Contacts of the helix formed by residues 156 - 166 (chain B) in PDB entry 1GZ0
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 ASN 156 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A GLN 4.8 3.6 + - - -
166A GLU* 4.1 26.0 + - - +
168A ASN* 3.7 18.5 + - - +
82B GLU* 3.9 2.5 + - - +
154B VAL* 3.7 2.7 - - - -
155B THR* 1.3 87.6 - - + +
157B LEU* 1.3 68.7 + - - +
158B ALA* 3.4 16.3 - - - +
159B ARG* 3.0 38.6 + - + +
160B THR* 3.0 23.4 + - - -
162B ARG* 3.8 5.7 + - - -
203B ARG* 5.1 1.8 - - - +
205B LEU* 5.2 0.8 - - - +
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Residues in contact with LEU 157 (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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99B ILE* 3.5 30.3 - - + -
101B ASP* 3.5 39.7 - - + +
125B ILE* 4.2 17.3 - - + -
127B PRO* 4.0 17.9 - - + +
154B VAL* 3.8 12.8 + - + +
155B THR 4.1 1.2 + - - -
156B ASN* 1.3 74.4 - - - +
158B ALA* 1.3 58.7 + - - +
160B THR* 3.3 3.9 + - - -
161B MSE 2.8 45.0 + - - +
203B ARG* 3.3 23.4 - - - +
206B THR* 3.9 10.1 - - + +
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Residues in contact with ALA 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A GLU* 6.1 0.4 - - + -
156B ASN* 3.3 13.3 - - - +
157B LEU* 1.3 77.0 - - - +
159B ARG* 1.3 58.2 - - - +
161B MSE 3.2 11.5 + - - +
162B ARG* 2.9 34.0 + - - +
205B LEU* 3.9 25.4 - - + +
206B THR* 5.4 1.9 + - - +
209B HIS* 3.6 34.1 - - + +
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Residues in contact with ARG 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLU* 5.5 5.6 + - - +
155B THR* 4.1 23.2 - - - +
156B ASN* 3.0 31.5 + - - +
158B ALA* 1.3 73.0 - - - +
160B THR* 1.3 65.6 + - - +
162B ARG* 3.2 32.1 + - + +
163B MSE 3.2 20.1 + - - +
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Residues in contact with THR 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLU* 3.1 9.6 + - + +
85B LEU* 3.6 30.1 - - + -
99B ILE* 5.9 0.2 - - + -
125B ILE* 4.5 10.5 - - + -
154B VAL* 2.8 39.8 - - + +
156B ASN 3.0 5.2 + - - -
157B LEU* 3.7 9.4 - - + -
159B ARG* 1.3 76.7 - - - +
161B MSE 1.3 64.0 + - + +
163B MSE 3.2 11.2 + - + +
164B LEU* 3.0 29.9 + - + +
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Residues in contact with MSE 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ILE* 4.1 18.8 - - + -
157B LEU* 2.8 32.7 + - + +
158B ALA* 3.2 6.3 + - - +
160B THR* 1.3 76.0 - - - +
162B ARG* 1.3 59.0 + - - +
164B LEU* 3.0 10.2 + - - +
165B GLN* 2.9 32.7 + - - +
171B ILE* 3.6 30.8 - - + +
194B VAL* 4.2 4.5 - - + -
206B THR* 3.1 53.8 - - + +
209B HIS* 3.7 29.8 - - + +
210B CYS* 3.8 4.5 - - - -
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Residues in contact with ARG 162 (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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166A GLU* 5.5 9.2 + - - +
156B ASN* 3.8 6.7 + - - -
158B ALA* 2.9 18.8 + - - +
159B ARG* 3.2 48.4 - - + +
160B THR 3.2 0.2 - - - -
161B MSE 1.3 76.7 - - - +
163B MSE 1.3 61.7 + - - +
165B GLN* 2.9 24.3 + - - +
166B GLU* 3.0 30.4 + - + +
209B HIS* 3.8 23.3 + - + +
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Residues in contact with MSE 163 (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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82B GLU 4.9 2.0 - - - +
85B LEU* 3.4 48.0 - - + -
86B PRO* 4.2 17.0 - - + -
89B ILE* 3.7 23.3 - - + -
159B ARG 3.2 8.5 + - - +
160B THR* 3.2 15.2 + - + +
162B ARG* 1.3 79.6 - - - +
164B LEU* 1.3 66.6 + - + +
166B GLU* 3.4 20.4 + - - +
167B GLU* 3.2 24.5 + - + +
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Residues in contact with LEU 164 (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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85B LEU* 4.8 0.7 - - + -
89B ILE* 3.4 30.7 - - + -
97B LEU* 3.8 13.7 - - + -
99B ILE* 3.8 27.8 - - + -
125B ILE* 4.3 16.4 - - + -
160B THR* 3.0 22.3 + - + +
161B MSE 3.0 13.9 + - + +
163B MSE 1.3 85.3 - - + +
165B GLN* 1.3 57.1 + - - +
167B GLU* 2.9 21.5 + - - +
169B ILE* 3.2 35.3 + - + +
171B ILE* 4.4 6.7 - - + -
192B ALA* 4.7 7.4 - - + -
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Residues in contact with GLN 165 (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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161B MSE 2.9 19.7 + - - +
162B ARG* 2.9 22.3 + - - +
164B LEU* 1.3 76.6 - - - +
166B GLU* 1.3 59.4 + - + +
167B GLU 3.1 0.9 - - - -
168B ASN* 3.3 13.3 + - - +
169B ILE 4.0 7.9 - - - +
171B ILE* 3.3 17.2 - - + +
209B HIS* 3.2 29.8 + - - +
210B CYS 4.8 0.6 - - - -
211B ASP* 3.1 32.0 + - - +
155C THR* 5.6 4.0 - - + +
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Residues in contact with GLU 166 (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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162B ARG* 3.0 32.5 + - + +
163B MSE 3.8 13.1 - - - +
164B LEU 3.2 0.2 - - - -
165B GLN* 1.3 77.2 - - + +
167B GLU* 1.3 68.7 + - - +
168B ASN 3.2 3.9 + - - -
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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