Contacts of the strand formed by residues 176 - 181 (chain C) in PDB entry 3P8Z
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 176 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A PRO* 3.5 20.6 - - - +
71C VAL* 3.6 9.3 - - + -
72C ILE* 2.8 55.1 + - + +
74C GLU* 3.8 18.4 + - - +
141C ASP 3.1 10.7 + - - +
142C THR* 3.3 7.5 - - - +
143C LEU* 2.8 25.9 + - - +
175C ASN* 1.3 77.8 - - - +
177C PHE* 1.3 60.1 + - - +
221C SER* 3.3 5.9 + - - -
222C ASN* 2.8 33.7 + - - +
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Residues in contact with PHE 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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71C VAL* 3.4 12.5 - - - +
143C LEU 3.0 15.5 - - - +
172C LEU* 3.9 36.3 - - + -
175C ASN* 3.5 16.8 - - - -
176C GLN* 1.3 74.7 - - - +
178C CYS* 1.3 63.4 + - - +
179C ILE* 3.8 12.6 - - + -
200C HIS* 4.5 15.9 - - + -
201C GLY 4.1 6.1 - - - -
202C GLY* 4.5 0.4 - - - -
219C TRP* 3.5 53.6 - + - -
220C ILE* 3.4 18.0 - - - -
221C SER* 3.1 45.7 + - - -
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Residues in contact with CYS 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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62C LEU* 4.5 3.1 - - + -
65C PHE* 3.7 30.5 - - - -
71C VAL* 3.9 20.8 - - + +
87C TRP* 3.9 11.2 - - + -
143C LEU 3.0 5.7 + - - -
144C LEU* 3.3 14.3 - - + -
145C CYS 3.0 24.3 + - - +
177C PHE* 1.3 76.4 - - - +
179C ILE* 1.3 61.7 + - - +
218C TYR* 3.9 16.8 - - - -
219C TRP 3.4 4.7 - - - -
220C ILE* 4.0 11.9 - - + -
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Residues in contact with ILE 179 (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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143C LEU* 3.9 25.6 - - + -
145C CYS* 3.4 10.8 - - + -
164C VAL* 4.4 7.0 - - + -
165C LEU* 4.7 10.1 - - + -
168C VAL* 3.8 40.4 - - + -
172C LEU* 4.1 9.4 - - + -
177C PHE* 3.8 23.6 - - + -
178C CYS* 1.3 79.6 - - - +
180C LYS* 1.3 75.2 + - - +
181C VAL* 3.4 2.1 + - + +
218C TYR* 3.3 3.8 - - - -
219C TRP* 2.8 50.4 + - + +
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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
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145C CYS 2.8 13.3 + - - +
146C ASP* 3.5 31.0 + - - +
147C ILE 3.7 10.9 - - - +
148C GLY* 2.5 49.4 + - - +
161C THR* 5.7 0.5 - - - +
164C VAL* 4.3 8.1 - - - +
165C LEU* 5.4 0.7 - - - +
179C ILE* 1.3 82.6 - - - +
181C VAL* 1.3 66.2 + - - +
182C LEU* 3.8 19.3 + - - +
216C GLU* 3.7 27.1 + - + +
217C MET 3.7 0.2 - - - -
218C TYR* 3.5 28.7 - - + +
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Residues in contact with VAL 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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161C THR* 3.7 24.0 - - + -
165C LEU* 4.4 9.2 - - + -
179C ILE* 3.8 9.4 - - + +
180C LYS* 1.3 77.2 - - - +
182C LEU* 1.3 66.9 + - - +
183C ASN 4.0 0.2 - - - +
184C PRO* 3.7 29.3 - - + +
189C VAL* 4.2 0.2 - - + -
193C LEU* 4.1 22.2 - - + -
204C LEU* 3.8 22.7 - - + -
216C GLU* 3.4 0.3 - - - -
217C MET 2.6 36.6 + - - +
219C TRP* 4.1 8.7 - - + -
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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