Contacts of the strand formed by residues 160 - 166 (chain A) in PDB entry 4EFH
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 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A LEU* 3.6 29.6 - - + -
154A ASP 3.2 7.2 - - - +
155A SER* 2.8 22.4 + - - +
159A VAL* 1.3 72.3 - - - +
161A HIS* 1.3 65.9 + - - +
162A THR* 5.4 0.9 - - + -
177A ARG* 3.5 2.8 - - - -
178A LEU* 2.8 47.6 + - + +
180A LEU 2.6 25.1 + - - -
181A ALA* 3.7 0.2 - - - +
261A LEU* 4.9 1.7 - - - +
274A ILE* 4.0 16.2 - - + -
277A THR* 6.3 0.2 - - + -
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Residues in contact with HIS 161 (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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73A HIS 5.2 1.6 - - - -
75A ILE* 6.1 1.0 - - + +
108A ALA* 4.5 7.6 - - + -
109A PRO* 3.5 48.9 + - + +
110A LEU* 5.4 1.7 - - + +
137A GLN* 5.8 0.4 + - - -
152A VAL 3.5 0.9 - - - +
153A LEU* 3.5 4.2 - - - +
154A ASP* 2.8 43.6 + - + +
159A VAL* 3.5 33.2 - - + +
160A THR* 1.3 74.7 - - - +
162A THR* 1.3 62.9 + - - +
163A VAL* 3.9 16.6 - - + -
175A ILE* 4.3 5.2 - - + -
176A LEU 3.3 8.7 - - - +
177A ARG* 3.6 35.1 - - + +
277A THR* 6.0 0.2 - - - -
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Residues in contact with THR 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ILE* 4.6 3.8 - - - -
152A VAL 3.2 5.2 - - - -
153A LEU* 3.9 16.2 - - + -
160A THR* 5.4 1.6 - - + -
161A HIS* 1.3 75.5 - - - +
163A VAL* 1.3 61.7 + - - +
164A PRO* 4.1 0.2 - - - -
175A ILE* 3.6 4.2 - - - -
176A LEU* 3.0 37.3 + - - +
274A ILE 4.4 0.4 - - - +
277A THR* 3.4 15.3 + - + +
278A THR* 3.2 40.4 - - - +
281A SER* 2.9 29.3 + - - -
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Residues in contact with VAL 163 (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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109A PRO* 3.6 25.1 - - + -
136A ILE* 5.0 2.2 - - + -
138A ALA* 3.5 31.2 - - + -
139A VAL* 5.0 0.2 - - + -
151A ILE* 3.4 6.7 - - - +
152A VAL 2.7 31.2 + - - +
154A ASP* 5.7 0.2 - - + -
161A HIS* 3.9 10.3 - - + +
162A THR* 1.3 78.8 - - - +
164A PRO* 1.3 67.8 - - - +
165A ILE* 3.5 13.0 + - + +
170A ALA* 3.9 17.7 - - + -
175A ILE* 3.8 24.0 - - + -
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Residues in contact with PRO 164 (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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150A GLY 3.7 5.2 - - - +
151A ILE* 3.9 9.6 - - + -
162A THR 3.8 2.5 - - - +
163A VAL* 1.3 87.0 - - - +
165A ILE* 1.3 57.9 + - - +
170A ALA* 3.5 4.7 - - - -
171A LEU* 3.0 29.9 + - + +
174A ALA* 3.5 41.7 - - + +
175A ILE* 4.2 4.5 - - + -
281A SER* 3.7 20.2 - - - +
285A CYS* 3.5 20.4 - - - -
293A LEU* 4.2 13.0 - - + -
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Residues in contact with ILE 165 (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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138A ALA 4.0 1.6 - - - +
139A VAL* 3.9 37.7 - - + +
142A LEU* 3.7 14.8 - - + -
148A THR 3.4 19.7 - - - +
149A THR* 3.3 6.1 - - - +
150A GLY 2.7 36.7 + - - +
152A VAL* 3.7 25.4 - - + -
163A VAL* 3.5 21.1 - - + +
164A PRO* 1.3 78.3 - - - +
166A TYR* 1.3 63.5 + - - +
167A GLU 4.1 0.2 - - - -
168A GLY* 3.8 19.1 - - - +
169A TYR 3.4 10.5 - - - +
170A ALA* 4.2 2.0 - - - -
171A LEU* 4.8 1.6 - - - -
293A LEU* 4.2 5.0 - - - +
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Residues in contact with TYR 166 (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 THR* 3.8 22.4 - - + -
165A ILE* 1.3 72.8 - - - +
167A GLU* 1.3 79.7 + - + +
168A GLY 3.3 0.2 - - - -
169A TYR* 2.9 31.2 + - - +
171A LEU* 4.1 24.8 - - + +
289A ILE* 3.8 34.8 - - + -
292A ASP* 5.4 3.4 - - - -
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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