Contacts of the strand formed by residues 150 - 160 (chain H) in PDB entry 1GC1
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 150 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146H THR* 2.7 17.8 + - - -
147H SER 4.6 3.8 + - - +
148H GLY* 5.1 1.4 - - - -
149H GLY* 1.3 80.3 + - - +
151H ALA* 1.3 64.8 + - - +
198H THR* 3.9 14.4 - - - +
199H VAL* 3.3 33.7 - - - +
200H PRO* 3.8 7.3 - - + +
118L PHE* 4.0 12.7 - - - -
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Residues in contact with ALA 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141H PRO* 4.9 5.2 - - + -
143H SER 4.6 4.5 - - - +
144H LYS 4.1 9.6 - - - +
146H THR* 3.4 12.5 + - - -
150H THR* 1.3 77.2 - - - +
152H ALA* 1.3 60.4 + - - +
153H LEU* 5.1 0.2 - - + -
198H THR* 3.2 5.4 - - - -
199H VAL* 2.5 36.1 + - + +
201H SER* 3.7 7.6 + - - -
204H LEU* 3.4 37.9 - - + -
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Residues in contact with ALA 152 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141H PRO* 3.7 10.5 - - - +
142H SER* 4.0 6.5 + - - +
146H THR* 4.8 0.6 - - - +
151H ALA* 1.3 77.8 - - - +
153H LEU* 1.3 63.9 + - - +
196H VAL* 5.8 0.2 - - + -
197H VAL 3.5 7.0 - - - +
198H THR* 3.7 20.6 - - + -
118L PHE* 4.1 28.0 - - + -
120L PHE* 3.4 26.9 - - + -
137L LEU* 4.7 6.5 - - + -
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Residues in contact with LEU 153 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139H LEU* 3.2 17.5 - - - +
141H PRO* 3.9 12.6 - - + -
152H ALA* 1.3 78.8 - - - +
154H GLY* 1.3 61.8 + - - +
169H TRP* 4.0 6.7 - - + -
196H VAL* 3.2 8.2 - - - +
197H VAL* 2.8 49.0 + - + +
199H VAL* 3.4 33.2 - - + -
204H LEU* 4.2 13.0 - - + -
209H TYR* 4.2 15.0 - - + -
226H VAL* 3.7 32.8 - - + +
120L PHE* 4.3 2.5 - - - -
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Residues in contact with GLY 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138H PRO* 3.2 6.1 - - - +
139H LEU* 2.7 39.6 + - - +
153H LEU* 1.3 81.0 - - - +
155H CYS* 1.3 62.5 + - - -
169H TRP* 3.3 14.1 - - - -
195H SER 3.0 13.5 - - - -
196H VAL* 4.0 1.3 - - - -
226H VAL* 3.5 6.2 - - - +
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Residues in contact with CYS 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136H VAL* 4.0 11.7 - - + -
137H PHE 3.1 9.2 - - - +
138H PRO* 4.2 3.8 - - - -
139H LEU* 4.0 7.4 - - - +
154H GLY* 1.3 82.4 - - - -
156H LEU* 1.3 60.0 + - - +
157H VAL* 3.7 9.5 + - + +
167H VAL* 5.4 0.2 - - + -
169H TRP* 4.0 2.7 - - - -
193H LEU 3.8 0.2 - - - +
194H SER* 3.2 6.4 - - - -
195H SER* 2.8 37.4 + - - +
211H CYS* 2.0 53.2 - - + -
224H LYS* 4.2 10.8 - - - -
226H VAL* 4.6 1.1 - - - -
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Residues in contact with LEU 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135H SER 3.0 5.7 - - - +
136H VAL* 3.5 0.9 - - - -
137H PHE* 2.6 47.1 + - + +
139H LEU* 4.2 13.9 - - + +
155H CYS* 1.3 70.3 - - - +
157H VAL* 1.3 58.9 + - - +
158H LYS* 3.6 16.2 - - + -
192H SER* 4.1 15.7 - - - +
193H LEU 3.8 3.6 - - - +
194H SER* 3.5 19.1 - - - +
126L GLN* 3.2 31.4 - - - +
133L SER* 3.9 17.7 - - - +
135L VAL* 4.4 14.6 - - + -
180L THR* 4.5 12.3 - - + +
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Residues in contact with VAL 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134H PRO* 3.5 20.2 - - + -
135H SER 3.6 3.6 - - - -
136H VAL* 4.4 3.4 - - + +
155H CYS* 4.2 13.5 - - + +
156H LEU* 1.3 72.8 - - - +
158H LYS* 1.3 59.4 + - - +
160H TYR* 3.4 7.1 - - + -
165H VAL* 4.3 7.0 - - + -
167H VAL* 4.1 15.0 - - + -
192H SER* 3.4 3.3 - - - -
193H LEU* 2.8 48.3 + - + +
195H SER 5.5 1.8 - - - +
213H VAL* 3.5 44.6 - - + -
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Residues in contact with LYS 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134H PRO* 3.4 1.4 - - - +
135H SER* 2.8 38.1 + - - -
137H PHE* 4.4 15.0 - - + -
156H LEU* 3.6 12.1 - - + -
157H VAL* 1.3 73.8 - - - +
159H ASP* 1.3 93.9 + - + +
160H TYR* 3.4 2.7 - - - -
186H GLN* 2.9 26.1 + - - -
191H TYR 3.8 0.2 - - - -
192H SER* 2.9 26.2 - - - +
126L GLN* 3.4 26.0 - - - +
131L THR* 5.1 9.0 - - + +
133L SER* 4.0 15.0 + - - -
180L THR* 6.2 2.0 - - - -
182L THR* 4.9 9.3 - - - +
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Residues in contact with ASP 159 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H LYS* 2.6 43.7 + - - +
133H GLY 3.7 0.2 - - - +
134H PRO* 4.4 0.2 - - - -
135H SER* 4.8 6.9 + - - +
158H LYS* 1.3 100.3 + - + +
160H TYR* 1.3 56.9 + - - +
186H GLN* 2.8 23.4 + - - -
188H SER* 4.8 0.7 + - - -
190H LEU* 3.9 26.5 - - + +
191H TYR 3.0 10.3 + - - -
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Residues in contact with TYR 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H LYS 3.4 13.9 - - - +
134H PRO* 3.4 31.9 - - + -
157H VAL* 3.4 27.6 - - + -
158H LYS 4.3 0.2 - - - -
159H ASP* 1.3 77.6 - - - +
161H PHE* 1.3 60.7 + - - +
162H PRO 3.4 19.3 - - - -
163H GLN* 2.6 47.7 + - - -
165H VAL* 3.8 11.0 - - + +
183H ALA* 3.3 7.8 - - - +
190H LEU* 3.6 3.7 - - - -
191H TYR* 2.8 48.9 + - + -
193H LEU* 3.1 25.5 - - + +
215H HIS* 3.8 7.9 - + + -
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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