Contacts of the helix formed by residues 141 - 153 (chain A) in PDB entry 6V99
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 ASP 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A SER* 3.5 6.5 + - - -
140A MET* 1.3 71.0 - - - +
142A TYR* 1.3 63.9 + - - +
143A GLU* 3.1 12.3 + - - +
144A TYR* 3.3 35.0 + - + +
145A MET 4.3 0.3 + - - -
255A SER* 2.8 22.7 + - - +
257A VAL* 3.6 8.4 - - + +
297A TRP* 3.7 13.7 - - + -
7C GLN* 3.3 16.7 - - - +
11C ARG* 2.6 46.6 + - - -
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Residues in contact with TYR 142 (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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50A ALA* 4.0 1.9 + - - -
53A ASN* 3.3 37.9 + - + +
54A ALA* 3.5 15.9 - - - -
57A SER* 2.9 26.1 + - - +
59A ILE* 4.2 17.9 - - + -
130A VAL* 4.4 11.9 - - + -
132A LEU* 3.5 38.5 - - + +
138A TYR* 2.7 23.9 + - - -
140A MET* 3.8 34.1 - - + -
141A ASP* 1.3 70.2 - - - +
143A GLU* 1.3 63.7 + - - +
144A TYR 3.2 0.7 - - - -
145A MET* 3.2 12.6 + - + +
146A LEU* 3.0 29.2 + - + +
208A ILE* 4.7 4.9 - - + -
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Residues in contact with GLU 143 (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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7A GLN 4.8 0.3 - - - +
8A PRO* 3.7 12.4 - - - +
9A LEU* 2.8 29.2 + - - +
10A ALA* 2.9 33.6 + - - +
57A SER* 4.4 4.9 + - - +
141A ASP* 3.1 17.1 + - - +
142A TYR* 1.3 78.3 - - - +
144A TYR* 1.3 62.1 + - - +
146A LEU* 3.3 6.4 + - - +
147A GLN* 2.9 39.2 + - - +
6C VAL* 3.9 24.5 - - + +
7C GLN* 4.9 0.7 - - - -
8C PRO* 4.2 9.6 - - + +
11C ARG* 3.8 9.4 - - - +
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Residues in contact with TYR 144 (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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141A ASP* 3.3 40.9 + - + -
142A TYR 3.2 0.8 - - - -
143A GLU* 1.3 77.6 - - - +
145A MET* 1.3 63.4 + - - +
147A GLN* 3.2 3.3 + - - +
148A GLN* 3.0 23.9 + - - +
250A HIS* 4.1 8.9 - - + -
254A ASP* 4.0 16.4 - - + +
255A SER* 3.7 25.6 - - - -
6C VAL* 3.7 34.0 - - + +
7C GLN* 2.8 31.1 + - + +
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Residues in contact with MET 145 (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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140A MET* 3.9 19.7 - - + -
141A ASP 4.3 0.8 + - - +
142A TYR* 3.2 17.9 + - + +
144A TYR* 1.3 78.0 - - - +
146A LEU* 1.3 58.3 + - - +
148A GLN* 3.4 2.5 + - - +
149A HIS* 2.9 30.6 + - - +
157A THR* 3.3 28.6 - - + +
158A ILE 3.6 2.9 - - - -
159A GLY 3.3 29.4 - - - +
208A ILE* 3.7 27.6 - - + +
210A VAL* 3.6 22.6 - - + +
250A HIS* 3.7 31.0 + - + +
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Residues in contact with LEU 146 (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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9A LEU* 3.3 22.3 - - + +
10A ALA* 3.7 38.4 - - + +
13A ALA* 4.2 8.1 - - + -
59A ILE* 5.1 1.1 - - + -
128A TYR* 3.9 31.2 - - + -
130A VAL* 3.8 26.7 - - + -
142A TYR* 3.0 22.6 + - + +
143A GLU* 3.6 9.6 - - - +
144A TYR 3.3 0.2 - - - -
145A MET* 1.3 77.5 - - - +
147A GLN* 1.3 62.6 + - - +
149A HIS* 3.2 6.4 + - + +
150A VAL* 3.1 21.5 + - - +
210A VAL* 4.0 12.3 - - + -
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Residues in contact with GLN 147 (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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9A LEU* 3.6 15.1 - - + +
143A GLU* 2.9 34.6 + - - +
144A TYR 3.8 3.8 - - - +
146A LEU* 1.3 76.9 - - - +
148A GLN* 1.3 61.9 + - - +
150A VAL* 3.5 0.9 + - - +
151A ASP* 3.0 45.4 + - - +
6C VAL* 3.5 46.1 + - + +
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Residues in contact with GLN 148 (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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144A TYR 3.0 16.8 + - - +
145A MET* 3.8 4.7 - - - +
147A GLN* 1.3 77.9 - - - +
149A HIS* 1.3 57.1 + - - +
151A ASP* 4.8 3.4 - - - -
152A SER* 2.8 43.8 + - - +
157A THR* 4.1 5.2 - - + +
180A ASP* 5.9 0.2 - - - +
248A VAL* 3.5 17.6 - - + +
249A ALA 3.0 31.5 + - - -
250A HIS* 2.9 31.9 + - - +
251A ARG 5.1 0.3 + - - -
254A ASP* 5.2 3.1 - - - +
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Residues in contact with HIS 149 (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 TYR* 4.9 3.8 - + - -
145A MET 2.9 16.9 + - - +
146A LEU 3.2 4.4 + - - +
148A GLN* 1.3 76.7 - - - +
150A VAL* 1.3 66.7 + - + +
152A SER* 3.5 2.9 + - - -
153A GLY* 3.4 16.8 + - - -
154A ALA* 3.0 29.4 + - - +
155A ASP 3.8 13.5 - - - -
157A THR* 3.0 32.6 + - - +
210A VAL* 3.5 39.7 + - + -
211A PHE* 3.6 1.8 - - - -
212A HIS* 3.3 44.7 + + - -
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Residues in contact with VAL 150 (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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9A LEU* 3.7 20.9 - - + -
128A TYR* 3.8 33.7 - - + +
146A LEU* 3.1 16.5 + - + +
147A GLN* 4.1 3.1 - - + +
149A HIS* 1.3 79.7 - - + +
151A ASP* 1.3 68.7 + - - +
153A GLY* 3.6 9.9 + - - -
212A HIS* 4.6 13.1 - - + +
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Residues in contact with ASP 151 (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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147A GLN* 3.0 36.3 + - - +
148A GLN* 4.2 2.7 - - - +
150A VAL* 1.3 86.3 - - - +
152A SER* 1.3 60.1 + - - +
153A GLY 3.3 0.2 - - - -
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Residues in contact with SER 152 (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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148A GLN* 2.8 27.1 + - - -
149A HIS* 3.5 4.0 + - - -
151A ASP* 1.3 76.8 - - - +
153A GLY* 1.3 58.5 + - - +
154A ALA* 3.1 23.0 + - - +
157A THR* 4.2 1.7 + - - -
246A LYS* 3.2 24.8 + - - +
248A VAL* 4.2 23.2 - - - +
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Residues in contact with GLY 153 (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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149A HIS 3.4 7.9 + - - -
150A VAL* 3.6 6.7 + - - -
151A ASP 3.3 3.8 + - - -
152A SER* 1.3 77.1 + - - +
154A ALA* 1.3 67.9 + - - +
155A ASP* 3.6 7.3 + - - +
212A HIS* 6.2 2.9 - - - -
246A LYS* 4.5 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