Contacts of the strand formed by residues 217 - 225 (chain N) in PDB entry 2GTL
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 GLN 217 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118N HIS* 3.6 20.6 + - + +
119N GLY* 4.6 2.1 - - - -
208N HIS* 3.4 49.3 + - + -
209N ARG 3.7 0.2 - - - -
210N VAL* 3.7 12.3 - - + -
215N LEU 4.0 9.2 - - - +
216N HIS* 1.3 90.7 + - - +
218N CYS* 1.3 62.9 + - - +
219N ALA 3.5 0.4 - - - +
220N ASP* 4.6 3.8 + - - -
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Residues in contact with CYS 218 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117N TRP* 3.4 21.7 - - + -
118N HIS* 3.1 7.0 + - - -
119N GLY* 2.8 25.7 + - - -
120N CYS* 2.0 50.0 - - - +
191N LEU* 3.8 23.1 - - - -
209N ARG* 2.8 13.5 + - + +
211N THR* 4.3 6.1 - - - -
216N HIS* 3.4 9.8 + - - -
217N GLN* 1.3 72.4 - - - +
219N ALA* 1.3 62.9 + - - +
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Residues in contact with ALA 219 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115N SER* 4.0 7.6 - - - +
116N THR 3.2 14.6 - - - +
117N TRP* 3.4 30.5 - - + -
118N HIS* 3.4 9.7 - - - -
208N HIS* 3.0 31.6 + - - +
209N ARG* 3.1 11.3 + - + -
217N GLN 3.5 0.2 - - - -
218N CYS* 1.3 82.9 - - - +
220N ASP* 1.3 65.7 - - - +
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Residues in contact with ASP 220 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114N THR 3.6 1.6 - - - +
115N SER* 3.4 2.3 - - - -
116N THR* 3.0 45.5 + - - +
118N HIS* 3.1 25.0 + - - -
208N HIS* 3.6 26.5 + - + +
217N GLN* 4.6 1.7 + - - -
219N ALA* 1.3 73.4 - - - +
221N LEU* 1.3 60.9 + - - +
222N PHE* 4.3 19.3 - - + -
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Residues in contact with LEU 221 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113N GLY* 3.8 15.5 - - - +
114N THR 3.5 15.9 - - - +
115N SER* 3.9 15.0 - - - +
128N THR* 3.6 31.6 - - + +
130N ILE* 4.5 7.6 - - + -
193N VAL* 4.7 5.8 - - + -
207N CYS* 2.6 60.0 + - + +
208N HIS* 4.7 3.1 - - - +
209N ARG* 5.1 7.4 - - + -
219N ALA 5.2 0.4 - - - +
220N ASP* 1.3 76.0 - - - +
222N PHE* 1.3 68.1 + - - +
223N VAL* 3.3 28.3 - - + -
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Residues in contact with PHE 222 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113N GLY* 3.6 16.3 - - - -
114N THR 3.8 5.9 + - - -
199N ARG* 4.3 31.0 - - - +
205N ALA 3.7 4.5 - - - +
206N GLU* 3.9 38.8 - - + -
207N CYS 5.4 0.2 - - - -
208N HIS* 5.6 1.1 - + - -
220N ASP* 4.3 26.5 - - + -
221N LEU* 1.3 82.0 - - - +
223N VAL* 1.3 61.2 + - - +
224N THR* 4.6 0.5 + - - -
72O ASP 3.9 11.6 - - - +
73O ASP* 3.8 8.8 - - - +
74O PRO* 3.8 39.5 - - + -
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Residues in contact with VAL 223 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111N PHE* 3.7 32.1 - - + +
112N SER 2.9 14.4 - - - +
128N THR 5.4 0.7 - - - +
130N ILE* 4.6 6.1 - - + -
195N CYS* 4.6 2.0 - - - -
197N PHE* 5.5 0.2 - - + -
199N ARG* 5.9 0.2 + - - -
204N ARG* 3.6 5.0 - - - +
205N ALA* 3.1 46.6 + - + +
207N CYS* 3.7 23.1 - - - -
221N LEU* 3.3 30.5 - - + -
222N PHE* 1.3 73.3 - - - +
224N THR* 1.3 67.4 + - - +
72O ASP 4.9 1.0 - - - +
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Residues in contact with THR 224 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111N PHE* 3.5 4.6 - - - -
112N SER* 2.9 31.3 + - - +
203N GLU* 3.6 8.1 - - + +
204N ARG* 4.1 19.0 - - + +
222N PHE 4.6 0.7 + - - -
223N VAL* 1.3 78.9 + - - +
225N LEU* 1.3 75.0 + - - +
226N GLU* 3.3 2.1 + - - +
72O ASP* 3.7 32.2 + - + +
73O ASP* 5.7 0.5 - - - +
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Residues in contact with LEU 225 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109N ASN* 3.6 27.1 - - + +
110N VAL 3.1 36.1 - - - +
111N PHE* 3.7 14.3 - - + -
202N ASN 4.5 11.0 - - - +
203N GLU* 2.8 39.0 + - + +
224N THR* 1.3 81.2 - - - +
226N GLU* 1.3 73.2 + - - +
227N GLU* 3.7 1.7 + - - -
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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