Contacts of the strand formed by residues 117 - 122 (chain C) in PDB entry 1I2M
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 ILE 117 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ALA* 3.4 15.3 - - + +
88C ILE* 4.0 28.5 - - + -
105C HIS* 3.9 23.1 - - + +
108C LEU* 3.8 30.1 - - + -
109C VAL* 4.4 9.0 - - + +
113C GLU 5.6 0.2 - - - +
115C ILE* 3.5 22.3 + - + +
116C PRO* 1.3 80.1 - - - +
118C VAL* 1.3 64.4 + - - +
144C LEU* 3.7 27.6 - - + +
145C GLN 4.1 5.4 + - - -
163C TRP* 3.5 18.1 - - - -
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Residues in contact with VAL 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ALA 3.0 6.0 + - - +
87C ILE* 3.3 30.6 - - + +
88C ILE* 2.9 25.7 + - - +
117C ILE* 1.3 78.3 - - - +
119C LEU* 1.3 67.5 + - - +
120C CYS* 3.9 3.3 + - - -
144C LEU* 5.4 0.2 - - - -
145C GLN* 3.6 14.1 - - + +
147C TYR* 3.6 33.7 - - + -
160C PRO* 3.9 17.3 - - + -
163C TRP* 4.1 13.2 - - + -
164C LEU* 4.1 9.6 - - + -
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Residues in contact with LEU 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ILE* 3.4 35.4 - - + +
90C PHE* 3.8 28.0 - - + -
98C TYR* 4.2 15.7 - - + -
101C VAL* 4.2 12.1 - - + -
117C ILE 4.4 0.2 + - - -
118C VAL* 1.3 75.1 - - - +
120C CYS* 1.3 61.0 + - - +
138C PHE* 5.2 5.4 - - + +
141C LYS* 4.5 16.8 - - + +
144C LEU* 4.2 16.9 - - + +
145C GLN 2.7 16.4 + - - +
146C TYR* 3.2 25.8 - - + -
147C TYR 3.0 24.1 + - - -
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Residues in contact with CYS 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C PHE* 5.1 0.4 - - - -
87C ILE* 4.0 15.0 - - - -
88C ILE 2.8 14.0 + - - +
89C MET* 3.5 11.3 - - + +
90C PHE* 3.1 28.5 + - - -
118C VAL* 4.4 4.7 - - - -
119C LEU* 1.3 77.0 - - - +
121C GLY* 1.3 61.1 + - - +
122C ASN 3.5 1.2 + - - -
146C TYR* 4.2 1.1 - - - -
147C TYR* 3.4 6.7 - - - +
149C ILE* 3.9 24.9 - - + -
160C PRO* 3.2 40.6 - - - -
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Residues in contact with GLY 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C PHE* 3.8 8.3 - - - -
92C VAL* 3.4 17.9 - - - +
120C CYS* 1.3 70.5 - - - +
122C ASN* 1.3 60.5 + - - -
123C LYS* 5.0 0.5 - - - +
146C TYR* 3.4 24.4 - - - -
147C TYR 2.9 11.5 + - - -
148C ASP* 3.4 5.9 - - - +
149C ILE* 2.9 26.1 + - - +
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Residues in contact with ASN 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C THR 3.1 25.0 + - - +
22C GLY* 3.8 17.2 + - - -
26C PHE* 5.2 2.0 - - - +
89C MET* 3.8 14.0 - - + -
90C PHE 2.9 16.1 + - - +
91C ASP* 3.3 2.4 - - - +
92C VAL* 2.9 23.7 + - - -
120C CYS 3.5 1.0 + - - -
121C GLY* 1.3 71.5 - - - +
123C LYS* 1.3 71.5 + - - +
124C VAL* 3.0 13.2 + - + +
149C ILE* 3.4 28.0 - - + +
150C SER* 3.5 12.5 - - - -
151C ALA* 4.0 8.7 + - - +
157C PHE* 5.3 3.8 - - - -
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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