Contacts of the strand formed by residues 166 - 173 (chain B) in PDB entry 1EFP
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 GLY 166 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A GLU 3.3 9.0 - - - -
183A ALA* 4.5 4.7 - - - -
238A ASP* 4.2 6.8 - - - -
162B GLU* 4.0 1.7 - - - +
163B VAL* 2.7 34.6 + - - +
164B ASP 3.3 2.2 + - - -
165B GLY* 1.3 79.5 - - - +
167B LEU* 1.3 72.5 + - - +
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ASP* 3.5 5.2 - - - +
181A GLU* 2.8 68.1 + - + +
148B SER* 5.1 4.7 - - - +
160B THR* 5.2 12.1 - - - +
161B ARG 3.3 9.0 - - - +
162B GLU* 3.6 35.7 - - - +
163B VAL* 4.1 2.1 - - - +
166B GLY* 1.3 83.5 - - - +
168B GLN* 1.3 62.4 + - - +
169B THR* 4.3 1.3 - - - +
183B ARG* 4.8 13.2 - - - +
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Residues in contact with GLN 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A HIS* 4.1 32.8 + - - +
69A LEU* 4.7 5.9 - - - +
94A ASP* 5.4 2.3 - - - +
177A TRP* 3.9 20.8 - - + -
179A ALA 3.7 4.9 - - - -
180A ASP* 3.6 10.0 - - - +
160B THR* 4.2 0.2 - - - -
161B ARG* 2.7 69.1 + - - +
163B VAL* 3.8 22.3 - - + +
167B LEU* 1.3 74.6 - - - +
169B THR* 1.3 59.8 + - - +
170B ILE* 3.8 17.6 + - + +
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Residues in contact with THR 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A TRP* 3.8 1.2 - - - -
178A VAL* 2.8 36.4 + - + -
179A ALA* 3.0 28.7 + - - +
151B GLU* 5.8 0.4 - - - +
158B LYS* 4.7 13.9 - - + -
159B VAL 3.6 9.0 - - - +
160B THR* 3.1 34.3 - - + +
167B LEU* 5.5 1.2 - - - +
168B GLN* 1.3 71.7 + - - +
170B ILE* 1.3 74.0 + - - +
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Residues in contact with ILE 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU* 4.1 12.3 - - + -
175A SER* 5.1 5.8 - - - -
176A SER 3.2 15.5 - - - +
177A TRP* 4.1 8.3 - - + -
178A VAL* 4.1 4.7 - - - +
143B GLN 3.9 20.6 - - - +
144B ALA* 4.6 2.0 - - - -
157B ALA 3.7 0.2 - - - +
158B LYS* 3.4 4.9 - - - +
159B VAL* 3.0 39.3 + - + +
161B ARG* 3.7 24.7 - - - +
168B GLN* 3.8 26.7 - - + +
169B THR* 1.3 82.6 - - - +
171B ALA* 1.3 62.1 + - - +
172B VAL* 4.1 14.4 - - + -
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Residues in contact with ALA 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A SER* 3.3 6.2 - - - -
176A SER* 3.0 35.7 + - - +
178A VAL* 4.0 16.6 - - + +
156B LYS* 5.1 16.2 - - + +
157B ALA 3.2 9.2 - - - +
158B LYS* 4.7 9.2 - - + -
170B ILE* 1.3 75.8 - - - +
172B VAL* 1.3 61.9 + - - +
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A LEU 3.4 4.3 - - - -
175A SER* 4.2 7.9 - - - -
116B LEU* 6.4 0.2 - - + -
142B ALA* 3.6 18.8 - - + -
143B GLN 3.8 23.6 - - - +
144B ALA* 4.7 5.8 - - + -
156B LYS* 3.0 7.6 - - - +
157B ALA* 2.9 49.7 + - + +
159B VAL* 4.5 7.2 - - + -
170B ILE* 4.1 16.2 - - + -
171B ALA* 1.3 78.4 - - - +
173B SER* 1.3 69.9 + - - +
174B LEU* 6.3 0.2 - - + -
176B ALA* 3.9 14.8 - - + -
178B VAL* 5.8 2.2 - - + -
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Residues in contact with SER 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A GLY 5.4 2.2 - - - -
174A LEU* 3.2 29.4 + - - +
142B ALA* 3.9 9.2 + - - +
155B ALA 3.7 8.1 - - - -
156B LYS* 4.2 2.5 - - - -
172B VAL* 1.3 76.7 - - - +
174B LEU* 1.3 67.0 + - - +
175B PRO* 3.4 13.8 + - - +
176B ALA* 3.4 16.5 - - - +
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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