Contacts of the strand formed by residues 127 - 134 (chain C) in PDB entry 3G65
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 127 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A VAL* 4.8 14.9 + - - +
154A GLU* 3.4 28.5 + - - +
197A MET* 4.8 8.6 - - + +
198A CYS 4.0 3.8 - - - -
199A LEU* 3.6 22.6 - - + +
203A ASP* 2.9 31.7 + - - +
118C GLU* 3.4 6.6 - - - +
119C LEU* 2.9 57.7 + - + +
121C SER* 3.4 26.2 + - - +
123C SER* 3.0 30.2 + - - +
125C SER 4.2 1.6 - - - +
126C SER* 1.3 75.1 - - - +
128C ILE* 1.3 63.0 + - - +
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Residues in contact with ILE 128 (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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196A GLU 3.7 1.4 - - - +
197A MET* 3.6 3.2 - - - +
198A CYS* 2.8 55.8 + - + +
116C SER* 5.2 4.0 - - - -
117C VAL 3.3 11.4 - - - +
118C GLU* 5.1 5.6 - - + -
126C SER* 4.1 20.4 - - - +
127C ARG* 1.3 80.1 - - - +
129C VAL* 1.3 65.8 + - - +
130C THR* 4.0 21.5 - - + -
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Residues in contact with VAL 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PRO* 3.5 24.2 - - + -
195A THR* 4.2 3.4 - - + -
196A GLU 3.5 6.7 - - - +
197A MET* 3.4 34.8 - - + -
94C THR* 4.6 4.3 - - - +
115C VAL 3.3 5.5 - - - +
117C VAL* 2.8 44.1 + - + +
119C LEU* 3.8 17.9 - - + -
128C ILE* 1.3 75.2 - - - +
130C THR* 1.3 62.5 + - - +
131C HIS* 3.2 30.1 - - + +
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Residues in contact with THR 130 (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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194A VAL 3.6 3.5 + - - +
195A THR* 3.6 1.2 - - - +
196A GLU* 2.9 52.1 + - + +
108C LYS* 5.0 9.6 + - - +
114C THR* 4.5 14.6 - - + -
115C VAL 3.8 3.6 - - - -
116C SER* 4.3 12.6 - - - -
128C ILE* 4.0 19.3 - - + +
129C VAL* 1.3 77.0 - - - +
131C HIS* 1.3 62.8 + - - +
132C ASP* 4.2 2.9 + - - -
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Residues in contact with HIS 131 (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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158A PRO* 3.7 13.7 - - + -
193A MET* 3.8 19.7 - - + +
194A VAL 3.9 3.1 - - - -
195A THR* 3.2 40.0 + - + +
90C ARG* 4.6 5.4 - - + -
91C ALA* 3.8 42.7 + - + +
94C THR* 3.8 7.4 + - - -
113C LEU 3.6 0.5 - - - +
114C THR* 3.1 6.3 - - - -
115C VAL* 2.8 49.6 + - + +
117C VAL* 4.7 2.2 - - + -
129C VAL* 3.2 24.1 - - + +
130C THR* 1.3 72.3 - - - +
132C ASP* 1.3 63.1 + - - +
133C ILE* 3.6 3.2 + - + -
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Residues in contact with ASP 132 (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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179A ARG* 4.8 7.4 + - - -
192A ALA 4.2 0.7 - - - +
193A MET* 3.2 17.8 - - - +
194A VAL* 3.2 35.4 + - + +
196A GLU* 6.2 0.3 - - - +
106C THR* 4.3 1.4 - - - +
108C LYS* 3.2 29.4 + - - +
109C HIS* 5.9 1.4 - - - -
110C PHE* 6.0 1.3 - - + -
112C CYS* 4.0 19.7 - - - -
114C THR* 2.8 28.7 + - - +
130C THR* 5.2 4.2 + - - -
131C HIS* 1.3 72.0 - - - +
133C ILE* 1.3 60.5 + - - +
134C PRO* 3.1 14.0 - - - +
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Residues in contact with ILE 133 (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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193A MET* 3.5 20.0 - - - -
83C LEU* 4.2 22.2 - - + -
84C THR 5.4 0.2 - - - +
87C ASN* 3.9 19.3 - - + +
88C LEU* 3.7 36.8 - - + +
91C ALA* 4.0 2.9 - - + -
112C CYS* 3.1 2.4 - - - -
113C LEU* 2.7 49.4 + - + +
115C VAL* 3.7 26.2 - - + -
131C HIS 3.6 2.9 + - - +
132C ASP* 1.3 70.6 - - - +
134C PRO* 1.3 75.8 - - + +
135C ILE 3.2 0.2 + - - -
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Residues in contact with PRO 134 (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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191A LYS* 3.3 42.0 - - + +
192A ALA 3.6 16.4 - - - +
193A MET* 3.8 4.7 - - - -
82C GLU 4.2 0.5 - - - +
83C LEU* 4.0 12.3 - - - +
84C THR 5.0 1.4 + - - -
87C ASN* 3.7 22.5 + - - +
110C PHE* 4.2 4.7 - - + -
111C PRO 4.1 0.7 - - - +
112C CYS* 3.7 10.8 - - - -
132C ASP 3.1 9.8 - - - +
133C ILE* 1.3 90.1 - - - +
135C ILE* 1.3 60.0 + - - +
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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