Contacts of the strand formed by residues 131 - 140 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121P PRO* 4.0 23.1 - - + -
125P GLU* 3.1 2.9 - - - -
126P LEU* 4.1 4.5 - - + -
130P LYS* 1.3 74.6 - - - +
132P THR* 1.3 58.9 + - - +
133P LEU* 4.5 0.6 - - - +
180P SER* 3.6 0.2 - - - -
181P LEU* 2.5 58.2 + - + +
182P THR 4.1 0.2 - - - -
183P PRO* 3.8 26.0 - - + +
186P TRP* 4.7 3.4 - - + -
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Residues in contact with THR 132 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119P PHE 4.4 0.9 - - - +
120P PRO 4.6 0.2 - - - -
121P PRO* 3.6 13.5 - - - +
125P GLU* 2.4 44.4 + - + +
130P LYS* 4.9 6.1 - - + -
131P ALA* 1.3 75.1 - - - +
133P LEU* 1.3 64.5 + - - +
134P VAL* 4.4 5.5 + - - +
178P TYR* 5.1 2.9 - - - -
179P LEU 3.3 9.0 - - - -
180P SER* 3.4 21.1 - - - +
159Q LEU* 4.2 20.2 - - + +
161Q LYS* 4.4 25.0 - - + +
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Residues in contact with LEU 133 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118P LEU* 4.5 0.9 - - + -
119P PHE 3.5 8.3 - - - +
121P PRO* 3.9 24.2 - - + -
131P ALA 4.5 0.7 - - - +
132P THR* 1.3 78.8 - - - +
134P VAL* 1.3 64.8 + - - +
135P CYS 4.0 0.7 - - - -
149P TRP* 3.9 29.2 - - + -
177P SER 3.7 0.3 - - - +
178P TYR* 3.3 10.7 - - - +
179P LEU* 2.7 39.2 + - + +
181P LEU* 3.6 28.9 - - + -
186P TRP* 4.8 2.0 - - + +
192P TYR* 3.9 31.9 - - + -
207P VAL* 4.3 15.9 - - + -
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Residues in contact with VAL 134 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117P THR 3.4 9.0 - - - +
118P LEU* 3.7 3.9 - - - +
119P PHE* 3.4 29.8 + - + +
132P THR* 4.7 6.1 - - - +
133P LEU* 1.3 80.7 - - - +
135P CYS* 1.3 58.3 + - - +
136P LEU* 3.5 31.6 + - + +
177P SER 3.8 2.5 - - - +
178P TYR* 3.8 12.6 - - + -
142Q LEU* 4.2 20.4 - - + -
159Q LEU* 3.5 26.9 - - + -
197Q SER* 3.7 18.4 - - - +
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Residues in contact with CYS 135 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116P VAL* 4.2 11.2 - - - -
117P THR 3.5 4.0 - - - -
118P LEU* 4.1 4.3 - - + -
134P VAL* 1.3 70.4 - - - +
136P LEU* 1.3 66.8 + - - +
137P ILE* 3.8 6.6 - - - +
147P VAL* 5.2 0.4 - - - -
149P TRP* 3.4 21.9 - - + -
176P SER* 3.6 1.2 - - - -
177P SER* 2.9 41.3 + - - +
194P CYS* 2.0 46.4 - - - -
196P VAL* 4.1 14.6 - - - -
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Residues in contact with LEU 136 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115P SER 3.1 17.3 - - - +
116P VAL* 4.5 0.7 - - - -
117P THR* 2.7 35.2 + - - +
119P PHE* 5.1 4.3 - - + -
134P VAL* 3.5 30.7 - - + +
135P CYS* 1.3 81.9 - - - +
137P ILE* 1.3 62.8 + - - +
138P SER* 4.3 1.7 - - - -
175P ALA 4.1 0.4 - - - -
176P SER* 3.6 16.8 - - - +
142Q LEU* 6.0 0.4 - - + -
184Q PHE* 3.7 36.1 - - + -
197Q SER* 4.7 9.4 - - - -
199Q VAL* 3.5 34.5 - - + -
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Residues in contact with ILE 137 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114P PRO* 3.6 23.1 - - + -
115P SER 3.9 3.4 - - - -
116P VAL* 4.8 2.5 - - + +
135P CYS* 3.8 20.0 - - - +
136P LEU* 1.3 70.0 - - - +
138P SER* 1.3 70.3 + - - +
140P PHE* 3.4 22.2 - - + -
145P VAL* 4.1 11.7 - - + -
147P VAL* 3.9 22.4 - - + -
175P ALA* 2.9 45.7 + - + +
176P SER 3.9 3.4 - - - +
177P SER* 4.1 6.1 - - - +
196P VAL* 3.6 25.6 - - + -
184Q PHE* 3.1 8.3 - - - -
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Residues in contact with SER 138 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114P PRO* 3.4 2.4 - - - +
115P SER* 2.8 43.2 + - - -
136P LEU 4.3 1.3 - - - -
137P ILE* 1.3 84.4 - - - +
139P ASP* 1.3 92.6 + - - +
140P PHE* 3.2 6.5 + - - -
173P TYR 3.9 6.3 - - - -
174P ALA* 4.2 3.8 - - - +
182Q HIS* 4.5 11.5 + - - -
184Q PHE* 4.3 13.0 - - - -
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Residues in contact with ASP 139 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112P ALA* 3.6 16.1 - - - +
113P ALA 3.7 8.4 - - - +
115P SER* 4.2 13.2 - - - -
138P SER* 1.3 96.2 + - - +
140P PHE* 1.3 59.3 + - - +
170P ASN* 3.6 21.3 - - - +
172P LYS* 3.9 22.0 + - + +
173P TYR 3.0 9.4 + - - -
174P ALA* 4.8 1.2 - - - +
182Q HIS* 5.9 0.4 - - - -
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Residues in contact with PHE 140 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112P ALA* 3.3 14.4 - - - +
114P PRO* 3.8 14.6 - - + -
137P ILE* 3.4 21.1 - - + -
138P SER 3.5 16.2 - - - -
139P ASP* 1.3 79.6 - - - +
141P TYR* 1.3 62.9 + - - +
142P PRO 3.4 19.1 - - - -
143P GLY* 3.9 4.7 - - - -
144P ALA 4.4 0.2 - - - -
145P VAL* 3.6 31.4 - - + -
165P PRO* 3.7 12.8 - - + -
172P LYS* 3.6 1.5 - - - +
173P TYR* 2.6 60.3 + - + +
174P ALA* 3.5 25.1 - - - -
175P ALA 3.7 2.5 - - - -
198P HIS* 3.8 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