Contacts of the strand formed by residues 131 - 140 (chain C) in PDB entry 4R2G
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 ALA 131 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121C PRO* 4.2 20.6 - - + -
125C GLU* 3.1 3.1 - - - -
126C LEU* 4.4 4.9 - - + -
130C LYS* 1.3 76.8 - - - +
132C THR* 1.3 65.4 + - - +
133C LEU* 4.3 0.9 - - + -
179C LEU 3.9 0.3 - - - +
180C SER* 4.6 0.2 - - - -
181C LEU* 2.8 57.3 + - + +
182C THR 4.0 13.5 - - - +
183C PRO* 4.1 6.7 - - + -
186C TRP* 4.7 2.9 - - + -
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Residues in contact with THR 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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120C PRO 4.5 1.2 - - - -
121C PRO* 3.7 17.9 - - - +
125C GLU* 2.6 31.5 + - - +
130C LYS* 5.8 1.8 - - + -
131C ALA* 1.3 80.0 - - - +
133C LEU* 1.3 67.6 + - - +
134C VAL* 4.0 5.1 + - - +
178C TYR* 5.2 5.8 - - + -
179C LEU 3.4 5.4 - - - -
180C SER* 3.9 21.8 - - - +
142D LEU* 5.5 1.9 - - - +
159D LEU* 3.5 21.0 - - - +
161D LYS* 4.4 26.2 - - + +
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Residues in contact with LEU 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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118C LEU* 4.5 0.7 - - + -
119C PHE 3.9 9.2 - - - +
121C PRO* 3.7 29.6 - - + -
131C ALA* 5.5 0.2 - - + -
132C THR* 1.3 76.3 - - - +
134C VAL* 1.3 63.0 + - - +
149C TRP* 3.4 31.3 - - + -
178C TYR* 3.6 7.4 - - - +
179C LEU* 3.0 40.6 + - + +
181C LEU* 3.7 27.1 - - + -
186C TRP* 4.5 4.7 - - + -
192C TYR* 3.5 32.8 - - + +
207C VAL* 4.1 10.8 - - + -
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Residues in contact with VAL 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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117C THR 3.8 1.2 - - - +
118C LEU* 3.3 7.4 - - - +
119C PHE* 3.0 44.8 + - + -
132C THR 4.0 3.3 + - - +
133C LEU* 1.3 78.2 - - - +
135C CYS* 1.3 61.9 + - - +
136C LEU* 3.5 32.5 - - + -
177C SER 3.8 3.4 - - - +
178C TYR* 4.0 17.7 - - + -
142D LEU* 4.4 9.6 - - + -
159D LEU* 3.5 31.9 - - + -
197D SER* 3.7 12.8 - - - +
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Residues in contact with CYS 135 (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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116C VAL* 3.8 21.3 - - - -
117C THR 3.9 1.6 - - - -
118C LEU* 4.5 3.8 - - + +
134C VAL* 1.3 74.1 - - - +
136C LEU* 1.3 62.9 + - - +
137C ILE* 4.0 6.0 + - - +
149C TRP* 3.6 15.0 - - + -
176C SER* 3.4 4.2 - - - -
177C SER* 2.8 45.0 + - - +
194C CYS* 2.0 46.7 - - + -
196C VAL* 4.3 8.1 - - - -
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Residues in contact with LEU 136 (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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115C SER 3.7 2.1 - - - +
116C VAL* 3.4 3.7 - - - -
117C THR* 2.9 48.0 + - + +
119C PHE* 4.8 5.8 - - + -
134C VAL* 3.5 25.4 - - + -
135C CYS* 1.3 78.7 - - - +
137C ILE* 1.3 62.7 + - - +
175C ALA 4.0 1.1 - - - -
176C SER* 3.8 20.0 - - - -
142D LEU* 5.9 0.7 - - + -
184D PHE* 3.8 24.7 - - + -
197D SER* 4.2 19.3 - - - +
199D VAL* 3.5 39.0 - - + -
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Residues in contact with ILE 137 (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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114C PRO* 3.6 28.7 - - + -
115C SER 4.0 2.2 - - - -
116C VAL* 4.0 6.7 - - + -
135C CYS* 4.6 11.4 - - - +
136C LEU* 1.3 75.9 - - - +
138C SER* 1.3 69.7 + - - +
140C PHE* 3.8 17.9 - - + -
145C VAL* 4.6 6.5 - - + -
147C VAL* 3.6 31.6 - - + -
174C ALA* 3.6 0.3 - - - -
175C ALA* 2.8 48.3 + - + +
176C SER 4.8 3.6 - - - +
177C SER* 4.8 0.9 - - - -
196C VAL* 3.6 24.5 - - + -
184D PHE* 3.2 10.0 - - - -
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Residues in contact with SER 138 (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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114C PRO* 3.4 3.3 - - - +
115C SER* 2.7 48.4 + - - -
136C LEU 5.4 0.2 - - - -
137C ILE* 1.3 79.6 - - - +
139C ASP* 1.3 77.9 + - - +
140C PHE* 3.5 4.7 - - - -
168C GLN* 6.2 0.7 - - - -
173C TYR 3.6 9.6 - - - -
174C ALA* 4.5 3.6 - - - -
182D HIS* 4.4 12.0 - - - -
184D PHE* 3.8 18.9 - - - -
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Residues in contact with ASP 139 (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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112C ALA* 3.6 10.2 - - - +
113C ALA 3.1 18.3 - - - +
115C SER* 4.7 11.2 - - - -
138C SER* 1.3 86.3 + - - +
140C PHE* 1.3 56.2 + - - +
170C ASN* 4.2 18.5 + - - +
172C LYS* 4.0 24.0 + - + +
173C TYR 3.1 8.9 + - - -
182D HIS* 4.2 15.9 + - - -
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Residues in contact with PHE 140 (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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112C ALA* 3.3 5.6 - - - +
114C PRO* 3.8 10.8 - - + -
137C ILE* 3.8 15.5 - - + -
138C SER* 3.8 9.2 - - - -
139C ASP* 1.3 73.9 - - - +
141C TYR* 1.3 61.3 + - - +
142C PRO 3.5 20.6 - - - -
143C GLY* 4.3 6.7 - - - -
144C ALA 4.4 0.4 - - - -
145C VAL* 3.4 41.7 - - + -
165C PRO* 4.4 4.3 - - + -
172C LYS* 3.8 3.5 - - - +
173C TYR* 2.6 76.9 + - + +
174C ALA* 3.2 10.8 - - - -
175C ALA* 3.9 9.9 - - + -
198C HIS* 3.5 28.0 - + + -
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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