Contacts of the helix formed by residues 134 - 142 (chain V) in PDB entry 1I84
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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131V PRO 6.4 0.4 - - - -
133V TYR* 1.3 76.6 - - - +
135V GLU* 1.3 65.5 + - - +
136V LYS* 2.9 28.2 + - - +
137V ILE* 2.7 27.3 + - - +
138V ILE* 2.7 15.9 + - - +
154V TYR* 3.6 4.8 + - - -
192V GLN* 5.1 2.7 - - - +
212V GLY* 3.2 26.1 + - - -
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Residues in contact with GLU 135 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134V SER* 1.3 69.4 + - - +
136V LYS* 1.3 66.7 + - - +
138V ILE* 2.9 22.5 + - + +
139V ASP* 3.0 25.5 + - - +
196V VAL* 3.7 15.5 - - + +
211V GLN 3.7 12.8 - - - +
212V GLY 2.6 36.1 + - - +
213V PRO* 2.9 16.8 - - - +
214V SER 2.8 15.3 - - - +
215V PHE* 2.7 45.6 - - + +
217V TYR* 3.7 8.6 + - - -
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Residues in contact with LYS 136 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9V ASP* 6.2 1.6 - - - +
10V GLU* 3.9 23.6 + - - +
134V SER* 2.9 13.5 + - - +
135V GLU* 1.3 81.0 - - - +
137V ILE* 1.3 74.8 + - + +
139V ASP* 3.3 5.6 + - - +
140V MET* 3.2 37.8 + - + +
211V GLN* 4.7 5.5 - - - +
212V GLY 4.3 3.7 - - - +
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Residues in contact with ILE 137 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10V GLU* 6.5 1.1 - - + -
13V LEU* 4.6 9.2 - - + -
131V PRO 4.6 5.8 - - - +
132V ILE* 3.9 31.4 - - + +
133V TYR 4.4 0.2 - - - +
134V SER* 2.7 33.7 + - - +
136V LYS* 1.3 90.2 - - + +
138V ILE* 1.3 64.9 + - - +
140V MET* 3.2 26.8 + - + +
141V TYR* 3.3 33.8 - - + -
154V TYR* 4.2 6.1 - - + -
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Residues in contact with ILE 138 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134V SER 2.7 26.9 + - - +
135V GLU* 3.2 13.5 - - + +
137V ILE* 1.3 72.2 - - - +
139V ASP* 1.3 64.8 + - - +
141V TYR* 3.2 5.5 + - - +
142V LYS* 3.0 24.0 + - + +
154V TYR* 3.1 49.4 - - + +
192V GLN* 4.5 7.2 - - + +
193V TYR* 4.0 15.4 - - + -
196V VAL* 3.4 19.5 - - + -
197V VAL* 3.4 29.2 - - + -
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Residues in contact with ASP 139 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135V GLU* 3.0 27.5 + - - +
136V LYS* 3.9 4.7 - - - +
138V ILE* 1.3 81.2 - - - +
140V MET* 1.3 65.5 + - - +
141V TYR 3.3 0.4 + - - -
142V LYS* 3.4 47.1 + - - +
144V LYS* 5.4 1.2 - - - -
196V VAL* 6.4 0.2 - - - -
215V PHE* 4.9 9.6 - - - -
121W GLU* 5.1 0.7 - - - +
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Residues in contact with MET 140 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10V GLU* 5.3 8.5 - - + +
14V PHE* 3.8 28.9 - - + -
136V LYS* 3.2 33.7 + - + +
137V ILE* 3.2 28.9 + - + +
138V ILE 3.1 0.2 - - - -
139V ASP* 1.3 80.1 - - - +
141V TYR* 1.3 61.9 + - + +
144V LYS* 3.2 22.8 - - - +
149V MET* 2.9 45.2 - - + +
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Residues in contact with TYR 141 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13V LEU* 4.3 7.4 - - + +
137V ILE* 3.3 39.2 + - + +
138V ILE 3.2 6.7 + - - +
140V MET* 1.3 83.1 - - + +
142V LYS* 1.3 65.8 + - - +
143V GLY 2.9 2.4 + - - -
144V LYS* 2.9 25.8 + - + +
145V LYS 5.6 1.1 - - - -
149V MET* 3.3 29.8 - - + -
150V PRO* 2.6 49.9 + - + +
152V HIS* 3.3 26.6 - + + +
154V TYR* 4.3 13.9 - - + +
155V ALA* 4.2 18.8 - - + -
158V ASP* 4.2 3.3 - - - +
193V TYR* 3.8 19.8 + - + +
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Residues in contact with LYS 142 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138V ILE 3.0 11.9 + - - +
139V ASP* 3.4 39.5 + - - +
140V MET 3.4 1.6 - - - +
141V TYR* 1.3 73.5 - - - +
143V GLY* 1.3 59.9 + - - +
144V LYS* 3.0 10.2 + - - +
193V TYR* 3.6 10.9 + - - +
196V VAL* 5.1 9.0 + - + +
197V VAL* 4.0 37.6 + - + +
215V PHE* 6.1 3.6 - - - -
114W THR* 5.9 0.3 - - - +
121W GLU* 3.2 29.9 + - - +
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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