Contacts of the strand formed by residues 170 - 176 (chain N) in PDB entry 1P7G
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 170 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145N VAL* 3.1 4.6 - - - -
146N TYR* 2.8 37.8 + - + +
168N ASP 2.9 23.8 + - - +
169N ALA* 1.3 77.8 + - - +
171N VAL* 1.3 63.6 - - - +
172N LEU* 3.5 3.4 + - + +
213N ALA* 4.1 15.3 - - + -
217N GLN 4.1 6.7 - - - +
218N ILE* 3.3 12.2 - - - +
219N ALA* 2.7 37.7 + - + +
168O ASP* 3.4 22.8 + - - +
170O GLN* 3.3 15.8 - - - +
218O ILE* 3.7 25.4 - - + +
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Residues in contact with VAL 171 (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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89N LEU* 4.4 11.9 - - + -
92N ILE* 3.9 33.6 - - + +
143N ILE* 4.2 14.6 - - + -
144N LEU 3.9 4.9 - - - +
145N VAL* 4.1 13.2 - - + -
165N HIS* 5.1 0.7 - - - +
169N ALA 4.8 2.5 - - - +
170N GLN* 1.3 72.2 - - - +
172N LEU* 1.3 65.4 + - - +
173N LEU 4.3 14.1 - - - +
174N ALA* 4.4 4.5 - - + -
209N ARG* 3.8 13.5 - - - -
219N ALA* 3.9 8.8 - - - +
167O ALA* 4.2 20.6 - - + -
168O ASP* 2.9 22.2 + - - +
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Residues in contact with LEU 172 (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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92N ILE* 5.1 0.2 - - - -
96N ASN* 3.3 19.4 + - - -
111N ILE* 4.5 5.2 - - + -
144N LEU* 2.7 24.6 + - + +
145N VAL 4.2 1.3 - - - -
146N TYR* 4.0 13.2 - - + +
153N LEU* 3.2 35.0 - - + -
170N GLN* 3.6 18.2 - - + +
171N VAL* 1.3 78.8 - - - +
173N LEU* 1.3 59.5 + - - +
206N VAL* 3.9 21.4 - - + +
209N ARG* 3.4 20.8 - - + +
210N LEU* 3.8 41.5 - - + +
213N ALA* 4.6 0.4 - - + -
219N ALA* 4.6 2.7 - - + -
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Residues in contact with LEU 173 (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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96N ASN* 3.3 14.8 - - + +
125N PHE* 4.2 16.4 - - + -
129N PHE* 4.2 7.9 - - + -
142N ALA 4.1 0.3 - - - +
143N ILE* 3.2 6.8 - - - +
144N LEU* 2.8 37.7 + - + +
171N VAL* 4.3 2.0 - - - +
172N LEU* 1.3 78.8 - - - +
174N ALA* 1.3 64.5 + - - +
197N TRP* 3.7 36.1 - - + -
198N TRP* 4.4 2.5 - - + -
201N VAL* 3.8 16.6 - - + -
203N TRP* 3.7 31.9 - - + -
206N VAL* 3.8 16.8 - - + -
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Residues in contact with ALA 174 (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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89N LEU* 4.6 8.7 - - + +
92N ILE* 4.6 6.3 - - + -
93N PHE* 3.3 19.4 - - - -
96N ASN* 2.7 17.9 + - - +
129N PHE* 4.6 0.4 - - - -
141N TRP* 3.8 22.4 - - + -
142N ALA 3.7 4.0 - - - -
143N ILE* 4.0 10.1 - - + -
171N VAL* 4.4 10.3 - - + -
173N LEU* 1.3 77.3 - - - +
175N LEU* 1.3 60.9 + - - +
176N ASP 4.1 0.2 - - - -
197N TRP* 3.5 13.6 - - - -
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Residues in contact with LEU 175 (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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93N PHE* 4.2 0.9 - - + -
129N PHE* 3.5 22.7 - - + -
133N ALA* 3.6 26.0 - - + -
141N TRP* 3.2 9.3 - - - -
142N ALA* 2.9 31.1 + - + +
174N ALA* 1.3 73.1 - - - +
176N ASP* 1.3 65.5 + - - +
177N VAL* 3.5 9.4 + - + +
193N TYR* 3.6 24.9 - - + +
194N VAL* 3.8 20.0 - - + -
197N TRP* 3.7 45.3 - - + +
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Residues in contact with ASP 176 (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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42N HIS* 2.8 31.9 + - - -
90N HIS* 3.4 6.4 + - - -
93N PHE* 3.7 19.0 - - + -
140N GLY 3.6 0.5 - - - +
141N TRP* 3.4 33.7 - - + -
175N LEU* 1.3 73.7 - - - +
177N VAL* 1.3 59.5 + - - +
178N TRP* 2.9 31.3 + - - -
180N HIS* 4.3 3.5 + - - -
181N ALA* 3.5 10.4 - - + +
193N TYR* 2.7 31.7 + - - -
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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