Contacts of the helix formed by residues 134 - 142 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131S PRO 6.4 0.7 - - - -
133S TYR* 1.3 76.0 - - - +
135S GLU* 1.3 65.7 + - - +
136S LYS* 2.9 28.9 + - - +
137S ILE* 2.7 26.5 + - - +
138S ILE* 2.7 15.7 + - - +
154S TYR* 3.6 5.1 + - - -
192S GLN* 5.1 2.9 - - - +
212S GLY* 3.2 25.6 + - - -
213S PRO* 5.4 0.2 - - - -
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Residues in contact with GLU 135 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134S SER* 1.3 69.2 + - - +
136S LYS* 1.3 65.5 + - - +
138S ILE* 2.9 21.4 + - + +
139S ASP* 3.0 25.5 + - - +
196S VAL* 3.7 15.3 - - + +
211S GLN 3.7 13.7 - - - +
212S GLY 2.6 36.5 + - - +
213S PRO* 2.9 16.5 - - - +
214S SER 2.8 15.1 - - - +
215S PHE* 2.7 45.7 - - + +
217S TYR* 3.7 8.6 + - - -
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Residues in contact with LYS 136 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9S ASP* 6.2 2.0 - - - +
10S GLU* 3.9 23.6 + - - +
134S SER* 2.9 13.4 + - - +
135S GLU* 1.3 83.3 - - - +
137S ILE* 1.3 74.7 + - + +
139S ASP* 3.3 5.5 + - - +
140S MET* 3.2 39.2 + - + +
211S GLN* 4.7 4.6 - - - +
212S GLY 4.3 4.6 - - - +
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Residues in contact with ILE 137 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10S GLU* 6.5 1.1 - - + -
13S LEU* 4.6 9.0 - - + -
131S PRO 4.6 5.6 - - - +
132S ILE* 3.9 31.6 - - + +
133S TYR 4.4 0.2 - - - +
134S SER* 2.7 32.1 + - - +
136S LYS* 1.3 89.6 - - + +
138S ILE* 1.3 64.8 + - - +
140S MET* 3.2 27.4 + - + +
141S TYR* 3.3 34.0 - - + -
154S TYR* 4.2 6.3 - - + -
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Residues in contact with ILE 138 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134S SER 2.7 25.9 + - - +
135S GLU* 2.9 13.9 + - + +
137S ILE* 1.3 74.4 - - - +
139S ASP* 1.3 63.7 + - - +
141S TYR* 3.2 6.1 + - - +
142S LYS* 3.0 23.7 + - - +
154S TYR* 3.1 48.9 - - + +
192S GLN* 4.5 7.6 - - + +
193S TYR* 4.0 15.2 - - + -
196S VAL* 3.5 20.2 - - + -
197S VAL* 3.4 29.2 - - + -
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Residues in contact with ASP 139 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135S GLU* 3.0 27.2 + - - +
136S LYS* 3.9 5.1 - - - +
138S ILE* 1.3 80.3 - - - +
140S MET* 1.3 64.6 + - - +
141S TYR 3.5 0.2 + - - -
142S LYS* 3.4 48.0 + - - +
144S LYS* 5.4 1.4 - - - -
196S VAL* 6.1 0.6 - - - +
215S PHE* 4.9 8.0 - - - -
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Residues in contact with MET 140 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10S GLU* 5.3 7.4 - - + +
14S PHE* 3.8 29.4 - - + -
136S LYS* 3.2 32.9 + - + +
137S ILE* 3.2 28.2 + - + +
138S ILE 3.1 0.4 - - - -
139S ASP* 1.3 80.3 - - - +
141S TYR* 1.3 62.6 + - + +
144S LYS* 3.2 23.1 - - - +
149S MET* 2.9 43.8 - - + +
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Residues in contact with TYR 141 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13S LEU* 4.3 6.7 - - + +
137S ILE* 3.3 37.9 + - + -
138S ILE 3.2 7.0 + - - +
140S MET* 1.3 83.1 - - + +
142S LYS* 1.3 67.0 + - - +
143S GLY 2.9 2.3 + - - -
144S LYS* 2.9 25.3 + - + +
145S LYS 5.6 1.3 - - - -
149S MET* 3.3 30.5 - - + -
150S PRO* 2.6 50.0 + - + +
151S PRO 4.3 0.2 + - - -
152S HIS* 3.3 24.9 - + + +
154S TYR* 4.3 13.0 - - + +
155S ALA* 4.2 18.2 - - + -
158S ASP* 4.2 2.9 - - - +
193S TYR* 3.8 19.5 + - + +
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Residues in contact with LYS 142 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138S ILE* 3.0 12.3 + - + +
139S ASP* 3.4 40.6 + - - +
140S MET 3.4 1.4 - - - +
141S TYR* 1.3 73.1 - - - +
143S GLY* 1.3 61.3 + - - +
144S LYS* 3.0 9.9 + - - +
193S TYR* 3.6 10.5 + - - +
196S VAL* 5.1 8.5 + - + +
197S VAL* 4.0 36.5 + - + +
215S PHE* 6.1 3.6 - - - -
110T HIS* 5.6 11.2 + - - -
114T THR* 5.9 5.8 - - - -
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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