Contacts of the helix formed by residues 125 - 140 (chain A) in PDB entry 2R0B
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 SER 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A SO4 2.9 7.5 + - - -
89A ASP* 2.7 37.3 + - - -
124A ILE* 1.3 81.5 - - - +
126A ARG* 1.3 60.6 + - - +
127A SER 3.5 0.2 - - - -
128A ALA 4.0 0.4 - - - -
129A ALA* 3.0 29.8 + - - +
158A ASN 3.6 12.8 - - - -
159A PRO* 3.9 4.9 - - - +
160A ASN* 3.1 22.1 + - - +
163A PHE* 3.4 6.0 - - - -
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Residues in contact with ARG 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A SO4 2.8 43.8 + - - +
63A ILE* 3.9 19.6 + - + +
64A ARG* 3.8 6.0 - - - +
65A GLN* 3.5 11.3 + - - +
68A GLU* 2.9 39.3 + - - -
87A ILE* 2.9 38.1 + - + -
88A ALA 3.6 1.3 - - - -
89A ASP* 3.5 27.7 - - + +
95A ILE* 5.7 0.7 - - - -
121A ASN* 3.4 11.4 - - - +
125A SER* 1.3 71.3 - - - +
127A SER* 1.3 66.2 + - - +
129A ALA* 3.1 4.0 + - - +
130A PHE* 3.1 33.1 + - + -
163A PHE* 3.6 27.8 - - + -
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Residues in contact with SER 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A SO4 2.7 20.5 + - - -
38A LEU* 3.6 15.9 - - - +
63A ILE* 3.8 11.8 - - - +
118A VAL* 3.9 4.1 - - - +
119A HIS* 3.8 7.9 - - - -
120A GLY 3.5 20.0 - - - -
123A GLY* 3.1 22.2 - - - -
126A ARG* 1.3 77.5 - - - +
128A ALA* 1.3 63.4 + - - +
130A PHE* 3.2 5.9 + - - +
131A VAL* 3.1 24.8 + - - +
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Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 3.8 13.8 - - + +
123A GLY 4.8 0.2 - - - +
124A ILE* 3.3 27.1 - - - +
125A SER 3.7 2.1 + - - +
126A ARG 3.3 0.4 - - - -
127A SER* 1.3 80.1 + - - +
129A ALA* 1.3 64.4 + - - +
131A VAL* 3.1 3.3 + - - +
132A ILE* 2.9 27.8 + - - +
150A VAL* 5.4 0.6 - - + +
157A ILE* 3.8 32.3 - - + -
159A PRO* 4.4 5.6 - - + -
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Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ILE* 3.7 26.2 - - + -
99A PHE* 4.7 1.6 - - - -
125A SER 3.0 19.9 + - - +
126A ARG 3.1 5.6 + - - +
128A ALA* 1.3 76.1 - - - +
130A PHE* 1.3 57.3 + - - +
132A ILE* 3.3 2.0 + - - -
133A ALA* 2.9 25.5 + - - +
159A PRO* 4.3 6.0 - - + +
163A PHE* 4.2 8.7 - - + -
167A LEU* 3.5 29.5 - - + +
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Residues in contact with PHE 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ILE* 5.8 1.8 - - + -
63A ILE* 3.9 19.5 - - + -
85A LEU* 3.9 3.1 - - + -
87A ILE* 3.3 36.6 - - + -
95A ILE* 3.8 31.4 - - + -
98A PHE* 3.8 13.0 - - + -
99A PHE* 3.6 22.7 - + - -
102A THR* 3.4 45.0 + - + +
106A ILE* 5.1 5.1 - - + +
118A VAL* 4.5 7.6 - - + -
126A ARG* 3.1 26.2 + - + -
127A SER 3.2 7.2 + - - +
129A ALA* 1.3 77.4 - - - +
131A VAL* 1.3 61.4 + - - +
133A ALA* 3.5 5.2 + - - +
134A TYR* 3.3 20.8 + - - +
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Residues in contact with VAL 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ILE* 4.0 21.1 - - + -
36A LEU* 4.1 18.2 - - + -
37A PHE 4.7 0.2 - - - +
38A LEU* 4.0 17.5 - - + -
106A ILE* 5.9 0.7 - - - -
118A VAL* 3.8 31.2 - - + -
127A SER 3.1 14.9 + - - +
128A ALA* 3.1 10.1 + - - +
130A PHE* 1.3 74.4 - - - +
132A ILE* 1.3 61.8 + - - +
134A TYR* 3.3 7.0 + - - +
135A ILE* 3.0 45.1 + - + +
150A VAL* 4.4 8.1 - - + -
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Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ALA 2.9 20.8 + - - +
129A ALA* 3.7 5.2 - - - +
131A VAL* 1.3 74.3 - - - +
133A ALA* 1.3 59.1 + - - +
135A ILE* 3.2 6.4 + - - +
136A MET* 2.9 52.6 + - + +
143A TYR* 3.9 17.5 - - + -
146A ALA* 4.0 11.7 - - + +
147A PHE* 4.1 13.5 - - + +
150A VAL* 4.0 19.3 - - + -
157A ILE* 3.8 26.9 - - + -
159A PRO* 4.0 20.9 - - + -
167A LEU* 4.0 5.6 - - + -
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Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PHE* 3.8 32.1 - - + +
102A THR* 5.7 1.1 - - - +
129A ALA 2.9 11.9 + - - +
130A PHE 3.7 6.1 - - - +
131A VAL 3.3 0.4 - - - -
132A ILE* 1.3 76.5 - - - +
134A TYR* 1.3 62.7 + - - +
136A MET* 3.4 5.1 + - - +
137A GLU* 3.2 25.6 + - - +
167A LEU* 3.6 23.8 - - + +
170A TYR* 4.7 11.0 - - + -
174A TYR* 5.0 0.5 + - - -
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Residues in contact with TYR 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 4.3 24.1 - - + +
36A LEU* 3.8 16.6 - - + -
102A THR* 6.2 0.2 - - - +
103A LYS* 3.8 22.9 - - + +
106A ILE* 3.4 44.0 - - + -
107A ASP* 3.3 27.1 + - - -
110A LEU* 3.7 16.1 - - + +
130A PHE 3.3 11.0 + - - +
131A VAL* 3.6 9.4 - - - +
132A ILE 3.2 0.4 - - - -
133A ALA* 1.3 78.4 - - - +
135A ILE* 1.3 60.1 + - - +
137A GLU* 4.1 2.1 - - - -
138A THR* 2.9 68.9 + - + +
139A PHE* 4.3 2.7 - + - -
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Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ILE* 3.8 18.4 - - + -
33A LEU* 3.4 23.8 - - + -
131A VAL* 3.0 23.9 + - + +
132A ILE* 3.2 5.6 + - - +
134A TYR* 1.3 74.8 - - + +
136A MET* 1.3 66.5 + - - +
139A PHE* 2.9 35.2 + - + +
140A GLY 3.9 0.3 + - - -
141A MET* 3.6 29.5 + - + -
146A ALA* 3.9 12.1 - - + -
149A TYR* 4.3 9.0 - - + -
150A VAL* 3.4 32.8 - - + -
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Residues in contact with MET 136 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ILE* 2.9 36.3 + - - +
133A ALA* 3.8 4.7 - - - +
135A ILE* 1.3 77.4 - - - +
137A GLU* 1.3 57.7 + - - +
140A GLY* 3.0 25.1 + - - -
141A MET 3.2 22.0 + - - +
142A LYS 4.2 1.1 - - - +
143A TYR* 3.9 31.6 - - + +
146A ALA* 3.7 15.9 - - + -
167A LEU* 3.6 36.1 - - - +
168A GLN* 4.7 1.1 - - - +
170A TYR* 6.5 0.2 - - + -
171A GLU* 3.8 26.9 - - + +
174A TYR* 3.2 15.7 + - + +
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Residues in contact with GLU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LYS* 4.1 30.5 - - + +
133A ALA 3.2 12.1 + - - +
134A TYR 4.2 1.6 - - - +
136A MET* 1.3 81.1 - - - +
138A THR* 1.3 64.5 + - - +
140A GLY* 3.9 4.3 + - - -
170A TYR* 2.8 29.6 + - - -
174A TYR* 3.3 50.5 + - + +
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Residues in contact with THR 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LYS* 2.8 30.7 + - - +
107A ASP* 5.2 0.2 - - - +
134A TYR* 2.9 43.5 + - - +
137A GLU* 1.3 78.4 - - - +
139A PHE* 1.3 84.2 + - + +
140A GLY 3.5 0.6 + - - -
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Residues in contact with PHE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 3.8 40.6 - - + -
34A PRO* 5.5 4.5 - - + -
134A TYR* 4.3 3.1 - + - -
135A ILE* 2.9 24.2 + - + +
138A THR* 1.3 101.1 - - + +
140A GLY* 1.3 63.6 + - - +
141A MET* 3.3 24.9 + - + +
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Residues in contact with GLY 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A MET 3.0 11.3 + - - -
137A GLU 3.9 4.4 + - - -
138A THR 3.5 3.2 + - - -
139A PHE* 1.3 78.0 - - - +
141A MET* 1.3 60.2 + - - +
142A LYS* 4.1 1.0 + - - +
171A GLU* 5.9 0.4 - - - -
174A TYR* 6.3 0.9 - - - -
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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