Contacts of the strand formed by residues 174 - 183 (chain C) in PDB entry 2P80
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 LYS 174 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C TYR* 3.4 4.7 - - - -
173C ASP* 1.3 91.9 - - + +
175C ILE* 1.3 62.0 - - - +
176C TYR* 2.5 37.0 + - + -
234C THR* 2.8 34.5 + - - +
235C ALA* 4.6 0.6 - - - +
239C GLU* 3.6 26.2 - - - +
240C LYS 3.2 3.2 + - - -
241C VAL* 3.0 21.7 - - + +
242C LEU 2.9 23.2 + - - -
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Residues in contact with ILE 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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23C PRO 4.3 0.7 - - - +
24C PHE* 4.9 0.2 - - - -
25C VAL* 3.9 31.1 + - + +
28C HIS* 3.9 24.0 - - + +
72C LEU* 4.7 1.3 - - + -
155C MET* 3.3 35.7 - - + -
172C TYR* 3.9 19.3 - - + +
174C LYS* 1.3 76.8 - - - +
176C TYR* 1.3 79.7 + - - +
177C TYR* 6.1 0.2 - - + -
242C LEU* 3.2 28.3 - - + +
244C VAL* 4.5 6.3 - - + -
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Residues in contact with TYR 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PRO* 3.4 21.1 - - + +
24C PHE* 3.6 33.2 - + - -
25C VAL* 4.8 0.4 - - - -
174C LYS* 2.5 51.8 + - + -
175C ILE* 1.3 83.7 - - - +
177C TYR* 1.3 61.5 + - - +
178C VAL* 4.0 0.9 - - + -
233C MET* 3.5 44.2 - - + -
234C THR* 3.4 18.9 + - - -
241C VAL* 3.9 16.6 - - + -
242C LEU 3.1 7.2 + - - +
243C ILE* 3.4 10.0 - - + +
244C VAL* 3.0 24.9 + - - +
320C PHE* 4.4 6.1 - + + -
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Residues in contact with TYR 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C PRO* 4.0 16.2 - - + +
23C PRO* 2.9 34.0 + - - +
24C PHE 5.4 0.7 - - - +
25C VAL* 4.4 7.2 - - + +
69C PRO* 3.7 15.8 - - + +
70C GLY 3.6 19.7 - - - -
72C LEU* 3.7 33.2 - - + -
152C GLY* 3.2 18.2 - - - -
153C ALA* 3.9 17.3 - - + -
176C TYR* 1.3 73.9 - - - +
178C VAL* 1.3 65.5 + - - +
179C GLY* 3.7 15.7 + - - -
221C ASN* 5.3 0.9 + - - -
244C VAL* 3.4 20.9 - - + -
245C HIS 4.4 0.4 - - - -
246C SER* 2.7 38.1 + - - -
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Residues in contact with VAL 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PRO* 4.7 1.3 - - + -
177C TYR* 1.3 78.5 - - - +
179C GLY* 1.3 58.9 + - - +
220C PHE* 3.5 40.8 - - + -
221C ASN* 6.1 0.7 - - - +
227C LEU* 3.6 24.5 - - + -
233C MET* 4.3 17.5 - - + -
243C ILE* 4.5 13.7 - - + -
244C VAL 2.9 11.5 + - - +
245C HIS* 3.2 45.5 - - + +
303C TYR* 4.7 8.7 - - + -
318C ALA* 5.7 0.7 - - + -
320C PHE* 4.9 2.7 - - + -
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Residues in contact with GLY 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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69C PRO* 3.0 35.8 - - - +
177C TYR* 3.7 16.7 + - - -
178C VAL* 1.3 72.2 - - - +
180C GLU* 1.3 64.2 + - - -
181C GLN* 3.9 1.4 + - - +
219C VAL 3.9 0.2 - - - +
220C PHE* 3.5 1.5 - - - -
221C ASN* 3.2 25.7 + - - +
222C GLY 4.9 0.5 + - - -
246C SER* 3.7 5.8 - - - -
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Residues in contact with GLU 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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69C PRO* 5.5 0.5 - - - +
151C ASN* 4.7 6.6 - - - +
179C GLY* 1.3 75.0 - - - -
181C GLN* 1.3 67.7 + - - +
218C VAL* 2.7 29.7 - - + +
219C VAL 3.2 8.5 - - - +
220C PHE* 3.2 27.6 - - + -
245C HIS* 2.9 20.3 + - - +
246C SER 3.0 12.8 + - - +
247C GLN* 3.7 28.5 + - + +
248C ALA 4.9 0.7 + - - -
250C ARG* 5.3 2.6 - - - +
252C THR* 3.0 31.9 + - - -
305C ASN* 3.8 13.7 + - - +
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Residues in contact with GLN 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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68C VAL* 4.3 11.2 - - + +
69C PRO* 6.0 1.1 - - + +
146C VAL 3.2 17.4 + - - +
147C VAL* 3.3 21.6 + - - +
149C GLY* 3.4 8.8 - - - -
151C ASN* 2.8 30.3 + - - +
179C GLY 5.0 2.5 - - - +
180C GLU* 1.3 78.9 - - - +
182C ASP* 1.3 81.4 + - - +
183C PHE* 3.2 39.3 + - + -
217C HIS 3.6 1.6 - - - +
218C VAL* 3.5 2.3 - - - -
219C VAL* 2.9 34.5 + - + +
222C GLY 5.4 2.7 - - - +
247C GLN* 4.2 1.3 - - - +
249C ASN* 4.9 4.2 - - - +
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Residues in contact with ASP 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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147C VAL* 4.2 2.6 - - - +
181C GLN* 1.3 91.1 + - - +
183C PHE* 1.3 60.4 + - - +
184C TYR* 2.5 34.0 + - - -
215C PRO* 3.7 17.9 - - + -
217C HIS 3.6 5.8 - - - -
218C VAL* 4.0 4.9 - - + -
247C GLN* 2.9 20.3 + - - +
249C ASN* 2.9 31.6 + - - +
250C ARG* 3.6 16.0 - - - +
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Residues in contact with PHE 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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50C ILE* 4.6 9.0 - - + -
52C ILE* 4.2 27.6 - - + -
59C VAL* 3.9 28.3 - - + -
68C VAL* 4.5 12.3 - - + -
147C VAL* 2.7 31.6 - - - -
148C SER 3.9 6.3 - - - -
149C GLY* 4.7 0.9 - - - -
181C GLN* 3.2 33.0 - - + -
182C ASP* 1.3 71.6 - - - +
184C TYR* 1.3 76.0 + - - +
185C VAL* 4.1 15.9 - - + -
215C PRO* 3.1 19.6 - - - +
216C THR* 3.3 5.1 + - - +
217C HIS* 2.9 18.2 + - + +
219C VAL* 4.5 14.1 - - + -
222C GLY* 4.6 5.4 - - - -
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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