Contacts of the strand formed by residues 191 - 200 (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 TYR 191 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B THR* 6.1 1.4 - - - +
125B THR* 6.1 0.7 - - + +
159B ASP* 2.9 25.3 + - - -
160B TYR* 2.8 50.7 + + + +
161B PHE* 3.7 29.7 - + - -
163B GLU* 3.8 39.0 - - + +
183B ALA* 3.8 22.2 - - + -
184B VAL 3.6 11.2 - - - -
185B LEU* 3.6 32.3 - - + +
186B GLN* 3.4 0.4 + - - -
190B LEU* 1.3 72.8 - - - +
192B SER* 1.3 59.8 + - - +
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Residues in contact with SER 192 (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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179A THR* 6.0 1.0 - - - +
156B LEU* 3.8 10.9 - - - +
157B VAL 3.3 9.2 + - - -
158B LYS* 3.5 23.3 - - - +
160B TYR* 4.4 0.9 - - - -
182B PRO 4.6 0.3 - - - +
183B ALA* 3.5 0.5 - - - -
184B VAL* 3.0 34.1 + - - +
186B GLN* 3.5 26.8 + - - -
191B TYR* 1.3 74.7 - - - +
193B LEU* 1.3 63.4 + - - +
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Residues in contact with LEU 193 (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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156B LEU* 3.6 5.3 - - - +
157B VAL* 2.7 62.1 + - + +
160B TYR* 3.7 13.5 - - + +
163B GLU* 5.1 1.3 - - - +
165B VAL* 3.7 24.2 - - + +
167B VAL* 4.0 17.9 - - + -
180B THR* 4.3 10.3 - - + -
181B PHE* 3.3 26.2 - - - +
182B PRO* 5.0 2.0 - - + -
183B ALA* 4.0 12.8 - - + +
192B SER* 1.3 79.5 + - - +
194B SER* 1.3 68.4 + - - +
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Residues in contact with SER 194 (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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134A VAL* 4.3 10.9 - - - +
177A SER* 5.0 9.2 - - - -
179A THR* 5.1 2.8 + - - -
139B LEU* 3.9 17.0 - - - +
155B CYS 3.3 6.5 - - - -
156B LEU* 3.4 26.7 - - - +
180B THR* 3.9 0.3 - - - -
181B PHE* 3.0 45.9 + - - +
193B LEU* 1.3 75.7 - - - +
195B SER* 1.3 59.7 + - - +
196B VAL* 4.8 3.8 - - - -
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Residues in contact with SER 195 (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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154B GLY* 3.1 3.3 - - - -
155B CYS* 2.9 35.1 + - - +
167B VAL* 3.6 31.6 - - - +
169B TRP* 3.0 23.7 + - - -
178B VAL* 4.3 1.0 - - - +
179B HIS 3.4 4.3 + - - -
180B THR* 2.7 26.0 + - - +
193B LEU* 4.5 1.0 - - - +
194B SER* 1.3 73.7 - - - +
196B VAL* 1.3 61.4 + - - +
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Residues in contact with VAL 196 (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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119A PHE* 5.0 4.9 - - + -
134A VAL* 5.9 2.2 - - + -
136A LEU* 3.9 36.1 - - + -
138A ASN* 4.7 1.3 - - - +
139B LEU* 4.0 21.3 - - + -
153B LEU 3.4 11.4 - - - +
169B TRP* 4.6 1.1 - - - -
177B GLY 5.6 0.2 - - - +
178B VAL* 3.3 7.6 - - - +
179B HIS* 2.7 61.0 + - + +
181B PHE* 3.7 23.8 - - + -
194B SER* 4.8 2.7 - - - -
195B SER* 1.3 79.9 - - - +
197B VAL* 1.3 63.3 + - - +
198B THR* 6.1 0.2 - - + -
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Residues in contact with VAL 197 (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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152B ALA* 3.5 0.7 - - - -
153B LEU* 2.9 64.5 + - + +
169B TRP* 3.9 20.6 - - + -
174B LEU* 3.7 20.9 - - + -
176B SER 3.8 14.1 - - - +
177B GLY 3.3 6.1 - - - +
178B VAL* 3.7 24.9 - - + -
196B VAL* 1.3 78.0 - - - +
198B THR* 1.3 70.1 + - - +
199B VAL* 3.9 6.5 - - + -
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Residues in contact with THR 198 (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* 4.2 9.2 - - + -
136A LEU* 4.9 2.0 - - + -
138A ASN* 3.8 35.2 + - - +
139A ASN* 5.1 1.4 + - - -
150B THR* 3.6 23.8 - - + +
151B ALA 3.1 3.6 - - - +
152B ALA* 3.7 24.7 - - + -
176B SER 4.4 6.4 - - - +
177B GLY* 3.3 18.5 + - - -
196B VAL* 6.1 0.4 - - + -
197B VAL* 1.3 76.7 - - - +
199B VAL* 1.3 64.4 - - - +
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Residues in contact with VAL 199 (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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150B THR* 3.6 6.3 - - - -
151B ALA 2.7 36.2 + - - +
153B LEU* 3.8 20.0 - - + -
174B LEU* 4.5 7.9 - - + -
197B VAL* 3.9 17.5 - - + -
198B THR* 1.3 77.3 - - - +
200B PRO* 1.4 69.9 - - + +
203B SER* 3.6 7.2 - - - +
204B LEU* 4.2 9.2 - - + -
209B TYR* 3.4 46.0 - - + +
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Residues in contact with PRO 200 (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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148B GLY 6.2 1.1 - - - -
149B GLY 3.5 10.5 - - - +
150B THR* 4.6 1.6 - - + +
199B VAL* 1.4 92.1 - - + +
201B SER* 1.3 63.2 + - - +
202B SER* 3.2 15.5 - - - +
203B SER* 2.8 38.0 + - - +
204B LEU 3.9 0.9 + - - -
209B TYR* 4.9 0.4 - - - +
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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