Contacts of the strand formed by residues 177 - 185 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150C ALA* 3.3 26.2 + - + +
171C PRO* 4.1 1.0 - - - +
172C VAL 3.4 6.5 - - - +
173C GLY 3.4 25.2 + - - +
174C GLU* 3.8 8.7 + - - +
175C GLU 4.1 1.0 + - - -
176C HIS* 1.3 72.8 - - - +
178C TYR* 1.3 64.1 + - - +
196C ALA* 3.5 7.3 - - - +
197C VAL* 2.9 40.0 + - + +
198C ARG* 3.4 22.7 - - - +
199C PHE* 2.8 49.8 + - - +
200C VAL 5.3 0.8 - - - -
201C PRO* 5.6 0.6 - - - +
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Residues in contact with TYR 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B THR* 5.2 1.9 + - - -
76B GLN* 3.5 33.9 + - + +
143B ASP* 5.1 10.9 - - - -
172C VAL 3.0 30.6 + - - +
176C HIS* 3.8 35.5 - - + +
177C GLN* 1.3 80.8 - - - +
179C LEU* 1.3 63.3 + - - +
180C LYS* 3.3 20.6 + - - +
193C THR* 3.8 31.2 - - + -
195C GLU 3.4 4.5 - - - +
196C ALA* 4.0 21.1 - - + -
197C VAL* 3.6 4.5 - - - -
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Residues in contact with LEU 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C MET* 4.0 13.5 - - - -
66C ARG* 4.4 5.6 - - + -
67C MET* 3.7 31.4 - - + -
70C LEU* 3.5 29.2 - - + -
169C VAL* 3.5 26.7 - - + -
170C LEU 3.7 17.5 - - - +
171C PRO* 4.1 4.0 - - + -
178C TYR* 1.3 70.2 - - - +
180C LYS* 1.3 59.3 + - - +
193C THR* 3.8 1.0 - - - +
194C VAL* 2.8 39.7 + - + +
195C GLU* 2.9 15.0 + - + +
197C VAL* 3.4 21.3 - - + +
199C PHE* 5.3 0.2 - - + -
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Residues in contact with LYS 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C ILE* 5.0 4.4 - - + +
168C LEU 3.9 0.5 - - - +
169C VAL* 3.4 6.5 - - - +
170C LEU* 2.7 41.4 + - + +
172C VAL* 4.0 28.4 + - + +
178C TYR* 3.6 26.7 - - - +
179C LEU* 1.3 78.6 - - - +
181C ARG* 1.3 61.2 + - - +
182C VAL* 4.2 0.7 - - + -
191C ILE* 4.0 24.9 - - + +
192C ASP 3.4 9.6 - - - +
193C THR* 3.7 19.0 + - - +
194C VAL* 4.6 1.8 - - - -
156D THR* 4.2 22.6 - - - +
159D MET* 5.5 6.7 - - - +
160D THR* 5.4 2.8 + - - -
189D PHE* 5.7 7.1 - - - -
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Residues in contact with ARG 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C LEU* 3.9 33.5 + - + +
72C GLU* 4.3 6.1 + - - -
167C ILE* 3.8 23.3 - - + -
168C LEU 3.3 4.3 - - - -
169C VAL* 4.6 5.6 - - + +
179C LEU 4.4 0.2 + - - -
180C LYS* 1.3 73.4 - - - +
182C VAL* 1.3 67.3 + - - +
183C ARG* 3.7 33.2 - - + +
190C ILE 3.5 0.9 - - - +
191C ILE* 3.4 3.5 - - - +
192C ASP* 2.8 67.4 + - - +
194C VAL* 4.3 13.1 - - + +
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Residues in contact with VAL 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C ILE* 4.2 17.5 - - + -
159C MET* 4.0 29.8 - - + -
162C LEU* 4.0 7.9 - - + +
166C GLY 3.9 0.5 - - - +
167C ILE* 3.3 3.8 - - - +
168C LEU* 2.7 71.1 + - + +
170C LEU* 4.2 12.8 - - + -
180C LYS 4.9 0.4 - - - -
181C ARG* 1.3 80.4 - - - +
183C ARG* 1.3 60.0 + - - +
189C PHE* 4.4 11.2 - - + -
190C ILE 3.2 6.3 - - - +
191C ILE* 4.3 11.7 - - + -
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Residues in contact with ARG 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C GLU* 3.1 39.0 + - - -
165C GLY* 4.8 5.8 + - - +
166C GLY 3.5 9.6 - - - +
167C ILE* 3.6 15.2 - - + +
181C ARG* 3.7 34.7 - - + +
182C VAL* 1.3 78.0 - - - +
184C ARG* 1.3 70.1 + - - +
185C ARG* 3.8 27.2 + - + +
189C PHE* 3.2 4.5 - - - -
190C ILE* 2.8 43.0 + - + +
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Residues in contact with ARG 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C MET 3.5 8.9 + - - -
160C THR* 3.2 21.8 + - - +
162C LEU* 2.7 42.2 + - + +
163C ASP 3.6 19.2 - - - +
164C GLU* 4.5 5.0 + - - +
165C GLY* 3.2 25.8 + - - -
166C GLY 3.0 11.1 + - - +
182C VAL 4.3 0.2 - - - -
183C ARG* 1.3 75.1 - - - +
185C ARG* 1.3 62.0 + - - +
186C GLY 3.6 23.4 + - - +
187C GLY* 5.5 3.2 - - - -
188C GLU 3.5 6.1 - - - +
189C PHE* 3.8 34.1 - - + -
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Residues in contact with ARG 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C GLU* 4.0 0.9 - - - -
183C ARG* 3.8 23.3 + - + +
184C ARG* 1.3 72.6 - - - +
186C GLY* 1.3 62.1 + - - +
187C GLY 3.3 0.9 + - - -
188C GLU* 2.9 38.2 + - + +
190C ILE* 3.8 40.5 - - + +
188D GLU* 5.7 2.0 + - - -
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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