Contacts of the helix formed by residues 121 - 130 (chain A) in PDB entry 4I1Q
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 ALA 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A LEU* 3.7 16.0 - - + +
117A LEU* 3.1 21.6 + - + +
119A ASP 3.5 0.2 - - - -
120A GLN* 1.3 79.8 - - + +
122A VAL* 1.3 68.0 + - + +
124A THR* 4.0 1.3 - - - -
125A MET* 3.2 29.8 + - - +
209A ILE* 3.7 7.2 - - + +
213A ILE* 4.0 31.9 - - + -
216A LEU* 6.1 0.2 - - + -
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Residues in contact with VAL 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 4.7 6.9 - - + +
64A LEU* 3.9 28.5 - - + +
65A LYS* 4.4 24.2 - - + +
68A LEU* 4.0 25.1 - - + -
117A LEU* 3.2 12.9 + - + +
118A ALA* 3.6 7.9 - - - +
121A ALA* 1.3 76.2 - - + +
123A ARG* 1.3 61.0 + - + +
125A MET* 3.1 9.3 + - - +
126A GLU* 3.0 41.5 + - - +
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Residues in contact with ARG 123 (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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115A GLU 5.0 0.8 + - - -
118A ALA* 2.8 38.2 + - - +
119A ASP* 2.9 37.8 + - - +
122A VAL* 1.3 71.9 - - + +
124A THR* 1.3 64.0 + - - +
126A GLU* 3.5 23.6 + - - +
127A ILE* 3.1 34.7 + - + +
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Residues in contact with THR 124 (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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119A ASP 3.3 13.1 + - - -
120A GLN* 3.1 26.5 + - - +
121A ALA 3.8 2.2 + - - -
122A VAL 3.3 0.4 - - - -
123A ARG* 1.3 77.0 - - - +
125A MET* 1.3 60.7 + - - +
127A ILE* 3.6 10.5 + - - +
128A TYR* 3.3 20.4 + - - +
205A CYS* 5.4 4.9 - - - -
208A THR* 4.5 15.0 - - + -
209A ILE* 3.6 22.7 - - + -
212A ASN* 4.6 2.4 + - - -
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Residues in contact with MET 125 (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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57A GLY* 3.4 31.6 - - - +
60A LEU* 4.1 15.9 - - + -
61A TYR* 4.0 20.4 - - + +
64A LEU* 3.6 13.2 - - + -
121A ALA 3.2 10.8 + - - +
122A VAL* 3.1 10.5 + - - +
124A THR* 1.3 73.8 - - - +
126A GLU* 1.3 59.7 + - - +
128A TYR* 3.5 25.4 - - + -
129A VAL* 2.8 45.1 + - + +
205A CYS* 4.0 15.0 - - - -
206A TYR* 5.6 0.9 - - + -
209A ILE* 3.0 34.1 - - + -
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Residues in contact with GLU 126 (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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61A TYR* 3.9 25.0 + - + +
65A LYS* 5.0 4.3 - - - +
122A VAL* 3.0 31.1 + - - +
123A ARG* 3.2 31.6 + - + +
125A MET* 1.3 74.1 - - - +
127A ILE* 1.3 67.1 + - + +
129A VAL* 3.9 7.7 - - + +
130A ALA* 3.2 25.8 + - - +
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Residues in contact with ILE 127 (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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123A ARG* 3.1 26.4 + - + +
124A THR* 4.1 8.5 - - - +
126A GLU* 1.3 77.1 - - + +
128A TYR* 1.3 64.7 - - - +
130A ALA* 3.6 12.5 + - - +
131A GLN* 3.8 12.0 - - + +
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Residues in contact with TYR 128 (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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53A GLN* 3.2 23.4 + - - +
57A GLY* 4.5 7.2 - - - -
124A THR 3.3 15.7 + - - +
125A MET* 3.1 31.5 + - + +
127A ILE* 1.3 75.3 - - - +
129A VAL* 1.3 73.5 + - + +
130A ALA 3.0 2.3 + - - -
131A GLN* 3.1 43.9 + - - +
132A PHE* 3.8 24.8 - + - -
198A LEU* 5.3 0.7 - - + -
201A SER* 4.3 10.1 - - - -
202A ARG* 3.1 33.0 - - - +
205A CYS* 3.6 35.7 - - + -
206A TYR* 4.2 7.6 + + - -
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Residues in contact with VAL 129 (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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57A GLY* 3.6 22.4 - - - +
58A HIS* 4.0 3.8 - - - +
61A TYR* 4.2 20.6 - - + -
125A MET* 2.8 52.5 + - + +
126A GLU* 3.9 9.4 - - + +
128A TYR* 1.3 72.1 - - + +
130A ALA* 1.3 63.8 + - - +
132A PHE* 3.0 43.2 + - + +
133A SER 4.5 0.3 + - - -
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Residues in contact with ALA 130 (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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126A GLU 3.2 21.4 + - - +
127A ILE* 3.7 8.1 - - - +
128A TYR 3.0 1.8 + - - -
129A VAL* 1.3 77.6 - - - +
131A GLN* 1.3 62.7 + - - +
132A PHE 3.0 1.9 + - - -
133A SER* 3.5 11.5 + - - +
134A GLU* 3.0 15.1 - - - +
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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