Contacts of the strand formed by residues 169 - 176 (chain A) in PDB entry 4EWE
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 THR 169 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A PHE* 4.0 19.6 - - + -
92A TRP* 3.8 28.9 - - + -
116A LEU* 4.8 3.6 - - + -
118A VAL* 3.9 16.7 - - + +
153A SER* 2.8 22.8 + - - +
154A GLY* 3.7 8.2 + - - -
165A THR* 3.5 10.3 + - - +
167A THR* 2.8 20.7 + - - +
168A PRO* 1.3 71.7 + - - +
170A LEU* 1.3 66.6 + - - +
171A TYR* 4.6 4.3 - - + -
190A TRP* 4.0 5.8 - - - -
241A ILE* 4.6 2.9 - - + -
242A ALA 3.2 12.1 - - - +
243A GLY* 4.5 0.3 - - - -
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Residues in contact with LEU 170 (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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153A SER 3.5 16.4 - - - +
154A GLY* 3.8 2.7 - - - -
155A GLU 3.6 31.4 - - - +
169A THR* 1.3 74.4 - - - +
171A TYR* 1.3 62.4 + - - +
172A LEU* 3.7 21.1 - - + -
184A GLN* 4.3 1.6 - - + +
185A PRO 4.1 19.7 - - - +
186A ILE* 4.4 6.7 - - + -
187A PRO* 5.0 4.0 - - + -
190A TRP* 3.8 12.2 - - + -
240A LEU* 3.9 24.7 - - + -
241A ILE* 3.3 4.9 - - - -
242A ALA* 2.8 44.6 + - + +
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Residues in contact with TYR 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PHE* 4.2 4.5 - - - -
64A VAL* 3.9 24.8 + - + -
66A TYR* 3.9 17.1 - + + +
92A TRP* 4.4 3.4 - + - -
114A LEU* 3.7 32.1 + - - +
116A LEU* 4.1 29.0 - - + +
152A ILE* 2.9 54.7 + - + +
153A SER* 3.0 24.7 + - - +
169A THR* 4.6 2.7 - - + -
170A LEU* 1.3 75.6 - - - +
172A LEU* 1.3 66.1 + - - +
239A VAL* 3.9 22.7 - - + -
240A LEU 3.5 2.9 - - - -
241A ILE* 3.9 18.6 - - + -
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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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149A VAL* 3.6 10.1 - - + -
150A ALA 3.4 2.9 - - - -
151A VAL* 3.9 22.4 - - + -
153A SER 4.1 0.2 - - - +
155A GLU 4.3 0.2 - - - +
156A ALA* 3.7 22.9 - - + -
170A LEU* 3.7 31.2 - - + -
171A TYR* 1.3 88.2 - - - +
173A ASP* 1.3 60.9 + - - +
174A PHE* 3.7 23.3 + - + -
184A GLN* 3.7 35.2 - - + +
239A VAL* 3.2 6.2 - - - +
240A LEU* 2.8 41.2 + - + +
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Residues in contact with ASP 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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66A TYR* 2.8 44.0 + - + +
68A LEU* 4.6 1.3 - - - +
149A VAL* 3.2 4.2 - - - -
150A ALA* 2.8 38.9 + - + +
152A ILE* 4.2 3.1 - - + +
171A TYR* 5.5 0.2 - - + -
172A LEU* 1.3 71.6 - - - +
174A PHE* 1.3 59.7 + - - +
175A LYS* 3.5 11.6 + - - -
237A HIS* 3.0 24.4 + - - -
238A PHE 3.9 2.9 - - - -
239A VAL* 4.1 9.0 - - + -
1003A EDO 2.9 25.0 + - - -
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Residues in contact with PHE 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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147A VAL* 4.0 21.3 - - + -
148A THR 3.4 1.6 - - - -
149A VAL* 3.9 20.0 - - + -
172A LEU* 3.7 41.1 - - + -
173A ASP* 1.3 73.5 + - - +
175A LYS* 1.4 60.5 + - - +
176A LEU* 4.1 8.7 - - + -
182A HIS* 3.5 36.3 - + - -
184A GLN* 4.0 4.3 - - + -
228A VAL* 5.3 3.4 - - + -
236A SER 3.8 0.2 - - - +
237A HIS* 3.3 8.7 - - - -
238A PHE* 2.9 69.8 + + + +
240A LEU* 3.8 22.7 - - + -
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Residues in contact with LYS 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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69A GLU* 6.2 4.3 - - - -
146A GLY 3.7 3.1 - - - +
148A THR* 2.9 39.8 + - - +
173A ASP* 3.3 5.1 + - - -
174A PHE* 1.4 75.9 - - - +
176A LEU* 1.3 63.0 + - - +
177A ASP* 4.2 1.9 + - - +
235A ARG* 3.0 46.2 - - - +
236A SER 3.2 3.4 - - - -
237A HIS* 3.1 31.9 + - + -
1003A EDO 2.1 56.3 + - - +
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Residues in contact with LEU 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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146A GLY 3.6 3.1 - - - -
147A VAL* 4.0 26.9 - - + -
174A PHE* 4.1 14.8 - - + -
175A LYS* 1.3 78.0 - - - +
177A ASP* 1.3 66.7 + - - +
180A ALA* 4.2 10.5 - - + +
182A HIS* 5.0 0.2 - - + -
201A VAL* 4.2 1.8 - - + -
228A VAL* 4.0 20.0 - - + +
229A GLU* 4.0 8.3 - - - +
230A ASN* 3.0 37.3 + - + +
235A ARG* 3.4 5.8 - - - -
236A SER* 2.9 36.6 + - - +
238A PHE* 3.7 28.7 - - + -
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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