Contacts of the strand formed by residues 118 - 125 (chain A) in PDB entry 1IME
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 GLU 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A TRP* 3.6 27.4 - - + +
111A PHE* 2.9 25.0 + - + +
113A VAL* 4.2 19.1 - - + +
116A LYS* 3.4 3.7 + - + +
117A ILE* 1.3 74.8 - - - +
119A PHE* 1.3 66.4 + - + +
134A ARG* 2.6 33.6 + - - -
135A LYS* 2.9 47.5 + - - +
226A ILE* 4.3 1.7 - - - +
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Residues in contact with PHE 119 (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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5A TRP* 3.8 13.7 - - + -
8A CYS* 3.9 10.5 - - + -
9A MET* 3.6 55.0 - - + -
12A ALA* 3.8 20.9 - - + -
87A TRP* 4.0 9.6 - + - -
109A ILE* 4.9 4.7 - - + -
110A GLY* 3.8 0.2 - - - -
111A PHE* 3.1 67.9 + + + -
117A ILE* 3.5 7.6 - - - +
118A GLU* 1.3 82.2 - - + +
120A GLY* 1.3 62.9 + - - +
121A VAL* 4.5 7.0 - - + -
133A ALA 3.2 14.8 - - - +
134A ARG* 4.0 5.8 - - - -
226A ILE* 3.9 8.1 - - - -
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Residues in contact with GLY 120 (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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9A MET* 4.2 1.0 - - - +
109A ILE 3.2 11.2 - - - -
119A PHE* 1.3 76.7 - - - +
121A VAL* 1.4 65.0 + - - +
132A THR* 3.5 5.4 - - - -
133A ALA 3.1 28.9 + - - +
223A GLY* 3.6 23.6 - - - -
226A ILE* 3.6 4.8 - - - +
227A ILE* 4.2 1.9 - - - +
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Residues in contact with VAL 121 (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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9A MET* 4.5 7.4 - - + -
12A ALA* 4.4 12.6 - - + +
13A VAL* 3.9 30.3 - - + +
16A ALA* 3.8 22.0 - - + -
107A VAL 4.4 0.7 - - - -
108A SER* 3.5 2.3 + - - -
109A ILE* 2.8 44.1 + - + +
119A PHE* 4.5 6.1 - - + -
120A GLY* 1.4 78.6 - - - +
122A VAL* 1.3 65.9 + - - +
123A TYR 4.3 0.2 - - - -
130A MET* 3.5 28.5 - - - -
131A TYR 3.5 5.8 - - - +
132A THR* 4.2 4.9 - - + -
223A GLY 4.4 0.6 + - - -
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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
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106A ALA* 3.8 24.2 - - + -
107A VAL 3.3 5.6 - - - +
108A SER* 4.1 8.5 - - - +
121A VAL* 1.3 78.9 - - - +
123A TYR* 1.3 63.5 + - - +
124A SER 4.8 0.4 - - - +
130A MET* 3.8 0.7 - - - +
131A TYR* 2.9 39.9 + - + +
197A ALA* 4.1 14.4 - - + +
198A VAL* 5.1 3.1 - - + +
201A CYS* 4.1 18.4 - - - -
223A GLY 4.0 0.9 - - - -
224A ALA* 3.8 33.9 - - + +
227A ILE* 4.0 11.9 - - + +
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Residues in contact with TYR 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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16A ALA* 3.6 27.8 - - + +
17A ARG* 4.2 24.9 + - + +
20A GLY* 3.6 27.9 - - - -
21A GLU* 5.5 3.1 - - - +
106A ALA* 3.2 5.7 - - - -
107A VAL* 2.9 35.7 + - + +
121A VAL 4.3 0.2 - - - -
122A VAL* 1.3 74.2 - - - +
124A SER* 1.3 57.8 + - - +
125A CYS* 3.2 28.8 + - - -
128A GLY* 4.1 9.4 - - - -
129A LYS 3.6 31.2 - - - -
130A MET* 3.5 34.3 - - + -
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Residues in contact with SER 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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103A PRO 5.2 0.3 + - - -
104A PHE* 4.9 1.6 - - - -
105A VAL 3.5 15.4 + - - -
106A ALA* 4.3 2.0 - - - +
122A VAL* 4.0 2.0 + - - +
123A TYR* 1.3 69.3 - - - +
125A CYS* 1.3 54.6 + - - +
126A VAL 3.6 1.3 + - - -
127A GLU* 2.8 31.7 + - - +
128A GLY* 2.9 29.6 + - - -
129A LYS* 2.9 25.6 + - - -
131A TYR* 4.5 9.9 - - - -
198A VAL* 4.3 18.5 - - - +
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Residues in contact with CYS 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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20A GLY* 3.8 18.6 - - - +
23A VAL* 3.9 18.2 - - + -
24A CYS* 3.2 26.6 - - - -
105A VAL* 3.1 19.9 + - + +
106A ALA 4.7 0.4 - - - -
107A VAL* 3.7 30.1 - - - -
123A TYR* 3.2 21.3 + - + -
124A SER* 1.3 70.6 - - - +
126A VAL* 1.3 65.1 + - + +
128A GLY* 3.1 14.6 + - - -
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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