Contacts of the helix formed by residues 139 - 146 (chain X) in PDB entry 6CP3
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 TRP 139 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137X HIS 3.2 2.4 + - - -
138X GLY* 1.3 71.9 - - - -
140X VAL* 1.3 57.3 + - - +
141X PHE 3.1 9.7 + - - -
142X PHE* 3.3 33.3 + + - +
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Residues in contact with VAL 140 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137X HIS* 3.4 33.2 + - + +
139X TRP* 1.3 74.8 - - + +
141X PHE* 1.3 59.8 + - - +
142X PHE 3.1 1.8 - - - -
143X SER* 2.9 43.3 + - - +
248X LEU* 3.8 7.8 - - + +
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Residues in contact with PHE 141 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129X ASN 4.6 2.2 - - - -
130X THR* 4.3 10.8 - - - -
133X GLY* 3.5 42.4 - - - +
134X LEU* 3.6 37.7 - - + -
137X HIS* 3.5 20.0 - + + +
138X GLY 3.8 2.5 - - - +
139X TRP 3.1 1.4 - - - -
140X VAL* 1.3 78.3 - - - +
142X PHE* 1.3 64.2 + + - +
143X SER 3.1 3.7 + - - -
144X LEU* 3.5 24.5 + - + +
166X TYR* 3.2 32.5 - + - -
244X ASP 4.7 4.0 - - - -
245X ALA* 3.6 22.7 - - + -
248X LEU* 4.0 8.3 - - + +
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Residues in contact with PHE 142 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134X LEU* 3.6 34.8 - - + -
138X GLY 4.6 2.0 - - - -
139X TRP* 3.3 26.8 + + - +
140X VAL* 3.1 1.2 - - - -
141X PHE* 1.3 81.8 - + - +
143X SER* 1.3 56.1 + - - +
144X LEU* 3.2 6.8 + - - +
145X PHE* 3.5 50.1 + + + +
146X VAL* 4.9 2.8 + - - +
166X TYR* 5.8 5.4 - + - -
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Residues in contact with SER 143 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140X VAL* 2.9 37.2 + - - +
142X PHE* 1.3 76.2 - - - +
144X LEU* 1.3 62.5 + - - +
145X PHE 3.2 1.7 + - - -
146X VAL* 3.6 25.1 + - - +
248X LEU* 3.7 11.6 - - - +
249X HIS* 3.9 9.5 + - - -
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Residues in contact with LEU 144 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141X PHE* 3.9 17.5 - - + +
142X PHE 3.2 1.2 - - - -
143X SER* 1.3 77.4 - - - +
145X PHE* 1.3 76.1 + - + +
146X VAL 3.2 4.8 + - - -
147X PRO* 3.6 11.0 - - + +
162X GLU* 4.0 23.0 - - + +
166X TYR* 5.0 7.4 - - + -
169X ARG* 4.4 17.9 - - - +
244X ASP* 3.9 39.9 - - + +
245X ALA* 5.7 0.2 - - - -
248X LEU* 3.4 16.3 - - + +
249X HIS* 3.1 33.6 + - + +
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Residues in contact with PHE 145 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142X PHE* 3.5 50.0 - + + +
143X SER 3.2 1.4 - - - -
144X LEU* 1.3 86.4 - - + +
146X VAL* 1.3 59.0 + - + +
147X PRO* 3.5 8.8 - - - +
158X LEU* 4.3 2.4 - - - +
159X VAL* 3.3 46.5 + - + +
162X GLU* 3.6 27.8 - - + -
163X THR* 3.6 27.8 - - + -
166X TYR* 3.9 42.2 - + + -
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Residues in contact with VAL 146 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142X PHE 4.9 2.0 - - - +
143X SER* 3.6 27.9 - - - +
144X LEU 3.2 2.0 - - - -
145X PHE* 1.3 83.7 - - + +
147X PRO* 1.3 65.2 - - - +
148X ALA 3.5 6.8 + - - +
155X VAL* 4.3 21.1 - - + +
158X LEU* 5.4 1.8 - - + -
159X VAL* 4.3 13.0 - - + -
249X HIS* 4.5 2.3 + - - -
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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