Contacts of the strand formed by residues 118 - 125 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B TRP* 3.5 28.3 + - + -
111B PHE* 2.8 15.7 + - + +
113B VAL* 4.2 19.3 - - + +
116B LYS* 3.5 4.5 + - - +
117B ILE* 1.3 74.5 - - - +
119B PHE* 1.3 61.8 + - + +
134B ARG* 2.8 46.5 + - - +
135B LYS* 3.0 44.8 + - - +
226B ILE* 4.7 2.0 - - - -
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Residues in contact with PHE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B TRP* 4.0 7.9 - - + -
8B CYS* 3.8 13.7 - - + -
9B MET* 3.5 55.4 - - + -
12B ALA* 3.9 15.3 - - + -
87B TRP* 4.1 8.3 - + - -
109B ILE* 5.2 4.0 - - + -
110B GLY* 4.0 0.9 - - - -
111B PHE* 3.1 69.4 + + + -
117B ILE* 3.7 8.2 - - - +
118B GLU* 1.3 83.6 - - + +
120B GLY* 1.3 61.3 + - - +
121B VAL* 4.5 7.0 - - + -
133B ALA 3.1 15.5 - - - +
134B ARG* 3.8 15.5 - - - +
226B ILE* 3.7 8.7 - - - -
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Residues in contact with GLY 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B MET* 4.0 0.7 - - - +
109B ILE 3.6 8.1 - - - -
119B PHE* 1.3 75.5 - - - +
121B VAL* 1.4 65.3 + - - +
122B VAL 4.3 0.2 - - - -
132B THR* 3.3 6.0 - - - -
133B ALA 2.9 30.9 + - - +
223B GLY* 3.5 25.1 - - - -
226B ILE* 3.5 5.2 - - - +
227B ILE* 4.5 2.9 - - - -
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B MET* 4.7 3.1 - - + -
12B ALA* 3.9 20.0 - - + -
13B VAL* 3.9 23.8 - - + -
16B ALA* 3.7 17.9 - - + -
107B VAL 3.8 1.0 - - - +
108B SER* 3.6 0.3 - - - -
109B ILE* 2.9 43.6 + - + +
119B PHE* 4.5 10.1 - - + -
120B GLY* 1.4 78.7 - - - +
122B VAL* 1.3 67.6 + - - +
123B TYR 4.2 0.2 - - - -
130B MET* 3.6 28.5 - - - -
131B TYR 3.5 3.1 - - - -
132B THR* 3.9 9.6 - - + -
223B GLY 4.4 0.4 + - - -
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Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ALA* 3.9 22.7 - - + -
107B VAL 3.3 5.6 - - - +
108B SER* 4.1 9.4 - - - +
121B VAL* 1.3 78.8 - - - +
123B TYR* 1.3 63.0 + - - +
124B SER* 5.0 1.3 - - - +
130B MET* 3.8 1.5 - - - +
131B TYR* 2.9 36.3 + - + -
197B ALA* 4.0 14.4 - - + +
198B VAL* 5.5 1.6 - - + -
201B CYS* 4.1 16.6 - - - -
223B GLY 3.9 2.5 - - - -
224B ALA* 3.9 26.5 - - + +
227B ILE* 3.7 23.1 - - + -
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Residues in contact with TYR 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ALA* 3.5 26.2 - - + +
17B ARG* 3.9 22.6 + - + +
20B GLY* 3.6 27.8 - - - -
21B GLU* 4.6 3.0 - - - +
106B ALA* 3.2 5.5 - - - -
107B VAL* 3.0 32.8 + - + +
121B VAL 4.2 0.6 - - - -
122B VAL* 1.3 74.3 - - - +
124B SER* 1.3 63.7 + - - +
125B CYS* 3.5 15.1 + - + -
128B GLY* 4.1 26.0 - - - -
129B LYS 3.4 20.0 - - - -
130B MET* 3.8 31.6 - - + -
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Residues in contact with SER 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B PHE* 5.1 2.1 - - - -
105B VAL 3.6 11.9 + - - -
106B ALA* 4.3 2.7 - - - +
122B VAL* 4.0 1.7 + - - -
123B TYR* 1.3 72.5 - - - +
125B CYS* 1.3 58.6 + - - +
126B VAL 3.7 0.8 + - - -
127B GLU* 2.6 35.9 + - - +
128B GLY* 2.9 24.8 + - - -
129B LYS* 2.9 22.6 + - - -
131B TYR* 4.6 9.0 - - - -
198B VAL* 4.2 18.6 - - - +
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Residues in contact with CYS 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLY* 3.9 28.3 - - - +
23B VAL* 3.9 20.4 - - + -
24B CYS* 3.3 28.5 - - - -
105B VAL* 3.1 25.3 + - + +
107B VAL* 4.2 8.1 - - - -
123B TYR* 4.1 21.0 + - - -
124B SER* 1.3 69.1 - - - +
126B VAL* 1.3 67.4 + - - +
128B GLY* 3.1 13.3 + - - -
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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