Contacts of the helix formed by residues 156 - 167 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A GLU* 4.5 2.1 + - - +
154A VAL* 3.1 13.1 - - - +
155A THR* 1.3 86.2 + - + +
157A LEU* 1.3 69.5 + - - +
158A ALA* 3.9 13.5 - - - +
159A ARG* 3.4 34.7 + - + +
160A THR* 3.2 13.9 + - - -
162A ARG* 4.0 6.4 + - - -
203A ARG* 5.6 2.8 - - - +
205A LEU* 5.1 7.7 - - - +
165D GLN* 5.2 16.0 + - + +
211D ASP* 5.1 8.1 + - - -
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Residues in contact with LEU 157 (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* 3.9 24.2 - - + -
101A ASP* 3.5 29.8 - - + +
125A ILE* 4.4 14.1 - - + -
126A VAL 4.5 0.9 - - - -
127A PRO* 4.1 25.9 - - + +
154A VAL* 3.9 6.7 + - + +
155A THR 4.2 1.0 + - - -
156A ASN* 1.3 73.3 - - - +
158A ALA* 1.3 61.5 + - - +
160A THR* 3.1 4.7 + - - -
161A MSE 2.8 43.7 + - + +
203A ARG* 3.6 18.0 - - - +
206A THR* 3.2 30.7 - - + +
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Residues in contact with ALA 158 (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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156A ASN* 3.4 12.2 - - - +
157A LEU* 1.3 79.4 - - - +
159A ARG* 1.3 63.2 + - - +
161A MSE 3.3 7.9 + - - +
162A ARG* 3.0 35.5 + - - +
205A LEU* 4.2 22.0 - - + +
206A THR* 6.0 0.6 - - - +
209A HIS* 3.7 34.7 - - + +
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Residues in contact with ARG 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU* 2.9 34.8 + - - +
155A THR* 4.1 11.3 + - - -
156A ASN* 3.4 27.8 + - + +
157A LEU 3.2 0.4 - - - -
158A ALA* 1.3 78.9 - - - +
160A THR* 1.3 62.7 + - - +
162A ARG* 3.1 21.6 + - - +
163A MSE 3.0 20.6 + - + +
166D GLU* 2.7 33.8 + - - +
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Residues in contact with THR 160 (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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82A GLU* 3.5 9.2 + - - +
85A LEU* 3.9 26.4 - - + +
125A ILE* 4.3 19.1 - - + -
154A VAL* 3.1 32.0 - - + +
156A ASN 3.2 4.3 + - - -
157A LEU* 3.1 9.1 + - + +
159A ARG* 1.3 80.5 - - - +
161A MSE 1.3 57.9 + - + +
163A MSE 3.0 14.8 + - + +
164A LEU* 2.9 35.3 + - + +
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Residues in contact with MSE 161 (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* 4.4 16.2 - - + -
157A LEU* 2.8 39.4 + - + +
158A ALA* 3.7 6.3 - - - +
160A THR* 1.3 73.5 - - + +
162A ARG* 1.3 58.5 + - - +
164A LEU* 3.1 8.2 + - - +
165A GLN* 2.9 26.5 + - - +
171A ILE* 3.6 40.1 - - + +
194A VAL* 4.4 4.7 - - + -
206A THR* 3.3 46.4 - - + +
209A HIS* 3.7 32.1 - - + +
210A CYS* 4.0 4.5 - - - -
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Residues in contact with ARG 162 (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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156A ASN* 4.0 9.9 + - - -
158A ALA* 3.0 21.8 + - - +
159A ARG* 3.1 31.3 + - - +
161A MSE 1.3 75.3 - - - +
163A MSE 1.3 58.9 + - - +
165A GLN* 3.1 8.9 + - - +
166A GLU* 2.7 43.6 + - + +
209A HIS* 3.8 20.5 + - + -
204B ARG* 3.6 26.9 - - - +
205B LEU* 5.4 2.5 - - + -
208B GLU* 5.4 4.2 + - - -
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Residues in contact with MSE 163 (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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82A GLU 5.7 0.7 - - - +
85A LEU* 3.5 33.9 - - + -
86A PRO* 4.6 20.0 - - + -
89A ILE* 4.2 7.0 - - + -
159A ARG 3.0 12.1 + - - +
160A THR* 3.0 19.6 + - + +
162A ARG* 1.3 76.3 - - - +
164A LEU* 1.3 88.1 + - + +
166A GLU* 3.1 25.8 + - - +
167A GLU* 3.1 33.0 + - + +
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Residues in contact with LEU 164 (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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89A ILE* 3.3 32.1 - - + -
97A LEU* 4.0 18.4 - - + -
99A ILE* 3.8 28.7 - - + -
125A ILE* 4.3 16.4 - - + -
160A THR* 2.9 20.5 + - + +
161A MSE 3.1 12.3 + - - +
163A MSE 1.3 92.0 - - + +
165A GLN* 1.3 55.8 + - - +
167A GLU* 3.0 19.8 + - - +
169A ILE* 3.1 31.1 + - + +
171A ILE* 4.5 6.7 - - + -
192A ALA* 4.4 8.3 - - + -
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Residues in contact with GLN 165 (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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161A MSE 2.9 17.9 + - - +
162A ARG* 3.1 9.7 + - - +
164A LEU* 1.3 71.0 - - - +
166A GLU* 1.3 62.8 + - - +
167A GLU 2.8 5.8 + - - -
168A ASN* 3.1 14.6 + - - +
169A ILE 3.9 8.7 - - - +
171A ILE* 3.6 14.8 - - + +
209A HIS* 3.0 25.0 + - - +
211A ASP* 3.1 42.0 + - - +
156B ASN* 4.8 2.3 + - - -
203B ARG* 5.8 1.0 + - - -
204B ARG* 3.1 34.7 + - - +
205B LEU* 3.8 23.3 - - + +
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Residues in contact with GLU 166 (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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162A ARG* 2.7 32.7 + - - +
163A MSE 3.1 17.0 + - - +
165A GLN* 1.3 71.9 - - - +
167A GLU* 1.3 67.4 + - + +
168A ASN* 3.5 1.7 + - - +
156B ASN* 4.1 23.7 - - - +
158B ALA* 6.1 0.4 - - + -
162B ARG* 5.5 8.0 + - - +
205B LEU* 3.7 24.6 - - + +
209B HIS* 6.1 1.4 - - + -
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Residues in contact with GLU 167 (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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86A PRO* 5.5 9.4 - - + +
89A ILE* 4.8 11.6 - - + +
90A ALA* 6.1 1.6 - - - +
163A MSE 3.1 30.6 + - + +
164A LEU* 3.0 13.4 + - - +
165A GLN 2.8 1.0 - - - -
166A GLU* 1.3 88.2 - - + +
168A ASN* 1.3 62.0 + - - +
169A ILE* 3.2 7.4 + - + +
190A ARG* 2.6 37.9 + - - +
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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