Contacts of the strand formed by residues 142 - 151 (chain J) in PDB entry 3KYM
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 ALA 142 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116I PHE* 3.8 7.0 - - + -
132J PRO* 5.9 5.4 - - + -
140J SER 3.6 6.3 + - - +
141J THR* 1.3 77.7 + - - +
143J ALA* 1.3 62.6 + - - +
189J THR* 4.0 0.8 - - - -
190J VAL* 3.5 20.5 + - - +
192J SER* 5.1 0.4 - - - +
195J PHE* 3.2 40.3 - - + -
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Residues in contact with ALA 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116I PHE* 3.5 27.7 - - + -
118I PHE* 3.4 16.7 - - + -
135I LEU* 4.3 15.7 - - + -
132J PRO* 3.6 16.5 - - - +
142J ALA* 1.3 78.0 - - - +
144J LEU* 1.3 64.3 + - - +
188J VAL 3.3 13.0 - - - +
189J THR* 3.9 15.9 - - - -
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Residues in contact with LEU 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118I PHE* 4.1 5.8 - - - -
130J LEU 3.4 13.7 - - - +
131J ALA* 4.7 4.5 - - + -
132J PRO* 4.8 4.0 - - + -
143J ALA* 1.3 74.4 - - - +
145J GLY* 1.3 56.2 + - - +
160J TRP* 3.9 2.7 - - + -
187J VAL* 3.4 5.4 - - - +
188J VAL* 2.7 51.9 + - + +
200J TYR* 3.6 46.0 - - + -
217J VAL* 3.7 33.2 - - + +
218J GLU 5.6 1.3 - - - +
219J ARG* 5.5 13.2 - - + -
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Residues in contact with GLY 145 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129J PRO* 3.8 0.3 - - - +
130J LEU* 2.9 37.6 + - - +
144J LEU* 1.3 77.8 - - - +
146J CYS* 1.3 60.1 + - - -
160J TRP* 3.4 11.9 - - - -
186J SER 3.2 12.8 - - - -
187J VAL* 3.9 4.0 - - - -
217J VAL* 3.3 16.5 - - - +
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Residues in contact with CYS 146 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J VAL* 4.1 12.3 - - + -
128J PHE 3.5 6.7 - - - -
129J PRO* 5.2 0.4 - - - -
130J LEU* 4.0 5.3 - - - +
145J GLY* 1.3 75.6 - - - -
147J LEU* 1.3 59.3 + - - +
148J VAL* 4.0 7.4 + - + +
158J VAL* 5.8 0.4 - - + -
160J TRP* 3.4 13.0 - - + -
185J SER* 3.5 4.0 + - - -
186J SER* 2.8 36.3 + - - +
202J CYS* 2.0 52.3 - - + -
204J VAL* 5.2 0.2 - - + -
215J LYS* 4.2 8.5 - - - -
217J VAL* 4.3 3.8 - - - -
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Residues in contact with LEU 147 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124I GLN* 4.5 4.5 - - - +
131I SER* 3.9 27.1 - - - +
133I VAL* 4.5 11.0 - - + -
178I THR* 5.0 10.3 - - + +
126J SER 2.9 17.2 - - - +
127J VAL* 3.4 1.1 - - - -
128J PHE* 2.8 49.7 + - + +
130J LEU* 4.1 17.2 - - + +
146J CYS* 1.3 71.3 - - - +
148J VAL* 1.3 59.8 + - - +
149J LYS* 3.4 18.4 + - + +
183J SER* 4.4 13.5 - - - +
184J LEU 3.9 10.8 - - - +
185J SER* 3.7 17.0 - - - +
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Residues in contact with VAL 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125J PRO* 3.7 18.2 - - + -
126J SER 3.7 2.9 - - - -
127J VAL* 4.8 2.0 - - + +
146J CYS* 4.6 10.5 - - + +
147J LEU* 1.3 72.4 - - - +
149J LYS* 1.3 56.5 + - - +
151J TYR* 3.7 8.7 - - + -
156J VAL* 4.0 12.6 - - + -
158J VAL* 5.2 6.7 - - + -
183J SER* 3.5 4.6 - - - -
184J LEU* 2.9 52.4 + - + +
186J SER 5.3 0.9 - - - +
204J VAL* 3.5 48.2 - - + -
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Residues in contact with LYS 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124I GLN* 3.4 16.1 - - + +
129I THR* 4.2 16.4 - - - +
131I SER* 3.0 27.3 + - - -
180I THR* 4.8 7.4 + - - +
125J PRO* 3.1 1.8 - - - +
126J SER* 2.7 44.4 + - - +
128J PHE* 4.0 19.3 - - + -
147J LEU* 4.2 14.6 - - + +
148J VAL* 1.3 74.4 - - - +
150J ASP* 1.3 100.5 + - - +
151J TYR 3.6 1.8 - - - -
177J GLN* 4.1 12.1 - - - +
183J SER* 4.2 14.4 - - - +
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Residues in contact with ASP 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123J LYS* 3.7 25.6 + - - +
124J GLY 3.7 14.0 - - - +
126J SER* 5.7 1.1 - - - +
149J LYS* 1.3 105.0 - - - +
151J TYR* 1.3 59.6 + - - +
177J GLN* 3.5 16.8 + - - +
179J SER* 5.1 3.3 + - - -
181J LEU* 3.9 23.1 - - + +
182J TYR 3.2 11.2 + - - -
183J SER* 4.2 0.8 - - - -
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Residues in contact with TYR 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123J LYS 3.4 7.4 - - - +
125J PRO* 3.4 34.8 - - + -
148J VAL* 3.7 31.0 - - + -
150J ASP* 1.3 75.0 - - - +
152J PHE* 1.3 63.2 + - - +
153J PRO 3.7 16.6 - - - -
154J GLU* 3.4 18.3 + - - -
156J VAL* 3.5 33.1 - - + +
174J ALA* 3.1 24.9 - - - +
181J LEU* 3.6 3.1 - - - +
182J TYR* 2.8 64.6 + + + +
183J SER* 3.9 3.8 - - - -
184J LEU* 3.5 6.4 - - + +
206J HIS* 4.2 7.6 - + - +
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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