Contacts of the helix formed by residues 137 - 142 (chain A) in PDB entry 3GHZ
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 137 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A THR* 2.6 44.3 + - - +
135A GLU 3.7 8.3 - - - +
136A LYS* 1.3 85.9 - - + +
138A GLY* 1.3 63.5 + - - +
140A THR* 4.1 0.5 + - - -
141A GLY 3.0 6.8 + - - -
9B VAL* 4.3 3.4 - - + -
11B ALA* 3.9 18.8 - - + -
139B PHE* 3.7 31.3 - - + -
144B GLU* 3.4 49.4 - - + +
145B GLY* 3.7 7.0 - - - +
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Residues in contact with GLY 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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136A LYS 4.1 0.4 + - - -
137A LEU* 1.3 73.5 - - - +
139A PHE* 1.3 61.0 + - - -
140A THR 3.2 0.4 - - - -
141A GLY 3.1 0.2 + - - -
142A ARG* 2.8 44.2 + - - +
139B PHE* 3.6 15.8 - - - +
144B GLU* 4.9 1.2 + - - -
301B POP 3.2 26.9 - - - -
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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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7A PHE* 5.3 3.8 - + - -
9A VAL* 3.6 43.1 - - + -
138A GLY* 1.3 72.1 - - - -
140A THR* 1.3 82.0 + - + +
142A ARG* 3.6 8.4 + - - +
143A GLY 3.5 1.9 + - - -
144A GLU* 2.9 53.5 + - + +
145A GLY 3.6 4.8 + - - -
147A ALA* 4.4 4.9 - - + -
301B POP 2.9 37.9 + - - +
134C THR* 4.8 7.2 - - + -
137C LEU* 3.6 30.3 - - + -
138C GLY* 3.6 20.9 - - - +
140C THR* 5.8 0.7 - - - -
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Residues in contact with THR 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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99A ILE* 3.7 28.9 - - + +
100A ALA* 4.6 4.0 + - - -
101A GLN* 3.3 18.3 + - - +
134A THR* 2.9 35.9 + - - +
137A LEU 4.1 0.3 + - - -
138A GLY* 5.5 0.2 - - - -
139A PHE* 1.3 103.2 - - + +
141A GLY* 1.3 62.0 + - - +
143A GLY* 3.1 12.0 + - - -
145A GLY 3.4 18.0 - - - +
147A ALA* 3.9 12.8 - - + +
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Residues in contact with GLY 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A GLN* 3.6 16.0 - - - +
134A THR* 3.4 6.3 - - - -
136A LYS* 3.3 41.9 + - - +
137A LEU 3.0 24.0 + - - -
140A THR* 1.3 80.0 + - - +
142A ARG* 1.3 59.2 + - - +
143A GLY 3.1 1.1 + - - -
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Residues in contact with ARG 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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136A LYS* 4.4 9.0 - - - +
138A GLY* 2.8 29.2 + - - +
139A PHE* 3.6 5.6 - - - +
140A THR 3.3 0.4 - - - -
141A GLY* 1.3 74.4 - - - +
143A GLY* 1.3 61.4 + - - +
144A GLU* 2.9 50.1 + - - +
142B ARG* 4.1 9.3 - - - +
144B GLU* 5.4 0.2 + - - -
301B POP 3.0 41.2 + - - -
142C ARG* 4.2 7.3 - - - +
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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