Contacts of the strand formed by residues 168 - 177 (chain C) in PDB entry 3O8E
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 LEU 168 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165C THR* 3.0 36.8 + - - +
167C ALA* 1.3 84.7 - - + +
169C VAL* 1.3 67.6 + - - +
319C TYR* 4.6 21.3 - - + -
320C TYR* 3.4 28.3 - - - +
321C ILE* 3.8 19.5 - - + -
322C ARG* 3.8 6.7 - - - -
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Residues in contact with VAL 169 (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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162C LEU* 3.9 26.0 - - + -
163C VAL 3.4 10.5 - - - +
164C LYS* 4.7 5.8 - - + -
168C LEU* 1.3 77.0 - - - +
170C THR* 1.3 62.8 + - - +
171C ALA 3.3 5.9 + - - -
234C GLY 4.1 4.0 - - - +
235C PHE* 4.1 16.2 - - + +
318C PHE 3.6 8.0 - - - +
319C TYR* 3.7 5.8 - - - -
320C TYR* 3.1 53.4 + - + +
322C ARG* 3.6 31.2 - - + -
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Residues in contact with THR 170 (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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161C THR 3.2 6.6 - - - +
162C LEU* 3.6 0.2 - - - -
163C VAL* 2.8 47.1 + - + +
165C THR* 2.8 27.9 + - - +
169C VAL* 1.3 68.5 - - - +
171C ALA* 1.3 58.4 + - - +
172C PHE* 3.9 4.1 + - + +
317C THR* 3.9 14.1 - - + -
319C TYR* 3.2 35.7 + - + +
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Residues in contact with ALA 171 (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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160C LEU* 5.4 1.8 - - + -
161C THR 3.5 4.0 - - - -
162C LEU* 3.9 19.3 - - + -
169C VAL 3.3 0.8 + - - -
170C THR* 1.3 72.4 - - - +
172C PHE* 1.3 59.1 + - - +
173C VAL 4.2 0.2 - - - -
316C PHE 3.4 1.9 - - - +
317C THR* 3.1 10.6 - - - +
318C PHE* 3.0 73.9 + - + +
320C TYR* 4.1 6.5 - - + -
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Residues in contact with PHE 172 (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 ILE* 3.4 4.9 - - + +
160C LEU* 3.3 6.0 - - - +
161C THR* 2.8 63.8 + - + +
170C THR* 5.0 4.0 - - + +
171C ALA* 1.3 73.0 - - - +
173C VAL* 1.4 61.0 + - - +
174C TYR* 3.5 28.0 - + - -
315C PRO* 3.5 30.7 - - + -
316C PHE 3.5 2.7 - - - -
317C THR* 3.7 20.2 - - + +
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Residues in contact with VAL 173 (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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158C LEU* 3.9 24.2 - - + -
159C ILE 3.3 8.7 - - - +
160C LEU* 3.8 20.9 - - + -
172C PHE* 1.4 75.4 - - - +
174C TYR* 1.4 66.3 + - - +
292C ILE* 3.9 27.1 - - + -
294C TRP* 4.0 11.5 + - + -
314C SER 4.3 0.9 - - - +
316C PHE* 3.0 43.9 + - + +
318C PHE* 3.9 26.9 - - + -
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Residues in contact with TYR 174 (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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138C VAL* 6.0 2.3 - - - +
139C ASN 5.9 0.7 + - - -
157C LYS 4.0 0.3 - - - +
158C LEU* 4.4 0.9 - - - +
159C ILE* 2.9 61.7 + - + +
172C PHE* 3.5 26.9 - + - -
173C VAL* 1.4 76.3 - - - +
175C VAL* 1.3 67.0 + - - +
176C ILE* 3.7 30.9 - - + +
294C TRP* 4.4 5.4 - - - +
312C VAL* 5.1 4.7 - - + -
313C THR* 3.4 30.1 - - - +
314C SER 3.9 0.7 - - - +
315C PRO* 3.8 32.5 - - + -
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Residues in contact with VAL 175 (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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147C ILE* 3.9 20.2 - - + -
156C CYS* 4.3 9.9 - - - -
157C LYS 3.7 2.0 - - - +
158C LEU* 3.8 26.9 - - + -
174C TYR* 1.3 76.0 - - - +
176C ILE* 1.3 65.1 + - - +
182C PHE* 4.1 15.9 - - + -
193C PHE* 3.8 23.8 - - + -
294C TRP* 4.1 8.5 - - + -
311C LEU* 4.1 2.5 - - + +
312C VAL* 3.4 6.4 - - - +
313C THR* 3.1 46.7 + - + +
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Residues in contact with ILE 176 (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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139C ASN* 4.2 20.4 - - + +
156C CYS* 3.4 3.9 - - - +
157C LYS* 2.8 55.1 + - + +
159C ILE* 3.8 21.1 - - + -
174C TYR* 3.7 29.6 - - + +
175C VAL* 1.3 76.8 - - - +
177C GLY* 1.3 70.5 + - - +
178C VAL* 4.0 0.3 - - - +
182C PHE* 4.5 0.4 - - - -
310C THR* 4.4 4.3 - - + -
311C LEU 3.7 2.0 - - - -
312C VAL* 4.1 21.5 - - + -
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Residues in contact with GLY 177 (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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156C CYS* 4.5 0.2 - - - -
157C LYS* 5.6 0.2 - - - -
176C ILE* 1.3 80.5 - - - +
178C VAL* 1.3 62.0 + - - +
182C PHE* 3.6 19.3 - - - -
183C ASN* 3.3 23.6 + - - -
310C THR* 3.4 17.1 - - - +
311C LEU 2.9 13.2 + - - -
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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