Contacts of the helix formed by residues 156 - 167 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170B TRP* 5.4 0.6 - - - -
210B CYS 4.8 3.4 + - - -
211B ASP* 3.2 40.5 + - - +
82C GLU* 4.7 1.4 + - - +
154C VAL* 3.0 14.8 - - - +
155C THR* 1.3 83.0 + - + +
157C LEU* 1.3 67.1 + - - +
158C ALA* 3.3 23.4 - - - +
159C ARG* 3.8 21.1 + - + +
160C THR 3.3 12.5 + - - -
162C ARG* 4.9 4.0 + - - -
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Residues in contact with LEU 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C ILE* 4.0 20.9 - - + -
101C ASP* 3.0 42.8 - - + +
125C ILE* 4.5 10.8 - - + -
126C VAL 4.4 5.4 - - - +
127C PRO* 4.1 29.5 - - + +
130C ARG* 4.1 11.0 - - - +
154C VAL* 4.1 4.5 - - + +
155C THR 4.1 2.0 + - - -
156C ASN* 1.3 73.1 - - - +
158C ALA* 1.3 57.6 + - - +
160C THR* 3.3 5.4 + - + -
161C MSE 2.9 46.3 + - + +
206C THR* 3.6 20.6 - - + +
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Residues in contact with ALA 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C ASN* 3.3 12.5 + - - +
157C LEU* 1.3 76.7 - - - +
159C ARG* 1.3 64.5 + - - +
161C MSE 3.2 12.2 + - - +
162C ARG* 3.0 47.7 + - - +
205C LEU* 4.7 11.0 - - + +
206C THR* 6.0 1.0 - - - +
209C HIS* 3.8 21.9 - - + +
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Residues in contact with ARG 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C GLU* 2.9 30.5 + - - +
155C THR* 4.6 10.9 + - - +
156C ASN* 3.4 25.5 + - + +
158C ALA* 1.3 79.6 - - - +
160C THR* 1.3 63.1 + - - +
162C ARG* 3.5 25.9 + - - +
163C MSE 3.2 20.9 + - + +
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Residues in contact with THR 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C GLU* 3.7 10.6 + - - +
85C LEU* 3.8 28.4 - - + +
99C ILE* 6.1 0.2 - - + -
125C ILE* 4.4 11.4 - - + -
154C VAL* 2.9 39.9 - - + +
156C ASN 3.3 1.4 + - - -
157C LEU* 3.3 6.8 + - + +
158C ALA 3.2 0.4 - - - -
159C ARG* 1.3 78.6 + - - +
161C MSE 1.3 67.7 + - + +
163C MSE 3.2 14.3 + - + +
164C LEU* 3.0 35.9 + - + +
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Residues in contact with MSE 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ILE* 4.1 19.5 - - + -
157C LEU* 2.9 39.4 + - + +
158C ALA* 3.2 8.3 + - - +
160C THR* 1.3 77.5 - - + +
162C ARG* 1.3 60.9 + - - +
164C LEU* 3.1 7.8 + - + +
165C GLN* 3.0 30.1 + - - +
171C ILE* 3.5 36.0 - - + +
194C VAL* 4.4 4.9 - - + -
206C THR* 3.5 42.4 - - + +
209C HIS* 3.7 28.0 - - + +
210C CYS* 4.0 5.4 - - - +
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Residues in contact with ARG 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C ASN* 4.9 3.2 + - - -
158C ALA* 3.0 25.6 + - - +
159C ARG* 3.5 31.2 - - - +
161C MSE 1.3 75.4 - - - +
163C MSE 1.3 57.9 + - - +
165C GLN* 3.2 11.2 + - - +
166C GLU* 2.8 38.5 + - - +
209C HIS* 3.1 31.3 + - + -
204D ARG* 3.7 20.8 - - - +
205D LEU* 4.6 3.3 - - + +
208D GLU* 6.0 0.2 - - - -
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Residues in contact with MSE 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C GLU 5.9 0.2 - - - +
85C LEU* 3.6 31.9 - - + -
86C PRO* 4.3 22.9 - - + -
89C ILE* 4.1 10.1 - - + -
159C ARG* 3.2 10.6 + - - +
160C THR* 3.2 19.8 + - + +
162C ARG* 1.3 81.0 - - - +
164C LEU* 1.3 88.3 + - + +
166C GLU* 3.4 15.5 + - - +
167C GLU* 3.2 29.2 + - + +
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Residues in contact with LEU 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C LEU* 4.5 7.2 - - + -
89C ILE* 3.3 32.1 - - + -
97C LEU* 4.2 19.7 - - + -
99C ILE* 4.0 28.0 - - + -
125C ILE* 4.5 3.6 - - + -
160C THR* 3.0 23.9 + - + +
161C MSE 3.1 11.6 + - - +
163C MSE 1.3 93.4 - - + +
165C GLN* 1.3 54.6 + - - +
167C GLU* 2.8 29.2 + - - +
169C ILE* 3.2 23.5 + - + +
171C ILE* 4.2 10.5 - - + -
192C ALA* 4.5 4.3 - - + -
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Residues in contact with GLN 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C MSE 3.0 16.0 + - - +
162C ARG* 3.6 7.2 - - - +
164C LEU* 1.3 71.1 - - - +
166C GLU* 1.3 58.9 + - - +
167C GLU 2.8 4.7 - - - -
168C ASN* 2.8 23.7 + - - +
169C ILE 3.8 11.2 - - - +
171C ILE* 3.4 19.3 - - + +
209C HIS* 2.8 25.4 + - - +
210C CYS 4.2 0.4 - - - -
211C ASP* 3.1 35.0 + - - +
203D ARG* 5.6 6.0 + - + +
204D ARG* 3.1 33.7 + - - +
205D LEU* 3.9 22.2 - - + +
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Residues in contact with GLU 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C ARG* 2.8 22.0 + - - +
163C MSE 3.5 14.1 - - - +
164C LEU 3.2 0.2 - - - -
165C GLN* 1.3 75.8 - - - +
167C GLU* 1.3 65.3 + - - +
168C ASN* 3.3 2.6 + - - +
156D ASN* 3.1 34.6 + - - +
162D ARG* 4.5 27.0 + - - +
205D LEU* 3.6 23.3 - - + +
209D HIS* 5.8 0.2 - - - -
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Residues in contact with GLU 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C PRO* 6.4 0.9 - - + -
89C ILE* 4.6 21.8 - - + +
163C MSE 3.2 26.6 + - + +
164C LEU* 2.8 14.5 + - - +
166C GLU* 1.3 89.1 - - - +
168C ASN* 1.3 68.1 + - - +
169C ILE* 3.3 2.2 + - + +
190C ARG* 3.1 22.1 + - - +
156D ASN* 4.6 6.8 + - - +
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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