Contacts of the strand formed by residues 150 - 160 (chain B) in PDB entry 4LKC
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 150 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A PHE* 3.9 18.1 - - + -
145B SER* 5.4 1.0 + - - -
146B THR* 5.3 5.1 + - - -
149B GLY* 1.3 74.1 - - - -
151B ALA* 1.3 62.3 + - - +
198B THR* 3.6 33.2 - - + +
199B VAL 3.6 11.9 - - - +
200B PRO* 4.6 0.9 - - - +
201B SER* 3.9 3.8 + - - -
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Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A PHE* 4.4 2.9 - - - -
141B PRO* 4.9 2.2 - - + -
145B SER* 3.7 23.3 - - - +
150B THR* 1.3 73.8 - - - +
152B ALA* 1.3 60.3 + - - +
197B VAL 3.9 0.5 - - - +
198B THR* 3.1 3.9 - - - -
199B VAL* 2.7 42.8 + - + +
201B SER* 3.7 13.6 + - - +
204B LEU* 3.7 26.5 - - + -
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Residues in contact with ALA 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A PHE* 3.6 43.8 - - + -
119A PHE* 3.4 18.5 - - + -
136A LEU* 3.9 12.1 - - + -
141B PRO* 3.6 12.7 - - - +
142B SER 4.7 1.4 + - - -
145B SER* 5.4 0.4 + - - -
151B ALA* 1.3 73.5 - - - +
153B LEU* 1.3 63.2 + - - +
197B VAL 3.5 5.4 - - - +
198B THR* 3.7 14.4 - - + -
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Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PHE* 4.0 5.4 - - - -
139B LEU* 3.4 16.4 - - - +
141B PRO* 3.7 19.5 - - + -
151B ALA 4.5 0.4 - - - +
152B ALA* 1.3 78.6 - - - +
154B GLY* 1.3 59.8 + - - +
169B TRP* 3.6 27.6 - - + -
196B VAL* 3.4 5.9 - - - +
197B VAL* 2.9 53.5 + - + +
199B VAL* 3.8 29.2 - - + -
204B LEU* 4.7 4.9 - - + -
209B TYR* 3.9 24.7 - - + -
226B VAL* 3.9 10.3 - - + +
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Residues in contact with GLY 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B LEU* 2.8 42.4 + - - +
153B LEU* 1.3 78.8 - - - +
155B CYS* 1.3 57.8 + - - -
169B TRP* 3.5 13.2 - - - -
195B SER 3.1 13.2 - - - -
196B VAL* 4.1 0.2 - - - -
226B VAL* 3.4 14.7 - - - +
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Residues in contact with CYS 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B VAL* 4.1 12.8 - - + -
137B PHE 3.4 7.6 - - - +
138B PRO* 4.8 0.2 - - - -
139B LEU* 3.7 4.2 - - - +
154B GLY* 1.3 70.9 - - - -
156B LEU* 1.3 61.0 + - - +
157B VAL* 3.9 6.8 + - + +
167B VAL* 5.3 0.2 - - + -
169B TRP* 4.4 1.6 - - + -
194B SER* 3.3 4.2 - - - -
195B SER* 2.9 34.8 + - - +
211B CYS* 2.0 53.6 - - + -
213B VAL* 5.0 0.7 - - + -
224B LYS* 4.2 4.7 - - - -
226B VAL* 3.6 23.6 - - - -
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Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A GLN* 4.3 2.7 - - - +
132A SER* 3.5 34.8 - - - +
134A VAL* 4.8 10.8 - - + -
179A THR* 5.0 8.1 - - + +
135B SER 3.4 5.5 - - - +
136B VAL* 3.4 2.4 - - - +
137B PHE* 2.8 59.5 + - + +
139B LEU* 4.1 13.4 - - + +
155B CYS* 1.3 72.3 - - - +
157B VAL* 1.3 59.0 + - - +
158B LYS* 4.3 10.5 - - + -
192B SER* 3.8 17.0 - - - +
193B LEU 3.6 13.0 - - - +
194B SER* 3.4 20.4 - - - +
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Residues in contact with VAL 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B PRO* 3.5 29.6 - - + -
135B SER 3.6 3.8 - - - -
136B VAL* 4.7 4.5 - - + -
155B CYS* 4.5 7.6 - - + +
156B LEU* 1.3 72.3 - - - +
158B LYS* 1.3 59.2 + - - +
160B TYR* 3.8 15.6 - - + -
165B VAL* 4.3 8.5 - - + -
167B VAL* 4.2 4.9 - - + -
192B SER* 3.3 4.3 - - - -
193B LEU* 2.7 59.2 + - + +
195B SER 5.6 0.2 - - - +
213B VAL* 3.8 35.9 - - + -
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Residues in contact with LYS 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A GLN* 3.5 21.1 - - - +
130A THR* 4.2 18.0 - - - +
132A SER* 3.4 20.2 - - - +
179A THR* 6.4 0.4 - - - -
181A THR* 4.6 11.7 - - - +
134B PRO* 3.4 2.4 - - - +
135B SER* 2.9 40.9 + - - +
137B PHE* 4.4 11.9 - - + -
156B LEU* 3.8 11.9 - - + -
157B VAL* 1.3 74.5 - - - +
159B ASP* 1.3 97.6 + - - +
160B TYR* 3.8 1.1 - - - -
186B GLN* 3.6 14.1 + - - +
191B TYR 3.9 0.2 - - - -
192B SER* 3.5 16.2 - - - +
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Residues in contact with ASP 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B LYS* 3.6 21.3 + - - +
133B GLY 3.3 17.8 - - - +
135B SER* 5.9 1.4 - - - -
158B LYS* 1.3 104.5 + - - +
160B TYR* 1.3 56.9 + - - +
186B GLN* 3.0 21.7 + - - +
188B SER* 4.7 2.1 + - - -
190B LEU* 3.8 27.3 - - + +
191B TYR 2.9 13.7 + - - -
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Residues in contact with TYR 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B LYS* 3.3 13.9 - - - +
134B PRO* 3.7 31.9 - - + -
157B VAL* 3.8 26.9 - - + -
159B ASP* 1.3 76.3 - - - +
161B PHE* 1.3 63.9 + - - +
162B PRO 3.7 9.2 - - - -
163B GLU* 3.0 27.3 + - - -
165B VAL* 3.3 27.9 - - + +
183B ALA* 3.2 17.3 - - - +
190B LEU* 3.7 3.2 - - - +
191B TYR* 2.8 61.7 + + + +
192B SER* 4.1 2.0 - - - -
193B LEU* 3.7 5.3 - - + +
215B HIS* 3.7 17.5 - - + -
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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