1.3 66.0 + - - +
142A ARG* 2.9 16.8 + - - -
146A TYR* 2.8 21.8 + - - -
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Residues in contact with PHE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ILE* 4.1 8.2 - - + +
131A TRP* 3.8 32.5 - + + -
136A VAL 2.8 13.4 + - - +
137A GLN* 3.4 25.8 - - - +
139A CYS* 1.3 75.9 - - - +
141A ASN* 1.3 75.1 + - - +
142A ARG 3.1 4.9 + - - -
143A SER* 3.2 24.1 + - - -
146A TYR* 3.5 7.4 + - - -
148A LEU* 3.7 25.8 - - + -
152A ALA* 4.7 1.6 - - + -
153A ALA* 3.8 30.3 - - + -
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Residues in contact with ASN 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLN* 2.9 39.2 + - - +
138A ALA* 3.8 7.9 - - - +
139A CYS 3.1 0.6 - - - -
140A PHE* 1.3 90.6 - - - +
142A ARG* 1.3 63.1 + - + +
143A SER 3.5 0.9 - - - -
280A LYS* 5.5 5.0 + - - -
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Residues in contact with ARG 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LEU* 4.0 29.1 + - + +
93A ILE* 3.7 25.3 - - - +
138A ALA* 3.5 18.2 - - - +
139A CYS 2.9 12.7 + - - +
141A ASN* 1.3 82.4 - - + +
143A SER* 1.3 57.6 + - - +
144A ARG* 3.2 5.4 - - - -
145A GLU* 2.9 72.6 + - - +
146A TYR* 3.6 2.8 - - - -
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Residues in contact with SER 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A CYS 3.6 0.2 + - - -
140A PHE* 3.2 18.6 + - - -
141A ASN 3.5 1.7 - - - -
142A ARG* 1.3 71.9 - - - +
144A ARG* 1.3 58.8 + - - +
145A GLU 2.9 6.5 + - - -
146A TYR* 2.7 41.1 + - - +
148A LEU* 3.8 31.5 + - - +
232A LEU* 4.9 1.7 - - - +
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Residues in contact with ARG 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ARG* 3.0 4.4 + - - +
143A SER* 1.3 79.7 + - - +
145A GLU* 1.3 72.3 + - + +
146A TYR 3.3 3.2 + - - +
231A ASP* 3.8 38.4 + - - +
232A LEU* 3.6 32.7 - - + +
233A VAL* 5.2 9.0 + - - +
277A LYS* 5.5 1.1 - - - +
281A SER* 4.5 4.7 + - - -
282A PRO* 5.9 2.8 - - - +
285A ILE* 3.9 25.9 - - - +
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Residues in contact with GLU 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ARG* 5.0 4.5 + - - -
91A LEU* 3.6 21.2 - - + +
142A ARG* 2.9 64.0 + - - +
144A ARG* 1.3 93.5 + - + +
146A TYR* 1.3 65.8 + - + +
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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