Contacts of the strand formed by residues 112 - 117 (chain C) in PDB entry 2W7U
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 ARG 112 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C GLU* 2.6 40.6 + - - -
3C ASN* 5.1 1.8 - - - +
110C LYS 3.7 4.4 + - - +
111C ASP* 1.3 74.6 - - - +
113C ILE* 1.3 63.6 + - - +
132C THR* 3.8 14.9 + - - +
133C GLY 3.3 15.3 + - - -
134C THR* 3.2 25.1 + - - -
160C ASN* 4.1 13.3 - - - +
161C SER* 4.2 14.0 + - - -
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Residues in contact with ILE 113 (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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111C ASP* 4.1 2.9 - - + +
112C ARG* 1.3 80.7 - - - +
114C SER* 1.3 63.4 + - - +
115C VAL* 3.9 15.3 - - + -
132C THR* 3.4 7.4 - - - +
133C GLY 2.8 40.6 + - - +
134C THR* 4.0 5.8 - - - +
135C ILE* 3.8 25.1 - - + +
145C PHE* 3.9 33.9 - - + -
147C ALA* 4.1 10.3 - - + -
158C VAL* 3.9 12.1 - - + -
159C LEU 3.4 7.4 - - - +
160C ASN* 4.7 0.9 - - - +
166C ILE* 3.7 30.3 - - + -
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Residues in contact with SER 114 (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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113C ILE* 1.3 75.3 - - - +
115C VAL* 1.3 63.5 + - - +
116C ILE* 4.2 2.5 + - - +
130C GLU* 3.5 30.2 + - - -
131C SER 3.4 8.5 - - - -
132C THR* 4.3 7.4 - - - -
157C PRO 3.6 1.0 - - - +
158C VAL* 3.5 4.2 - - - +
159C LEU* 2.9 51.8 + - - +
160C ASN 4.5 4.2 + - - -
163C HIS* 4.7 4.5 - - - -
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Residues in contact with VAL 115 (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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113C ILE* 3.9 13.5 - - + -
114C SER* 1.3 77.6 - - - +
116C ILE* 1.3 63.3 + - - +
117C GLY 4.2 0.2 + - - -
129C PHE 3.7 1.2 - - - +
130C GLU* 3.5 1.4 - - - -
131C SER* 2.6 45.1 + - - +
145C PHE* 3.7 26.9 - - + -
147C ALA* 3.9 10.8 - - + +
148C TYR 5.3 2.2 - - - +
149C ALA* 5.8 0.7 - - + -
153C ASN* 4.3 15.8 - - - +
156C SER* 3.7 24.5 - - - +
157C PRO 3.6 4.9 - - - +
158C VAL* 4.2 8.5 - - + -
169C LEU* 4.6 12.3 - - + -
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Residues in contact with ILE 116 (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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14C PRO* 4.8 3.1 - - + -
15C TYR* 3.7 27.4 - - + -
18C VAL* 3.8 18.9 - - + +
25C THR* 3.8 2.3 - - - +
114C SER* 4.6 3.1 - - - +
115C VAL* 1.3 82.2 - - - +
117C GLY* 1.3 60.7 + - - +
128C MET* 3.7 30.1 - - + -
129C PHE 3.3 10.3 - - - +
130C GLU* 3.9 25.1 - - + +
156C SER* 3.4 5.3 - - - -
157C PRO* 3.3 33.5 + - + +
159C LEU* 3.8 28.7 - - + -
163C HIS* 5.6 0.9 - - + -
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Residues in contact with GLY 117 (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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18C VAL* 4.7 1.1 - - - -
25C THR* 3.6 11.4 - - - -
115C VAL 4.2 0.2 + - - -
116C ILE* 1.3 76.8 - - - +
118C TYR* 1.3 64.4 + - - -
119C PRO* 3.4 7.4 - - - +
128C MET* 3.5 7.1 - - - +
129C PHE 3.0 30.4 + - - -
153C ASN* 3.5 6.1 + - - -
156C SER* 3.4 14.8 - - - -
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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