Contacts of the strand formed by residues 174 - 183 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A TYR* 3.4 7.2 - - - +
173A ASP* 1.3 80.3 - - - +
175A ILE* 1.3 62.9 + - - +
176A TYR* 2.6 38.4 + - + -
234A THR* 2.5 42.8 + - - +
235A ALA* 4.1 2.0 - - - +
239A GLU* 3.8 20.4 + - - +
240A LYS 3.4 0.8 + - - +
241A VAL* 2.9 40.6 - - + -
242A LEU 3.0 20.1 + - - -
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Residues in contact with ILE 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 5.0 0.2 - - - -
25A VAL* 3.6 28.8 + - + +
28A HIS* 4.1 18.2 - - + +
72A LEU* 4.7 3.4 - - + -
155A MET* 3.3 35.7 - - + -
172A TYR* 4.0 22.7 - - + -
174A LYS* 1.3 79.3 - - - +
176A TYR* 1.3 79.5 + - - +
241A VAL* 4.6 0.4 - - - -
242A LEU* 3.2 29.8 - - + +
244A VAL* 4.2 7.2 - - + -
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Residues in contact with TYR 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PRO* 3.4 22.0 - - + +
24A PHE* 4.0 29.3 - + - -
25A VAL* 4.7 0.4 - - - -
174A LYS* 2.6 54.2 + - + -
175A ILE* 1.3 83.8 - - - +
177A TYR* 1.3 60.7 + - - +
178A VAL* 4.0 2.4 + - + -
233A MET* 3.6 43.3 - - + -
234A THR* 3.6 13.5 + - - -
241A VAL* 4.0 13.9 - - + -
242A LEU 3.0 7.0 + - - +
243A ILE* 3.5 7.8 - - + +
244A VAL* 3.0 25.5 + - - +
320A PHE* 4.3 4.5 - + + -
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Residues in contact with TYR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PRO* 4.1 13.3 - - + +
23A PRO* 2.9 35.0 + - - +
24A PHE 4.9 0.4 - - - +
25A VAL* 4.5 5.8 - - + +
69A PRO* 3.6 11.1 - - + +
70A GLY 3.7 19.3 - - - -
72A LEU* 3.8 36.8 - - + -
152A GLY* 3.3 17.8 - - - -
153A ALA* 3.9 17.9 - - + -
175A ILE* 6.1 0.2 - - + -
176A TYR* 1.3 72.9 - - - +
178A VAL* 1.3 65.9 + - - +
179A GLY* 3.6 19.0 + - - -
221A ASN* 5.2 0.7 + - - -
244A VAL* 3.4 21.5 - - + -
245A HIS 4.4 0.7 - - - -
246A SER* 2.4 40.4 + - - -
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Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PRO* 4.6 0.7 - - + -
177A TYR* 1.3 78.7 - - - +
179A GLY* 1.3 58.3 + - - +
220A PHE* 3.5 39.5 - - + -
221A ASN* 5.8 0.9 - - - +
227A LEU* 3.8 22.2 - - + -
233A MET* 4.3 21.5 - - + -
243A ILE* 4.5 13.9 - - + -
244A VAL 2.8 10.3 + - - +
245A HIS* 3.2 44.5 - - + +
303A TYR* 4.6 10.1 - - + -
318A ALA* 5.7 0.9 - - + -
320A PHE* 4.9 2.2 - - + -
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Residues in contact with GLY 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A PRO* 3.1 34.0 - - - +
177A TYR* 3.6 18.4 + - - -
178A VAL* 1.3 72.4 - - - +
180A GLU* 1.3 62.8 + - - -
181A GLN* 4.0 1.2 + - - +
219A VAL 3.8 0.2 - - - +
220A PHE* 3.4 3.3 - - - -
221A ASN* 3.2 24.8 + - - +
222A GLY 4.9 0.3 + - - -
245A HIS* 4.4 0.2 - - - -
246A SER* 3.8 5.6 - - - -
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Residues in contact with GLU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A PRO* 5.6 0.7 - - - +
151A ASN* 4.7 6.6 - - - +
178A VAL 3.6 1.2 + - - -
179A GLY* 1.3 74.9 - - - -
181A GLN* 1.3 69.9 + - - +
218A VAL* 2.7 29.6 - - + +
219A VAL 3.2 6.7 - - - +
220A PHE* 3.2 29.2 - - + -
245A HIS* 3.0 19.4 + - - +
246A SER 3.0 16.0 + - - +
247A GLN* 3.9 25.7 + - + +
248A ALA 5.0 0.9 + - - -
250A ARG* 5.1 3.3 - - - +
252A THR* 3.1 31.6 + - - -
305A ASN* 3.8 12.3 + - - +
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Residues in contact with GLN 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A VAL* 4.3 12.1 - - + +
69A PRO* 6.0 1.5 - - + +
146A VAL* 3.2 21.4 + - - +
147A VAL* 3.3 21.1 + - - +
149A GLY* 3.3 8.4 - - - -
151A ASN* 2.7 30.3 + - - +
179A GLY 5.1 1.8 - - - +
180A GLU* 1.3 78.5 - - - +
182A ASP* 1.3 82.2 + - - +
183A PHE* 3.2 39.7 + - + -
217A HIS 3.6 1.9 - - - +
218A VAL* 3.5 2.9 - - - -
219A VAL* 2.9 34.8 + - + +
222A GLY* 5.6 1.8 - - - +
247A GLN* 4.4 1.3 - - - -
249A ASN* 5.9 0.4 - - - +
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Residues in contact with ASP 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A VAL* 4.2 2.5 - - - +
181A GLN* 1.3 90.6 + - - +
183A PHE* 1.3 61.9 + - - +
184A TYR* 2.4 37.0 + - - -
215A PRO* 3.6 22.9 - - + -
217A HIS 3.5 6.1 - - - -
218A VAL* 4.1 8.5 - - + +
247A GLN* 3.0 19.5 + - - +
249A ASN* 3.5 17.8 + - - +
250A ARG* 3.5 20.9 - - - +
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Residues in contact with PHE 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE* 5.4 5.4 - - + -
52A ILE* 3.4 42.6 - - + -
59A VAL* 4.1 20.4 - - + -
68A VAL* 4.5 13.2 - - + -
147A VAL 2.8 31.6 - - - -
148A SER 3.7 15.0 - - - -
181A GLN* 3.2 32.5 - - + -
182A ASP* 1.3 71.0 - - - +
184A TYR* 1.3 78.2 + - - +
185A VAL* 4.0 9.2 - - + -
215A PRO* 3.1 18.5 - - - +
216A THR* 3.2 7.3 + - - +
217A HIS* 2.9 15.9 + - + +
219A VAL* 4.5 14.1 - - + -
222A GLY* 4.8 5.2 - - - -
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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