Contacts of the helix formed by residues 159 - 170 (chain A) in PDB entry 4BOS
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 SER 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A ASP* 2.9 18.8 + - - -
158A ASN* 1.3 78.0 - - - +
160A ALA* 1.3 62.0 + - - +
161A LEU* 3.2 3.1 - - - -
162A PHE* 3.0 19.0 + - - -
163A THR* 3.1 14.2 + - - -
176A PRO 5.6 0.4 - - - -
179A ALA* 3.5 27.9 - - - +
183A ARG* 3.0 23.7 + - - +
216A ASP* 4.1 9.2 + - - +
13F ILE* 5.7 0.3 - - - +
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Residues in contact with ALA 160 (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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154A VAL* 3.9 5.8 - - + +
155A PRO 3.8 16.2 - - - +
156A ALA* 4.8 2.0 - - - -
157A ASP* 3.8 1.4 + - - -
158A ASN 3.5 2.8 - - - -
159A SER* 1.3 72.3 - - - +
161A LEU* 1.3 59.4 + - - +
162A PHE 3.3 0.2 - - - -
163A THR* 4.0 7.8 - - - -
164A SER* 2.6 37.6 + - - -
267A HIS* 5.5 0.9 - - + -
268A TYR* 3.4 25.4 - - - +
76C GLY* 3.5 24.3 + - - +
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Residues in contact with LEU 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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159A SER 3.1 1.0 + - - -
160A ALA* 1.3 78.9 - - - +
162A PHE* 1.3 81.8 + - + +
164A SER* 3.7 0.5 - - - -
165A VAL* 3.0 35.2 + - + +
220A GLY* 4.0 21.3 - - - +
224A GLU* 4.2 12.1 - - + -
225A ILE* 3.9 30.1 - - + -
228A LEU* 4.3 9.0 - - + -
261A LEU* 3.9 16.2 - - + -
268A TYR* 3.8 37.8 - - + +
75C GLY 4.1 11.8 + - - +
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Residues in contact with PHE 162 (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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159A SER* 3.0 16.0 + - - +
161A LEU* 1.3 84.5 - - + +
163A THR* 1.3 59.0 + - - +
165A VAL* 3.2 1.1 + - - -
166A TYR* 2.8 31.7 + - - +
178A CYS* 4.4 0.2 - - - -
179A ALA* 4.3 9.9 - - + -
182A MET* 3.4 41.6 - - + +
183A ARG* 3.4 52.9 - - + -
186A ILE* 4.1 14.6 - - + -
213A ILE* 4.1 4.7 - - + -
220A GLY* 3.9 28.7 - - - -
224A GLU* 3.9 22.4 - - + -
228A LEU* 4.2 7.4 - - + -
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Residues in contact with THR 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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154A VAL* 3.9 15.0 - - + -
155A PRO* 4.9 4.7 - - + -
157A ASP* 5.0 3.5 + - - -
159A SER* 3.1 20.8 + - - -
160A ALA* 4.0 7.6 - - - -
162A PHE* 1.3 77.2 - - - +
164A SER* 1.3 56.7 + - - +
166A TYR* 3.5 2.1 + - - +
167A TYR* 2.9 28.1 + - - +
173A VAL 5.0 0.5 - - - +
174A LEU* 3.5 30.3 - - + -
175A ASN 4.8 2.4 + - - +
176A PRO* 4.0 29.2 + - + +
178A CYS* 4.1 10.9 - - - -
179A ALA* 4.6 0.5 - - - +
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Residues in contact with SER 164 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A VAL* 3.7 3.3 - - - +
160A ALA 2.6 27.5 + - - -
161A LEU 3.7 2.9 - - - -
163A THR* 1.3 71.1 - - - +
165A VAL* 1.3 66.4 + - - +
167A TYR* 3.3 4.1 + - - +
168A VAL* 3.1 26.9 + - - +
261A LEU* 3.9 11.4 - - - -
268A TYR* 3.3 11.0 + - - -
269A ASP* 3.3 26.0 - - - -
270A PRO* 3.5 23.2 - - - +
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Residues in contact with VAL 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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161A LEU* 3.0 28.0 + - + +
162A PHE 3.7 3.6 - - - +
164A SER* 1.3 74.5 - - - +
166A TYR* 1.3 65.4 + - - +
168A VAL* 3.2 10.9 + - + +
169A VAL* 2.9 31.4 + - + +
182A MET* 4.0 16.4 - - + -
225A ILE* 5.2 2.5 - - + -
228A LEU* 4.3 22.2 - - + -
232A TYR* 4.2 16.2 - - + -
236A ILE* 4.3 15.7 - - + -
261A LEU* 3.8 22.2 - - + -
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Residues in contact with TYR 166 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A PHE 2.8 18.2 + - - +
163A THR 3.6 2.9 - - - +
165A VAL* 1.3 79.8 - - - +
167A TYR* 1.3 61.7 + - - +
169A VAL* 4.1 5.4 - - - -
170A GLU* 3.1 61.0 + - + +
173A VAL* 3.6 25.7 - - + +
175A ASN* 4.0 28.3 + - + -
178A CYS* 3.6 36.8 - - + -
182A MET* 3.9 13.4 - - + +
232A TYR* 4.4 10.1 - - - -
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Residues in contact with TYR 167 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A THR* 3.6 22.1 + - + +
154A VAL* 5.2 2.0 - - + -
163A THR 2.9 17.7 + - - +
164A SER* 3.5 5.6 - - - +
165A VAL 3.2 0.4 - - - -
166A TYR* 1.3 78.7 - - - +
168A VAL* 1.3 58.4 - - + +
171A GLY 3.6 0.7 + - - -
172A GLY* 2.7 60.5 + - - -
173A VAL 3.3 28.7 + - - +
174A LEU* 3.6 24.0 - - + -
270A PRO* 3.4 33.9 - - + -
272A GLN* 2.5 32.2 + - + -
282A PRO* 5.2 2.9 - - - +
284A THR* 3.8 7.9 - - + -
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Residues in contact with VAL 168 (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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164A SER 3.1 6.2 + - - +
165A VAL* 3.2 18.8 - - - +
167A TYR* 1.3 77.0 - - + +
169A VAL* 1.3 65.4 + - + +
171A GLY 3.1 2.6 + - - -
259A VAL* 3.6 35.2 - - + -
260A LEU 3.6 18.2 - - - +
261A LEU* 4.0 6.5 - - + -
270A PRO* 3.6 27.1 - - + -
271A LEU 3.7 12.3 - - - +
284A THR* 2.7 32.2 + - - +
285A ILE* 3.5 8.5 - - - +
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Residues in contact with VAL 169 (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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165A VAL* 2.9 32.7 + - + +
166A TYR* 3.8 6.3 - - - +
168A VAL* 1.3 77.1 - - + +
170A GLU* 1.3 70.0 + - - +
171A GLY 3.2 2.8 + - - -
232A TYR* 3.7 52.3 - - + -
234A CYS* 3.9 27.4 - - - -
236A ILE* 5.2 2.0 - - + -
259A VAL* 4.4 7.9 - - + -
285A ILE* 3.7 14.0 - - - +
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Residues in contact with GLU 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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166A TYR* 3.1 54.5 + - + +
167A TYR 4.4 0.2 - - - +
169A VAL* 1.3 90.8 - - + +
171A GLY* 1.3 59.4 + - - +
172A GLY 3.4 1.0 + - - -
173A VAL* 3.7 28.4 - - + +
232A TYR* 3.9 13.0 - - - -
285A ILE* 5.0 0.7 - - - -
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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