Contacts of the strand formed by residues 170 - 176 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A VAL* 3.1 6.9 - - - -
146A TYR 3.0 28.4 + - - +
148A PRO* 5.0 1.8 - - + -
168A ASP 2.9 25.0 + - - +
169A ALA* 1.3 79.0 + - - +
171A VAL* 1.3 62.8 + - - +
172A LEU* 3.4 3.7 + - + +
213A ALA* 4.3 19.3 - - + -
217A GLN 3.7 18.4 - - - +
218A ILE* 3.2 19.3 - - - +
219A ALA* 2.9 30.8 + - + +
168D ASP* 3.1 34.4 + - - -
170D GLN* 3.1 7.5 - - - +
218D ILE* 4.6 8.4 - - + +
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Residues in contact with VAL 171 (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 LEU* 4.3 6.1 - - + -
92A ILE* 3.6 30.0 - - + +
143A ILE* 4.2 18.4 - - + -
144A LEU 3.7 4.0 - - - -
145A VAL* 4.1 11.9 - - + -
165A HIS* 4.9 1.3 - - - +
169A ALA 4.9 2.5 - - - +
170A GLN* 1.3 71.3 - - - +
172A LEU* 1.3 63.3 + - - +
173A LEU 4.0 18.4 - - - +
174A ALA* 4.1 16.2 - - + -
209A ARG* 3.7 14.2 - - - -
219A ALA 4.5 5.7 - - - +
167D ALA* 4.2 21.1 - - + -
168D ASP* 2.9 16.1 + - - +
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Residues in contact with LEU 172 (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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92A ILE* 4.9 0.4 - - - -
96A ASN* 3.2 16.4 + - - -
111A ILE* 4.8 3.1 - - + -
144A LEU* 2.8 24.4 + - + +
146A TYR* 4.1 7.2 - - + +
153A LEU* 3.7 29.8 - - + -
170A GLN* 3.6 19.1 - - + +
171A VAL* 1.3 76.3 - - - +
173A LEU* 1.3 62.0 + - - +
206A VAL* 3.6 22.7 - - + +
209A ARG* 3.5 24.9 - - + +
210A LEU* 4.0 40.4 - - + +
213A ALA* 4.2 12.6 - - + -
219A ALA* 5.0 0.2 - - + -
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Residues in contact with LEU 173 (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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96A ASN* 3.1 38.6 - - - +
125A PHE* 4.4 15.0 - - + -
129A PHE* 3.9 6.5 - - + -
143A ILE* 3.1 5.7 - - - +
144A LEU* 2.8 41.2 + - + +
171A VAL* 3.6 3.3 - - - -
172A LEU* 1.3 80.8 - - - +
174A ALA* 1.3 59.4 + - - +
197A TRP* 3.8 33.2 - - + -
198A TRP* 4.6 1.6 - - + -
201A VAL* 3.8 20.2 - - + -
203A TRP* 3.9 33.0 - - + -
206A VAL* 3.8 9.4 - - + -
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Residues in contact with ALA 174 (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 LEU* 4.5 7.0 - - + +
92A ILE* 4.6 7.2 - - + -
93A PHE* 3.2 21.0 - - + +
96A ASN* 2.6 16.8 + - - +
129A PHE* 4.5 0.4 - - - -
141A TRP* 3.8 19.5 - - + -
142A ALA 3.4 4.5 - - - -
143A ILE* 3.5 18.4 - - + -
171A VAL* 4.1 10.3 - - + -
173A LEU* 1.3 74.9 - - - +
175A LEU* 1.3 60.0 + - - +
176A ASP 4.1 0.4 - - - -
197A TRP* 3.8 10.0 - - - -
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Residues in contact with LEU 175 (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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93A PHE* 4.1 0.9 - - + -
129A PHE* 3.5 20.6 - - + -
133A ALA* 3.8 22.0 - - + -
141A TRP* 3.1 8.2 - - - -
142A ALA* 2.7 34.7 + - + +
174A ALA* 1.3 73.6 - - - +
176A ASP* 1.3 67.4 + - - +
177A VAL* 3.5 9.0 + - + +
193A TYR* 3.6 24.2 - - + +
194A VAL* 3.9 24.0 - - + -
197A TRP* 3.6 49.4 - - + +
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Residues in contact with ASP 176 (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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42A HIS* 2.8 30.7 + - - -
90A HIS* 3.2 8.8 + - - -
93A PHE* 3.5 19.3 - - + -
140A GLY 3.6 0.2 - - - +
141A TRP* 3.5 32.5 - - + -
175A LEU* 1.3 74.8 - - - +
177A VAL* 1.3 59.1 + - - +
178A TRP* 2.9 32.6 + - - +
180A HIS* 4.0 3.1 + - - -
181A ALA* 3.4 12.1 - - + +
193A TYR* 2.8 31.4 + - - -
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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