Contacts of the helix formed by residues 136 - 142 (chain G) in PDB entry 5IC4
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118G LEU* 3.6 30.5 - - + -
123G GLU 5.3 0.7 - - - +
125G GLY* 2.9 39.7 + - - +
126G ILE 4.1 6.1 - - - +
127G ILE* 3.8 18.4 - - + +
134G VAL 3.3 1.2 + - - -
135G ASP* 1.3 72.5 - - - +
137G LYS* 1.3 57.8 + - - +
139G ILE* 3.1 8.3 + - + +
140G THR* 2.9 37.8 + - + +
158G PHE* 6.5 0.2 - - + -
160G ILE* 3.6 33.2 - - + -
197H TYR* 4.2 17.5 - - + +
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Residues in contact with LYS 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201F PRO* 5.0 11.9 + - - +
203F TYR* 4.4 9.7 - - - -
125G GLY 4.6 0.4 + - - -
135G ASP* 3.2 6.9 - - + +
136G LEU* 1.3 79.5 - - - +
138G LYS* 1.3 52.0 + - - +
140G THR* 2.9 10.0 + - - +
141G ASN* 2.6 62.5 + - - +
190H GLU* 2.9 39.8 + - - -
195H TYR* 5.0 6.7 + - - -
268H MET* 6.0 1.4 - - - +
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Residues in contact with LYS 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G VAL* 3.9 38.3 - - + +
101G ARG* 4.8 8.9 - - - +
134G VAL* 5.0 5.2 - - + -
135G ASP* 3.2 23.9 + - + +
137G LYS* 1.3 79.3 - - - +
139G ILE* 1.3 62.1 + - - +
141G ASN* 3.7 12.8 + - - +
142G PHE* 3.1 34.0 + - + -
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Residues in contact with ILE 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96G ILE* 3.6 29.6 - - + -
97G VAL* 4.4 11.9 - - + -
100G MET* 3.6 37.9 - - + -
116G CYS* 5.1 0.7 - - - -
118G LEU* 4.9 12.8 - - + -
127G ILE* 4.9 7.4 - - + -
134G VAL* 3.9 16.8 - - + -
135G ASP 3.7 11.9 - - - +
136G LEU* 3.1 13.1 + - + +
138G LYS* 1.3 78.0 - - - +
140G THR* 1.3 62.2 + - + +
142G PHE* 3.4 15.0 - - + -
143G PHE* 3.4 16.5 - - - -
158G PHE* 4.1 13.2 - - + -
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Residues in contact with THR 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136G LEU* 2.9 23.6 + - + +
137G LYS* 2.9 29.8 + - - +
139G ILE* 1.3 72.9 - - + +
141G ASN* 1.3 60.6 + - - +
142G PHE 3.1 3.1 - - - -
143G PHE* 3.0 18.7 + - - -
144G ARG* 3.6 6.2 + - - +
158G PHE* 4.1 29.6 - - + -
193H PHE* 3.6 20.1 - - - -
195H TYR* 3.6 31.6 + - + -
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Residues in contact with ASN 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G LYS* 2.6 55.8 + - - +
138G LYS* 4.0 9.1 - - - +
139G ILE 3.3 0.2 - - - -
140G THR* 1.3 73.0 + - - +
142G PHE* 1.3 62.8 + - - +
143G PHE 3.2 0.9 + - - -
144G ARG* 3.4 28.7 + - - +
147G ARG* 3.2 47.0 - - - +
190H GLU* 4.3 1.2 - - - +
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Residues in contact with PHE 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G VAL* 3.8 32.3 - - + -
100G MET* 3.9 15.0 - - + +
101G ARG* 3.4 52.7 - - + -
104G SER* 3.4 29.2 + - - +
138G LYS* 3.1 34.8 - - + -
139G ILE* 3.4 14.6 + - - +
140G THR 3.1 0.4 - - - -
141G ASN* 1.3 78.9 - - + +
143G PHE* 1.3 63.1 + - + +
144G ARG 3.7 0.3 + - - -
147G ARG* 3.8 14.7 - - - +
148G CYS* 3.6 9.5 - - - +
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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