Contacts of the strand formed by residues 170 - 176 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145J VAL* 3.2 5.4 - - - -
146J TYR* 2.9 36.8 + - + +
148J PRO* 5.1 0.4 - - + -
168J ASP 3.0 23.2 + - - -
169J ALA* 1.3 81.3 + - - +
171J VAL* 1.3 62.9 + - - +
172J LEU* 3.4 4.1 + - + +
213J ALA* 4.3 16.2 - - + -
217J GLN 3.8 10.3 - - - +
218J ILE* 3.4 7.4 - - - +
219J ALA* 2.7 38.0 + - + +
168K ASP* 3.2 34.0 + - - +
170K GLN* 3.4 0.2 - - - +
218K ILE* 3.2 26.5 - - + +
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Residues in contact with VAL 171 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89J LEU* 4.4 5.8 - - + -
92J ILE* 3.8 27.8 - - + +
143J ILE* 4.2 25.4 - - + -
144J LEU 3.7 6.1 - - - +
145J VAL* 4.2 3.4 - - + -
165J HIS* 5.0 1.1 - - - +
169J ALA 5.2 1.3 - - - +
170J GLN* 1.3 70.4 - - - +
172J LEU* 1.3 62.2 + - - +
173J LEU 4.1 18.6 - - - +
174J ALA* 4.2 15.3 - - + -
209J ARG* 3.8 12.1 - - - -
219J ALA* 4.1 11.6 - - - +
167K ALA* 4.2 22.4 - - + -
168K ASP* 2.9 19.5 + - - +
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Residues in contact with LEU 172 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92J ILE* 4.9 0.2 - - - -
96J ASN* 3.3 18.4 + - - -
111J ILE* 4.5 2.9 - - + -
144J LEU* 2.8 23.4 + - + +
145J VAL 4.3 0.7 - - - -
146J TYR* 4.2 8.1 - - + +
153J LEU* 3.7 30.3 - - + -
170J GLN 3.7 15.0 - - - +
171J VAL* 1.3 77.2 - - - +
173J LEU* 1.3 62.1 + - - +
206J VAL* 3.7 22.6 - - + +
209J ARG* 3.4 47.9 - - + +
210J LEU* 3.6 20.9 - - + +
213J ALA* 4.4 9.6 - - + -
219J ALA* 4.4 3.1 - - + -
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Residues in contact with LEU 173 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96J ASN* 3.1 26.0 - - + +
125J PHE* 4.7 7.9 - - + -
129J PHE* 4.2 14.9 - - + -
143J ILE* 3.2 6.1 - - - +
144J LEU* 2.8 40.4 + - + +
171J VAL* 3.7 2.4 - - - +
172J LEU* 1.3 80.9 - - - +
174J ALA* 1.3 60.9 + - - +
197J TRP* 3.5 42.4 - - + -
198J TRP* 4.8 1.3 - - + -
201J VAL* 4.2 10.3 - - + -
203J TRP* 4.1 26.5 - - + -
206J VAL* 3.9 18.2 - - + -
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Residues in contact with ALA 174 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89J LEU* 4.7 11.4 - - + +
92J ILE* 4.8 2.7 - - + -
93J PHE* 3.1 21.9 - - - +
96J ASN* 2.8 16.9 + - - +
141J TRP* 3.9 18.6 - - + -
142J ALA 3.6 4.3 - - - -
143J ILE* 3.8 16.4 - - + -
171J VAL* 4.2 10.8 - - + -
173J LEU* 1.3 76.8 - - - +
175J LEU* 1.3 59.9 + - - +
197J TRP* 3.9 10.5 - - - -
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Residues in contact with LEU 175 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93J PHE* 4.0 1.6 - - + -
129J PHE* 3.8 20.1 - - + -
133J ALA* 3.8 24.0 - - + -
141J TRP* 3.2 8.8 - - - -
142J ALA* 2.9 30.3 + - + +
174J ALA* 1.3 73.6 - - - +
176J ASP* 1.3 65.3 + - - +
177J VAL* 3.6 5.5 + - + +
193J TYR* 3.3 29.8 - - + +
194J VAL* 4.0 24.0 - - + -
197J TRP* 3.5 48.9 - - + +
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Residues in contact with ASP 176 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42J HIS* 3.0 29.5 + - + -
90J HIS* 3.2 17.0 + - - -
93J PHE* 3.6 18.4 - - + -
141J TRP* 3.4 29.7 - - + -
175J LEU* 1.3 73.2 - - - +
177J VAL* 1.3 60.3 + - - +
178J TRP* 2.8 31.9 + - - +
180J HIS* 4.2 1.9 + - - -
181J ALA* 3.5 8.7 - - + +
193J TYR* 2.8 31.0 + - - -
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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