Contacts of the strand formed by residues 177 - 185 (chain B) in PDB entry 3LBF
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 GLN 177 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B ALA* 3.3 25.0 + - + +
172B VAL 3.1 10.5 - - - +
173B GLY* 3.6 16.1 + - - +
174B GLU* 3.0 26.4 + - - +
175B GLU 3.9 1.8 + - - -
176B HIS* 1.3 73.7 - - - +
178B TYR* 1.3 70.0 + - - +
196B ALA* 3.5 4.7 - - - +
197B VAL* 3.2 36.4 + - + +
198B ARG* 3.4 10.3 + - + +
199B PHE* 2.7 48.9 + - - +
200B VAL 5.3 0.8 - - - -
201B PRO* 5.6 1.6 - - - +
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Residues in contact with TYR 178 (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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172B VAL 2.9 28.4 + - - +
176B HIS* 3.7 25.1 - - + +
177B GLN* 1.3 78.8 - - - +
179B LEU* 1.3 64.2 + - - +
180B LYS* 3.5 22.6 + - - +
193B THR* 3.8 26.7 - - + -
195B GLU* 3.3 8.1 - - - +
196B ALA* 3.5 35.2 - - + +
197B VAL* 3.8 4.9 - - - -
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Residues in contact with LEU 179 (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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63B MET* 4.3 12.8 - - - -
66B ARG* 4.6 6.1 - - + -
67B MET* 3.8 30.3 - - + -
70B LEU* 3.8 25.6 - - + -
169B VAL* 3.7 23.8 - - + -
170B LEU 3.7 17.5 - - - +
171B PRO* 3.9 6.5 - - + -
178B TYR* 1.3 72.9 - - - +
180B LYS* 1.3 58.3 + - - +
193B THR* 3.7 3.8 - - - +
194B VAL* 2.8 45.0 + - + -
195B GLU* 2.7 19.7 + - + +
197B VAL* 3.5 13.6 - - + +
199B PHE* 5.3 0.7 - - + -
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Residues in contact with LYS 180 (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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156A THR* 5.8 7.6 - - - +
189A PHE* 6.3 1.0 - - - -
154B ILE* 5.0 4.7 - - + -
168B LEU 3.8 0.3 - - - +
169B VAL* 3.4 7.6 - - - +
170B LEU* 2.8 45.3 + - + +
172B VAL* 3.6 29.7 + - + -
178B TYR* 3.5 31.6 - - + +
179B LEU* 1.3 77.0 - - - +
181B ARG* 1.3 61.2 + - - +
191B ILE* 4.4 20.9 - - + -
192B ASP 3.3 7.4 - - - +
193B THR* 3.2 29.4 + - - +
194B VAL* 4.7 2.5 - - - -
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Residues in contact with ARG 181 (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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70B LEU* 4.0 33.0 + - + +
72B GLU* 4.5 4.9 + - - -
167B ILE* 3.9 22.9 - - + -
168B LEU 3.3 3.6 - - - -
169B VAL* 4.6 6.3 - - + +
180B LYS* 1.3 74.1 - - - +
182B VAL* 1.3 63.9 + - - +
183B ARG* 3.5 39.7 - - + +
190B ILE 3.4 1.2 - - - +
191B ILE* 3.4 3.3 - - - +
192B ASP* 2.6 68.4 + - - +
194B VAL* 4.5 15.3 - - + +
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Residues in contact with VAL 182 (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 ILE* 3.9 19.7 - - + -
159B MET* 4.1 16.6 - - + -
162B LEU* 4.1 3.5 - - + +
166B GLY 3.9 0.5 - - - +
167B ILE* 3.3 2.8 - - - -
168B LEU* 2.6 61.3 + - + +
170B LEU* 4.6 4.5 - - + -
180B LYS* 5.1 0.9 - - + -
181B ARG* 1.3 79.7 - - - +
183B ARG* 1.3 63.1 + - - +
189B PHE* 4.0 32.3 - - + -
190B ILE 3.3 5.2 - - - +
191B ILE* 3.9 22.0 - - + -
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Residues in contact with ARG 183 (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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72B GLU* 2.9 39.1 + - - -
165B GLY 5.7 2.1 + - - +
166B GLY 3.5 7.0 - - - +
167B ILE* 3.7 15.4 - - + +
181B ARG* 3.5 42.8 - - + +
182B VAL* 1.3 79.0 - - - +
184B ARG* 1.3 63.7 + - - +
185B ARG* 3.7 29.5 + - + +
189B PHE* 3.3 4.8 - - - -
190B ILE* 2.9 46.5 + - + +
192B ASP* 5.2 2.9 - - - +
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Residues in contact with ARG 184 (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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159B MET 3.4 9.1 + - - -
160B THR* 3.1 22.8 + - - +
162B LEU* 2.6 41.8 + - + +
163B ASP 3.6 17.0 - - - +
164B GLU* 3.8 6.5 - - - +
165B GLY* 3.1 26.3 + - - -
166B GLY 2.9 12.1 + - - +
182B VAL 4.3 0.2 + - - -
183B ARG* 1.3 72.9 - - - +
185B ARG* 1.3 60.6 + - - +
186B GLY 3.4 23.9 + - - +
187B GLY* 5.1 2.4 + - - -
188B GLU 3.4 7.6 - - - +
189B PHE* 3.6 34.4 - - + -
15C ALA 5.1 3.0 + - - -
16C GLN* 3.5 39.4 + - - +
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Residues in contact with ARG 185 (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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188A GLU* 4.9 11.9 + - - -
164B GLU* 3.6 4.7 - - - -
183B ARG* 3.7 27.3 + - + +
184B ARG* 1.3 73.9 - - - +
186B GLY* 1.3 58.8 + - - +
187B GLY 3.0 0.7 + - - -
188B GLU* 2.8 41.0 + - + +
190B ILE* 3.6 41.9 - - + +
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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