Contacts of the strand formed by residues 131 - 136 (chain D) in PDB entry 2GER
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 GLY 131 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123D ASN* 3.1 15.5 - - - -
125D PRO* 3.6 4.9 + - - -
126D VAL* 3.6 21.3 - - - +
129D ARG 3.5 2.0 - - - -
130D GLU* 1.3 85.8 - - - +
132D ALA* 1.3 60.3 + - - +
133D THR* 3.9 1.8 - - - -
156D VAL 3.8 4.1 + - - -
157D GLY* 3.4 3.4 - - - -
158D PHE* 2.9 24.9 + - - +
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Residues in contact with ALA 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D MET 3.6 5.9 - - - +
122D THR* 3.7 4.7 - - - +
123D ASN* 3.0 20.1 + - - +
130D GLU 5.0 1.1 - - - +
131D GLY* 1.3 74.1 - - - +
133D THR* 1.3 61.0 + - - +
158D PHE* 4.0 16.8 - - + -
170D VAL* 6.2 0.2 - - - -
174D SER* 2.8 36.8 + - - +
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Residues in contact with THR 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D CYS* 4.9 0.5 - - - +
121D MET 2.7 19.8 + - - -
122D THR* 2.9 27.5 - - + +
131D GLY 5.3 0.7 - - - -
132D ALA* 1.3 75.0 - - - +
134D VAL* 1.3 65.8 + - - +
135D TYR* 5.7 0.3 - - - +
149D MET* 6.0 0.2 - - - +
153D LEU* 3.3 43.2 - - + +
156D VAL 5.3 1.8 - - - +
158D PHE* 2.6 49.6 + - - +
159D CYS* 3.1 19.5 - - - -
160D THR* 3.4 2.9 + - - +
170D VAL* 5.7 0.2 - - - -
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Residues in contact with VAL 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D CYS* 3.6 1.7 - - - -
121D MET* 2.8 45.9 + - + +
132D ALA 4.3 0.2 + - - -
133D THR* 1.3 77.4 + - - +
135D TYR* 1.3 60.1 + - - +
160D THR* 3.3 18.6 - - + +
162D VAL* 3.0 44.2 - - + -
167D ILE* 3.8 14.3 - - + +
170D VAL* 3.4 36.6 - - + -
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Residues in contact with TYR 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D ILE* 4.7 5.2 - - + -
119D ARG 3.1 11.2 - - - +
133D THR* 5.7 0.4 - - - +
134D VAL* 1.3 76.0 - - - +
136D ALA* 1.3 63.7 + - - +
137D THR* 4.4 3.1 - - - -
146D GLY* 4.8 10.7 + - - -
147D ARG* 5.4 0.9 + - - -
149D MET* 3.6 37.5 - - + -
150D GLU* 3.3 53.6 + - + +
159D CYS* 3.9 13.9 - - - -
160D THR 3.0 15.8 + - - -
161D GLU* 3.0 44.0 + - + +
162D VAL 2.7 32.6 + - - -
167D ILE* 4.2 2.7 - - - -
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Residues in contact with ALA 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D ILE* 3.4 2.8 - - + +
118D ILE* 3.2 8.0 - - - -
119D ARG* 2.7 53.1 + - + -
135D TYR* 1.3 73.8 - - - +
137D THR* 1.3 62.7 + - - +
162D VAL 3.4 17.0 - - - +
164D GLU* 3.7 29.8 - - + +
167D ILE* 3.9 5.1 - - + +
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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