Contacts of the helix formed by residues 138 - 148 (chain A) in PDB entry 6B0B
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 PHE 138 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLY* 1.3 71.4 - - - +
139A PRO* 1.4 70.7 - - + +
141A PHE 3.5 1.9 + - - -
142A ALA* 2.9 31.9 + - + +
162A MET* 4.5 8.5 - - + -
163A LEU* 3.6 28.7 - - + -
166A LEU* 3.5 35.5 - - + +
167A ASP* 5.8 4.7 - - + -
170A SER* 5.1 1.2 - - - -
36D ARG* 3.1 42.0 - - + -
39D GLU* 3.1 27.6 - - - +
41D THR* 4.4 13.2 - - + -
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Residues in contact with PRO 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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138A PHE* 1.4 95.3 - - + +
140A GLU* 1.3 70.3 + - - +
142A ALA* 2.9 7.2 + - + +
143A ASP* 2.4 48.8 + - - +
39D GLU* 4.2 19.7 - - + +
74D LYS* 5.9 5.2 - - - +
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Residues in contact with GLU 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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79A TYR* 3.3 41.8 + - + +
105A ARG* 5.6 0.9 + - - -
107A PHE* 3.2 31.2 - - + -
135A VAL 4.8 0.9 - - - -
136A MET* 3.5 15.0 - - + -
137A GLY* 3.0 34.5 + - - +
139A PRO* 1.3 103.7 - - - +
141A PHE* 1.3 57.5 + - - +
143A ASP* 4.0 1.3 - - - -
144A CYS* 2.9 29.8 + - - +
174A LYS* 4.4 8.0 + - - -
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Residues in contact with PHE 141 (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 PHE* 3.9 17.6 - + + -
13A PHE* 3.3 45.5 - + + -
14A ASN* 5.0 2.0 - - - -
79A TYR* 6.5 0.7 - - + -
109A SER* 3.1 24.5 - - - -
136A MET* 3.5 41.1 - - + -
137A GLY 3.6 4.0 + - - +
138A PHE 3.5 0.6 + - - -
139A PRO 3.2 0.6 - - - -
140A GLU* 1.3 79.8 - - - +
142A ALA* 1.3 56.1 + - - +
144A CYS* 3.2 3.1 + - + +
145A TRP* 2.6 38.0 + - - +
162A MET* 5.4 5.6 - - + -
166A LEU* 3.5 46.0 - - + -
169A ASN* 4.6 6.5 - - - -
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Residues in contact with ALA 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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138A PHE* 2.9 31.5 + - + +
139A PRO* 3.5 7.6 - - + +
141A PHE* 1.3 76.4 - - - +
143A ASP* 1.3 64.4 + - - +
145A TRP* 3.5 11.8 + - - +
146A GLU* 3.5 9.9 - - - +
162A MET* 5.6 5.4 - - + +
166A LEU* 4.8 0.8 - - + +
39D GLU* 5.3 4.5 - - + +
41D THR* 5.3 4.0 - - + -
216D ARG* 3.3 35.3 + - - +
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Residues in contact with ASP 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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79A TYR* 3.5 31.3 + - + -
105A ARG* 5.3 0.9 + - - -
139A PRO* 2.4 39.4 + - - +
142A ALA* 1.3 70.3 - - - +
144A CYS* 1.3 61.3 + - - +
145A TRP 3.2 0.3 + - - -
146A GLU* 3.4 4.2 - - - +
147A ASN* 2.7 44.1 + - - +
74D LYS* 4.4 15.4 + - - -
216D ARG* 5.7 1.4 + - - -
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Residues in contact with CYS 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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9A PHE* 4.5 4.7 - - + -
13A PHE* 3.7 33.4 - - + -
31A CYS* 3.8 9.4 - - - -
79A TYR* 3.5 24.1 - - + -
140A GLU 2.9 21.5 + - - +
141A PHE* 3.9 4.5 - - + +
143A ASP* 1.3 74.1 - - - +
145A TRP* 1.3 64.2 + - - +
147A ASN 4.1 0.2 - - - -
148A PHE* 3.3 41.9 + - - +
149A VAL* 3.5 8.2 + - - +
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Residues in contact with TRP 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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6A ALA* 3.7 28.7 - - + -
9A PHE* 3.4 42.8 - + + -
141A PHE 2.6 20.9 + - - +
142A ALA* 3.6 8.1 - - - +
143A ASP 3.1 0.6 - - - -
144A CYS* 1.3 76.1 - - - +
146A GLU* 1.3 62.5 + - - +
149A VAL* 2.9 51.2 - - + +
150A ASP 5.0 4.3 - - - -
151A HIS* 2.9 39.9 + + - -
155A LEU* 4.3 15.0 - - + -
158A ASN* 4.4 13.7 - - - -
159A PRO* 5.1 6.9 + - + -
162A MET* 5.8 12.3 - - + -
214D TYR* 4.6 9.9 + - - -
216D ARG* 3.9 20.0 - - - -
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Residues in contact with GLU 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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44A ARG* 5.0 0.2 + - - -
142A ALA 3.5 7.0 - - - +
143A ASP* 3.4 6.2 - - - +
145A TRP* 1.3 76.8 - - + +
147A ASN* 1.3 108.1 + - - +
149A VAL 3.2 10.0 - - - +
150A ASP* 5.1 0.3 - - - -
151A HIS* 3.6 35.7 + - + +
216D ARG* 3.5 31.7 + - + +
218D GLU* 5.0 8.2 - - - +
220D ARG* 5.1 8.0 + - - -
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Residues in contact with ASN 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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33A GLN* 5.0 7.2 - - - +
44A ARG* 2.9 48.1 + - - +
79A TYR* 5.7 1.2 - - - -
143A ASP* 2.7 40.1 + - - +
146A GLU* 1.3 106.0 + - - +
148A PHE* 1.3 76.8 + - + +
149A VAL 4.4 0.3 - - - +
150A ASP* 5.3 0.9 - - - +
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Residues in contact with PHE 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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3A LEU 3.3 24.8 + - - +
4A LEU* 3.9 9.3 + - + -
31A CYS* 3.5 31.6 - - + -
32A TYR 3.2 36.6 - - - -
33A GLN* 3.8 22.2 - - + -
44A ARG* 4.1 7.9 - - + +
45A GLY* 3.3 30.1 - - - -
46A TYR* 4.4 3.4 - + + -
79A TYR* 4.8 9.4 - + - -
144A CYS* 3.3 36.6 + - - +
147A ASN* 1.3 89.5 - - + +
149A VAL* 1.3 66.9 + - + +
150A ASP* 3.4 3.5 + - - +
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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