Contacts of the helix formed by residues 138 - 144 (chain A) in PDB entry 2GQ3
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 LEU 138 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A GLY 3.4 2.8 + - - -
137A SER* 1.3 69.7 - - - +
139A TYR* 1.3 56.3 + - + +
141A ALA* 3.0 2.3 + - - +
142A LEU* 2.7 70.1 + - + +
171A TYR* 5.4 1.1 - - + -
172A ALA* 4.1 20.6 - - + -
175A PHE* 4.2 23.6 - - + -
260A VAL* 2.8 26.3 + - + +
262A LEU* 4.0 27.6 - - + -
549A THR* 3.9 11.7 - - + -
550A LEU* 4.4 7.9 - - + -
553A LEU* 4.1 16.8 - - + -
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Residues in contact with TYR 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A SER* 3.8 0.7 - - - +
138A LEU* 1.3 78.3 - - + +
140A ASP* 1.3 56.3 + - - +
142A LEU* 3.2 0.9 + - - +
143A TYR* 2.7 40.7 + - - +
168A VAL* 3.7 22.8 - - + +
169A ILE* 4.0 22.0 - - + +
172A ALA* 3.6 27.2 - - + +
173A ARG* 4.1 10.7 + - - -
249A VAL* 4.1 22.4 - - + -
253A ASP* 4.8 0.2 + - - -
257A VAL* 3.5 20.8 + - - +
258A LYS 3.5 28.7 - - - -
259A ASP* 3.1 24.2 + - - +
260A VAL* 3.7 17.7 - - + +
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Residues in contact with ASP 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A SER* 3.0 31.2 + - - +
139A TYR* 1.3 77.2 - - - +
141A ALA* 1.3 58.5 + - - +
143A TYR* 4.7 3.8 - - - +
144A GLY* 2.8 30.5 + - - -
145A THR* 5.2 0.2 - - - +
259A ASP* 4.8 1.8 - - - +
546A THR* 5.9 0.7 - - - -
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Residues in contact with ALA 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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137A SER 3.2 14.2 + - - +
138A LEU 3.0 9.0 + - - +
140A ASP* 1.3 77.5 - - - +
142A LEU* 1.3 53.5 + - - +
145A THR* 2.7 37.6 + - - +
546A THR* 4.2 19.3 - - + +
549A THR* 4.0 16.2 - - + -
550A LEU* 3.8 27.9 - - + +
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Residues in contact with LEU 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 LEU* 2.7 46.1 + - + +
139A TYR 3.9 2.0 - - - +
141A ALA* 1.3 72.3 - - - +
143A TYR* 1.3 64.7 + - - +
145A THR* 3.4 11.4 + - - +
147A VAL* 3.4 31.2 - - + -
148A ILE* 3.5 20.5 + - + +
164A ARG* 3.4 12.5 + - - -
168A VAL* 4.0 24.7 - - + +
171A TYR* 3.5 40.6 - - + +
172A ALA* 4.5 2.0 - - + +
550A LEU* 3.7 16.2 - - + -
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Residues in contact with TYR 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A TYR 2.7 23.7 + - - +
140A ASP* 4.3 3.6 - - - +
142A LEU* 1.3 73.3 - - - +
144A GLY* 1.3 60.1 + - - +
156A LYS* 3.6 20.6 - - + +
157A GLY 5.0 0.4 + - - -
159A THR 4.0 3.1 + - - -
160A TYR* 3.7 25.7 - + - -
161A ASN* 2.8 35.2 + - - +
164A ARG* 2.8 63.7 + - + +
165A GLY* 3.7 23.3 - - - -
168A VAL* 3.7 11.4 - - + +
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Residues in contact with GLY 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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140A ASP* 2.8 18.7 + - - +
143A TYR* 1.3 82.3 - - - +
145A THR* 1.3 63.1 + - - +
156A LYS* 3.6 18.3 - - - +
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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