Contacts of the helix formed by residues 121 - 132 (chain B) in PDB entry 2GH1
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 THR 121 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120B THR* 1.3 91.5 + - - +
122B PRO* 1.3 67.6 - - - +
123B GLU* 3.3 14.1 - - + +
124B THR* 3.1 31.4 + - - +
125B MSE 3.5 5.7 + - - -
304B GOL 3.1 23.9 + - - -
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Residues in contact with PRO 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LEU* 3.9 9.4 - - + +
119B MSE 3.7 22.4 - - + +
120B THR 3.6 7.0 - - - +
121B THR* 1.3 87.1 - - - +
123B GLU* 1.3 69.9 + - - +
125B MSE 3.3 4.8 + - + +
126B LEU* 2.9 29.8 + - + +
181B GLY 4.9 6.1 - - - +
183B ASP* 5.6 3.4 - - + +
186B ILE* 3.4 35.0 - - + -
193B TYR* 4.0 18.4 - - + +
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Residues in contact with GLU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B THR* 3.6 16.5 - - + +
122B PRO* 1.3 86.0 - - - +
124B THR* 1.3 58.2 + - - +
126B LEU* 3.3 11.2 + - - +
127B GLN* 2.9 27.5 + - - +
193B TYR* 3.3 47.2 + - + -
196B GLU* 4.6 7.4 - - - +
197B LEU* 4.1 12.8 - - + +
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Residues in contact with THR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B THR* 3.1 27.6 + - - +
123B GLU* 1.3 76.7 - - - +
125B MSE 1.3 64.6 + - - +
127B GLN* 3.1 11.5 + - + +
128B LYS* 3.0 28.5 + - + +
304B GOL 3.6 15.5 - - - +
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Residues in contact with MSE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B TYR* 3.7 23.6 - - + -
98B ALA 3.4 27.1 - - - +
99B THR* 3.8 7.9 - - - -
115B PHE* 3.4 27.6 - - + -
116B LEU* 4.0 8.5 - - + -
119B MSE 3.1 43.5 - - + -
121B THR 3.5 3.1 + - - +
122B PRO 3.3 8.6 + - - +
124B THR* 1.3 79.6 - - - +
126B LEU* 1.3 62.6 + - - +
128B LYS* 3.2 24.3 + - + -
129B MSE 3.1 25.1 + - + +
304B GOL 4.0 2.2 + - - -
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LEU* 3.7 31.0 - - + -
122B PRO* 2.9 20.3 + - + +
123B GLU* 3.5 4.7 - - - +
125B MSE 1.3 72.7 - - - +
127B GLN* 1.3 67.2 + - - +
129B MSE 3.1 11.0 + - - +
130B ILE* 2.9 28.7 + - - +
139B ILE* 3.9 16.8 - - + -
141B CYS* 3.8 18.2 - - - -
190B ILE* 4.6 5.6 - - + -
193B TYR* 3.6 37.5 - - + -
194B LEU* 4.0 17.0 - - + -
197B LEU* 3.7 9.9 - - + -
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Residues in contact with GLN 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B GLU 2.9 14.5 + - - +
124B THR* 3.2 14.6 - - + +
126B LEU* 1.3 75.6 - - - +
128B LYS* 1.3 64.2 + - + +
130B ILE* 3.4 10.1 + - - +
131B HIS* 3.0 65.8 + - + +
197B LEU* 3.9 29.3 - - + +
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Residues in contact with LYS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B TYR* 4.2 6.2 + - - -
98B ALA 3.2 26.7 - - - -
99B THR* 3.5 21.8 - - - +
100B GLU* 4.1 4.9 + - - +
101B ILE* 2.7 30.6 + - - +
102B GLU* 5.6 1.0 - - - +
124B THR* 3.0 19.5 + - + +
125B MSE 3.4 20.2 - - + +
126B LEU 3.1 0.2 - - - -
127B GLN* 1.3 74.7 - - + +
129B MSE 1.3 68.0 + - - +
131B HIS* 3.0 21.1 + - + +
132B SER* 3.3 10.6 + - - -
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Residues in contact with MSE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B TYR* 3.7 30.3 - - + -
110B ALA* 4.1 7.2 - - + +
111B ILE* 3.5 42.4 - - - +
112B CYS* 3.7 24.9 - - + -
115B PHE* 4.7 2.5 - - - -
116B LEU* 4.3 10.1 - - - -
125B MSE 3.1 21.9 + - + +
126B LEU* 3.1 20.8 + - - +
128B LYS* 1.3 76.3 - - - +
130B ILE* 1.3 63.3 + - - +
132B SER* 2.6 27.6 + - - -
133B VAL* 3.3 9.6 - - - +
139B ILE* 4.1 16.2 - - + -
141B CYS* 4.6 1.8 - - - -
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Residues in contact with ILE 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B LEU* 2.9 24.1 + - + +
127B GLN* 3.4 17.7 - - - +
129B MSE 1.3 75.7 - - - +
131B HIS* 1.3 60.6 + - + +
133B VAL* 2.9 33.3 + - - +
139B ILE* 3.5 24.9 - - + -
194B LEU* 4.7 3.1 - - + -
197B LEU* 4.5 15.3 - - + +
199B VAL* 3.6 22.2 - - + -
291B ILE* 3.5 38.2 - - + +
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Residues in contact with HIS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LYS* 3.1 28.4 + - - +
127B GLN* 3.0 54.2 + - + +
128B LYS* 3.0 13.4 + - + +
130B ILE* 1.3 80.5 - - + +
132B SER* 1.3 57.4 + - - +
133B VAL 3.2 2.1 - - - +
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Residues in contact with SER 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B VAL* 4.1 6.8 - - - +
46B TYR* 2.8 31.4 + - - -
103B LEU* 4.1 19.5 - - - -
105B ASP 4.5 4.3 - - - -
106B LYS* 3.3 11.0 - - - +
107B TYR* 2.8 29.4 + - - +
110B ALA* 4.1 1.6 - - - +
128B LYS 3.3 4.8 + - - -
129B MSE 2.6 21.4 + - - -
131B HIS* 1.3 75.7 - - - +
133B VAL* 1.3 59.2 + - - +
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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