Contacts of the strand formed by residues 158 - 164 (chain A) in PDB entry 4JYY
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 158 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A VAL* 4.0 6.1 - - - +
156A GLY 3.9 1.8 + - - -
157A SER* 1.3 75.9 - - - +
159A TRP* 1.3 65.5 + - - -
175A THR 3.2 13.0 - - - -
177A ASN 3.6 13.0 - - - -
194A VAL* 2.8 31.3 + - - +
195A TRP* 3.4 13.6 + - - +
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Residues in contact with TRP 159 (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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110A ASN* 3.4 43.5 - - + +
111A HIS* 3.8 10.5 - + - -
114A PHE* 3.7 24.9 - + + -
154A VAL* 4.0 5.6 - - - +
158A GLY* 1.3 74.2 - - - -
160A ALA* 1.3 59.9 + - - +
161A TRP* 3.3 42.0 - + + +
174A THR* 3.1 9.8 - - - -
175A THR* 2.9 35.5 + - - +
177A ASN 3.1 21.0 + - - -
178A GLN* 2.9 26.1 - - - +
191A GLY 4.7 1.3 - - - -
192A LEU 3.3 11.9 - - - -
193A ASP* 3.4 55.0 - - + -
194A VAL* 4.2 1.1 - - - +
195A TRP* 3.8 4.4 - - - +
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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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147A PHE* 3.6 18.3 - - + +
150A SER* 4.5 2.9 - - - -
151A ALA* 3.7 39.5 - - + +
154A VAL* 4.9 0.4 - - + +
159A TRP* 1.3 74.6 - - - +
161A TRP* 1.3 61.0 + - - +
172A ILE* 5.6 0.7 - - + -
173A MET 3.8 4.0 - - - +
174A THR* 4.2 7.4 - - + -
191A GLY* 3.1 3.5 - - - -
192A LEU 2.8 36.5 + - - +
194A VAL* 4.9 1.2 - - + +
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Residues in contact with TRP 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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109A TYR* 5.7 1.1 - + - -
110A ASN* 3.5 31.4 - - + -
113A PHE* 4.0 21.8 - + - -
147A PHE* 3.8 5.8 - - - -
159A TRP* 3.3 42.0 - + + +
160A ALA* 1.3 77.6 - - - +
162A LEU* 1.3 61.0 + - - +
163A VAL* 3.6 18.2 - - + -
172A ILE* 3.3 10.2 - - - +
173A MET* 2.8 44.1 + - + +
174A THR* 4.2 0.2 - - - -
175A THR* 2.8 33.0 + - + -
180A SER* 5.3 0.7 - - - -
181A PRO* 3.5 28.6 - - + +
188A PRO* 3.9 20.0 - - + -
190A ILE 3.5 7.4 - - - +
191A GLY* 3.6 24.7 - - - -
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Residues in contact with LEU 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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129A LEU* 4.7 11.0 - - + -
133A ILE* 4.8 7.9 - - + -
137A PHE* 3.8 20.9 - - + -
143A PHE* 3.7 35.4 - - + -
147A PHE* 3.8 3.1 - - + -
161A TRP* 1.3 71.0 - - - +
163A VAL* 1.3 54.3 + - - +
170A LEU* 4.2 14.1 - - + -
171A SER 3.5 16.2 - - - +
172A ILE* 4.3 1.1 - - + +
188A PRO* 3.6 2.3 - - - +
189A ILE* 2.7 59.5 + - + -
190A ILE* 2.9 28.7 + - + +
220A TRP* 4.8 4.3 - - + -
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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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161A TRP* 3.6 22.4 - - + -
162A LEU* 1.3 78.8 - - - +
164A ALA* 1.3 60.7 + - - +
169A LYS 3.7 0.2 - - - +
170A LEU* 3.3 10.0 - - - +
171A SER* 2.9 56.8 + - - +
173A MET* 3.9 16.6 - - + -
181A PRO* 3.7 25.8 - - + -
186A LEU* 4.1 25.6 - - + -
187A THR 3.2 10.3 - - - +
188A PRO* 4.3 2.5 - - + -
189A ILE* 4.2 1.1 - - - -
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Residues in contact with ALA 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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163A VAL* 1.3 76.0 - - - +
165A THR* 1.3 63.3 + - - +
168A GLY* 4.5 0.7 - - - -
169A LYS 3.2 6.5 - - - +
170A LEU* 3.8 16.6 - - + -
185A ASN 4.7 0.3 - - - +
186A LEU* 3.8 5.8 - - - -
187A THR* 2.8 34.5 + - - +
189A ILE* 4.0 14.4 - - + -
227A TYR* 4.1 4.3 - - + -
230A LEU* 3.7 26.5 - - + -
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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