Contacts of the strand formed by residues 141 - 151 (chain I) in PDB entry 1LK3
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 MET 141 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136I LEU* 3.9 3.3 - - - +
139I ASN* 2.9 25.5 + - - +
140I SER* 1.3 94.2 - - - +
142I VAL* 1.3 60.5 + - - +
188I THR* 3.8 26.7 - - + +
189I VAL* 3.4 21.5 - - - +
190I PRO* 3.7 16.8 - - + -
191I SER* 3.0 10.8 + - - -
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Residues in contact with VAL 142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I PRO* 4.5 11.0 - - + -
136I LEU* 3.5 36.1 - - + -
141I MET* 1.3 75.0 - - - +
143I THR* 1.3 74.6 + - - +
144I LEU* 4.1 16.9 + - + +
187I VAL 3.9 0.7 - - - +
188I THR* 3.4 3.0 - - - -
189I VAL* 2.8 54.7 + - + +
190I PRO 4.3 0.4 - - - +
191I SER* 3.7 13.2 - - - +
194I TRP* 4.5 12.6 - - + -
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Residues in contact with THR 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132I PRO* 4.4 1.2 - - - +
142I VAL* 1.3 76.8 - - - +
144I LEU* 1.3 69.5 + - - +
186I SER* 3.8 27.1 - - - +
187I VAL 3.4 6.3 - - - +
188I THR* 3.0 24.2 + - - +
113M THR* 5.0 9.4 - - - +
115M SER* 3.7 20.7 + - - +
117M PHE* 3.3 30.2 - - + -
134M LEU* 4.1 7.0 - - + -
136M ASN* 4.3 8.7 + - - +
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Residues in contact with LEU 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130I LEU* 3.6 7.6 - - - +
132I PRO* 3.7 24.7 - - + -
142I VAL* 4.1 13.2 - - + +
143I THR* 1.3 85.0 - - - +
145I GLY* 1.3 59.4 + - - +
160I TRP* 4.6 1.6 - - - -
186I SER* 3.1 7.9 - - - -
187I VAL* 2.9 38.2 + - + +
189I VAL* 4.9 6.3 - - + -
194I TRP* 3.5 54.3 - - + +
199I VAL* 3.9 24.2 - - + -
216I ILE* 4.1 14.6 - - + -
117M PHE* 4.4 2.5 - - - -
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Residues in contact with GLY 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130I LEU* 2.8 46.9 + - - +
144I LEU* 1.3 78.5 - - - +
146I CYS* 1.3 57.8 + - - -
160I TRP* 3.6 11.8 - - - -
185I SER 3.1 13.0 - - - -
186I SER* 4.0 1.1 - - - -
216I ILE* 3.2 13.7 - - - +
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Residues in contact with CYS 146 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127I VAL* 4.2 11.2 - - + -
128I TYR 3.3 7.4 - - - +
130I LEU* 3.8 4.6 - - - +
145I GLY* 1.3 78.0 - - - -
147I LEU* 1.3 60.6 + - - +
148I VAL* 3.9 8.7 + - + +
158I VAL* 5.7 0.7 - - + -
160I TRP* 3.8 3.1 - - + -
184I THR* 3.4 4.3 - - - +
185I SER* 2.9 34.3 + - - +
201I CYS* 2.0 53.4 - - + -
214I LYS* 4.2 3.4 - - - -
216I ILE* 3.8 16.8 - - - -
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Residues in contact with LEU 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126I SER 3.4 2.4 - - - +
127I VAL* 3.4 4.0 - - - +
128I TYR* 2.8 57.3 + - + +
130I LEU* 4.2 15.1 - - + +
146I CYS* 1.3 70.6 - - - +
148I VAL* 1.3 58.1 + - - +
149I LYS* 4.3 12.1 - - + -
182I THR* 3.6 27.4 - - + -
183I LEU 3.7 4.0 - - - +
184I THR* 3.6 18.4 - - - +
123M GLN* 4.2 3.1 - - - +
130M SER* 3.5 34.1 - - - +
132M VAL* 4.6 11.9 - - + -
177M THR* 4.7 8.1 - - + +
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Residues in contact with VAL 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125I PRO* 3.6 25.4 - - + -
126I SER 3.5 3.4 - - - -
127I VAL* 4.5 4.0 - - + +
146I CYS* 4.3 12.1 - - + +
147I LEU* 1.3 73.9 - - - +
149I LYS* 1.3 58.5 + - - +
151I TYR* 3.8 15.5 - - + -
156I VAL* 4.5 7.6 - - + -
158I VAL* 4.4 5.2 - - + -
182I THR* 3.3 4.3 - - - -
183I LEU* 2.8 54.7 + - + +
185I SER* 5.7 0.4 - - - +
203I VAL* 3.9 37.7 - - + -
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Residues in contact with LYS 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125I PRO* 3.5 1.3 - - - +
126I SER* 2.9 45.7 + - - +
128I TYR* 4.2 15.9 - - + +
147I LEU* 3.7 9.4 - - + -
148I VAL* 1.3 73.9 - - - +
150I GLY* 1.3 70.8 + - - +
151I TYR* 3.6 2.2 - - - -
177I GLN* 5.6 5.5 - - - +
182I THR* 3.5 25.3 + - + +
123M GLN* 3.6 28.9 - - - +
130M SER* 4.1 12.0 + - - +
177M THR* 6.3 0.4 - - - +
179M SER* 4.6 10.3 + - - -
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Residues in contact with GLY 150 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123I THR* 3.0 26.2 - - - +
124I ALA 3.4 5.6 - - - +
149I LYS* 1.3 81.8 - - - +
151I TYR* 1.3 58.6 + - - +
180I LEU* 3.9 27.2 - - - +
181I TYR 3.0 10.4 + - - -
182I THR* 3.5 2.7 + - - -
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Residues in contact with TYR 151 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123I THR 3.2 12.1 - - - +
125I PRO* 3.7 30.5 - - + -
148I VAL* 3.8 23.8 - - + -
150I GLY* 1.3 75.4 - - - +
152I PHE* 1.3 64.4 + - - +
153I PRO 3.5 19.7 - - - -
154I GLU* 2.8 31.9 + - - -
156I VAL* 3.5 30.4 - - + +
174I ALA* 3.2 17.5 - - - +
180I LEU* 3.6 2.4 - - - -
181I TYR* 2.7 76.1 + - + +
182I THR* 4.1 1.8 - - - -
183I LEU* 3.6 13.0 - - + +
205I HIS* 3.8 2.7 - - - +
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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