Contacts of the helix formed by residues 156 - 167 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166C GLU* 3.1 34.3 + - - +
167C GLU* 4.6 7.1 + - - +
168C ASN* 4.4 10.4 - - - +
82D GLU* 4.1 2.8 + - - -
154D VAL* 3.7 3.9 - - - +
155D THR* 1.3 84.6 + - - +
157D LEU* 1.3 59.3 + - - +
158D ALA* 3.2 11.0 + - - +
159D ARG* 2.8 66.9 + - + +
160D THR* 2.9 12.8 + - - -
162D ARG* 5.0 2.1 + - - -
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Residues in contact with LEU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C ASN* 4.8 3.8 + - - -
99D ILE* 3.7 26.0 - - + -
101D ASP* 3.6 29.8 - - + +
125D ILE* 4.4 16.6 - - + -
127D PRO* 4.0 16.6 - - + +
154D VAL* 3.6 12.4 - - + +
155D THR 4.0 1.4 + - - -
156D ASN* 1.3 71.0 - - - +
158D ALA* 1.3 57.6 + - - +
160D THR* 3.2 2.7 + - - -
161D MSE 2.8 50.3 + - + +
203D ARG* 3.5 30.7 - - - +
206D THR* 3.6 12.1 - - + +
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Residues in contact with ALA 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C GLU* 5.3 0.2 - - + -
156D ASN* 3.2 8.8 + - - +
157D LEU* 1.3 78.2 - - - +
159D ARG* 1.3 62.5 + - - +
161D MSE 3.3 10.6 + - - +
162D ARG* 3.0 46.7 + - - +
205D LEU* 3.9 31.2 - - + +
206D THR* 5.5 1.9 + - - +
209D HIS* 3.6 13.4 - - + +
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Residues in contact with ARG 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D GLU* 4.1 19.1 + - - -
155D THR* 4.6 14.6 - - - +
156D ASN* 2.8 49.3 + - + +
158D ALA* 1.3 76.2 - - - +
160D THR* 1.3 65.9 + - - +
162D ARG* 2.9 36.6 + - + +
163D MSE 3.1 10.9 + - - +
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Residues in contact with THR 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D GLU* 3.7 6.5 + - + +
85D LEU* 3.7 20.2 - - + -
99D ILE* 6.0 0.4 - - + -
125D ILE* 4.5 14.1 - - + -
154D VAL* 2.9 37.4 - - + +
156D ASN 2.9 5.1 + - - -
157D LEU* 3.6 9.9 - - + -
159D ARG* 1.3 75.5 - - - +
161D MSE 1.3 59.5 + - + +
163D MSE 3.0 31.0 + - + +
164D LEU* 2.8 28.5 + - + +
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Residues in contact with MSE 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D ILE* 4.2 13.0 - - + -
157D LEU* 2.8 39.4 + - + +
158D ALA* 3.6 5.8 - - - +
160D THR* 1.3 74.5 - - - +
162D ARG* 1.3 65.6 + - - +
164D LEU* 3.0 9.9 + - - +
165D GLN* 2.9 28.7 + - - +
171D ILE* 3.4 41.0 - - + +
194D VAL* 4.0 11.9 - - + -
206D THR* 3.8 43.5 - - + +
209D HIS* 4.1 18.4 - - + +
210D CYS* 4.2 1.8 - - - -
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Residues in contact with ARG 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C GLU* 4.5 24.9 + - - +
156D ASN* 5.0 2.0 + - - -
158D ALA* 3.0 31.6 + - - +
159D ARG* 2.9 30.9 + - + +
161D MSE 1.3 74.0 - - - +
163D MSE 1.3 58.6 + - - +
165D GLN* 2.9 30.9 + - - +
166D GLU* 3.0 25.8 + - - +
209D HIS* 2.7 51.1 + - + -
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Residues in contact with MSE 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D LEU* 3.9 21.8 - - + -
86D PRO* 3.8 28.3 - - + -
89D ILE* 4.0 8.3 - - + -
159D ARG 3.1 4.8 + - - +
160D THR* 3.0 37.2 + - + +
162D ARG* 1.3 79.8 - - - +
164D LEU* 1.3 84.9 + - + +
166D GLU* 3.1 12.5 + - + +
167D GLU* 3.0 36.6 + - + +
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Residues in contact with LEU 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D ILE* 3.2 31.4 - - + -
97D LEU* 3.6 18.2 - - + -
99D ILE* 3.7 30.1 - - + -
125D ILE* 4.4 10.5 - - + -
160D THR* 2.8 22.1 + - + +
161D MSE 3.0 11.8 + - - +
163D MSE 1.3 86.0 - - + +
165D GLN* 1.3 62.7 + - - +
167D GLU* 3.1 12.4 + - - +
168D ASN 3.5 0.2 + - - -
169D ILE* 3.2 28.8 + - + +
171D ILE* 4.2 9.9 - - + -
192D ALA* 4.2 15.5 - - + -
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Residues in contact with GLN 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ASP* 4.4 2.1 - - - +
155A THR* 3.1 21.2 - - + +
156A ASN* 5.2 15.5 - - + +
161D MSE 2.9 16.2 + - - +
162D ARG* 2.9 19.6 + - - +
164D LEU* 1.3 76.2 - - - +
166D GLU* 1.3 65.4 + - - +
168D ASN* 3.0 13.5 + - - -
169D ILE 4.3 7.1 + - - +
171D ILE* 3.8 10.8 - - + -
209D HIS* 2.8 40.4 + - - +
210D CYS 4.7 0.4 - - - -
211D ASP* 3.4 27.6 + - - +
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Residues in contact with GLU 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A THR* 3.9 16.5 + - + +
159A ARG* 2.7 38.1 + - - +
162D ARG* 3.0 27.2 + - - +
163D MSE 3.1 14.1 + - + +
165D GLN* 1.3 76.5 - - - +
167D GLU* 1.3 66.9 + - - +
168D ASN* 3.1 14.3 + - - +
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Residues in contact with GLU 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D PRO* 4.9 15.3 - - + +
89D ILE* 4.2 26.9 - - + +
90D ALA* 5.5 3.6 + - - +
163D MSE 3.0 32.4 + - - +
164D LEU 3.6 8.7 - - - +
165D GLN 3.1 1.0 - - - -
166D GLU* 1.3 85.8 - - - +
168D ASN* 1.3 63.1 + - - +
169D ILE* 3.5 5.9 + - + +
190D ARG* 2.5 35.7 + - - +
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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