Contacts of the strand formed by residues 173 - 179 (chain W) in PDB entry 5A0Q
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 ILE 173 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15W GLY* 5.4 0.7 - - - -
16W ALA 3.2 9.2 - - - +
17W ASP* 4.4 0.9 - - - +
155W VAL 4.7 0.7 - - - +
156W SER* 2.9 43.3 - - - +
159W ILE* 4.0 17.5 - - + -
160W ALA* 4.1 15.0 - - + +
163W ILE* 3.7 19.5 - - + -
171W SER 4.3 0.4 - - - -
172W ASN* 1.3 73.4 - - - +
174W ASP* 1.3 73.3 + - - +
175W LEU* 5.0 5.6 - - + -
189W TYR* 3.0 23.7 + - - +
190W THR* 3.1 41.0 + - + +
192W PRO* 4.3 5.4 - - + -
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Residues in contact with ASP 174 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15W GLY* 3.3 2.6 - - - -
16W ALA* 2.4 46.2 + - + +
17W ASP 5.1 0.2 - - - +
18W THR* 3.1 23.3 - - - +
31W CYS 4.3 5.0 - - - +
32W SER* 4.8 0.3 - - - -
33W LYS 4.7 6.9 + - - -
34W ILE* 4.0 19.9 + - + +
172W ASN 3.6 0.2 - - - +
173W ILE* 1.3 79.6 - - - +
175W LEU* 1.3 64.8 + - - +
185W PHE* 5.1 6.0 - - + -
186W LEU 4.0 6.3 - - - +
187W ARG* 2.7 44.2 + - - +
188W PRO* 4.4 0.3 - - - +
189W TYR* 4.3 0.2 - - - -
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Residues in contact with LEU 175 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13W VAL* 3.4 33.9 - - + -
14W LEU 3.6 4.7 - - - +
15W GLY* 4.3 0.4 - - - -
152W LYS* 3.9 38.4 - - + +
155W VAL* 3.9 17.5 - - + -
156W SER* 4.3 6.5 - - - +
173W ILE* 5.0 2.2 - - + -
174W ASP* 1.3 78.3 - - - +
176W CYS* 1.3 60.6 + - - +
177W VAL* 3.7 21.5 - - + -
186W LEU* 3.1 43.3 + - + +
189W TYR* 3.4 28.9 - - + +
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Residues in contact with CYS 176 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12W ILE 3.8 1.0 - - - +
14W LEU* 2.9 40.9 + - + +
34W ILE* 3.7 26.0 - - + +
42W TYR* 3.3 43.3 - - - -
175W LEU* 1.3 74.2 - - - +
177W VAL* 1.4 60.2 + - - +
178W ILE* 4.7 0.7 - - - +
184W ASP 3.2 17.5 - - - +
185W PHE* 4.0 18.4 - - + -
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Residues in contact with VAL 177 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8W TYR* 3.0 31.6 - - + +
12W ILE 3.9 2.7 - - - -
13W VAL* 4.4 3.8 - - + +
148W GLU* 4.9 2.7 - - + +
152W LYS* 3.6 35.4 - - - +
175W LEU* 3.7 16.6 - - + -
176W CYS* 1.4 73.8 - - - +
178W ILE* 1.3 69.5 + - - +
179W SER* 4.2 6.7 - - - +
183W LEU* 4.0 3.1 - - - +
184W ASP* 3.3 51.8 + - + +
186W LEU* 5.0 2.2 - - + -
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Residues in contact with ILE 178 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8W TYR* 3.6 2.9 + - - -
11W GLY* 3.3 5.5 - - - -
12W ILE* 2.9 51.1 + - + +
14W LEU* 5.3 3.8 - - + -
40W ASN 3.3 21.5 - - - +
41W ILE* 4.8 0.4 - - - +
42W TYR* 3.3 39.7 - - + -
101W GLY 4.6 10.3 - - - +
102W GLY* 4.0 9.6 - - - -
103W VAL* 3.4 28.0 - - + +
176W CYS 4.7 2.7 - - - +
177W VAL* 1.3 76.2 - - - +
179W SER* 1.3 61.7 + - - +
182W LYS 4.9 0.2 - - - -
183W LEU* 3.8 13.5 - - + -
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Residues in contact with SER 179 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8W TYR* 3.6 13.8 + - - -
10W ASP* 3.4 20.9 - - - -
103W VAL* 4.6 5.6 - - - -
148W GLU* 3.8 8.3 + - - -
177W VAL* 4.4 3.5 - - - +
178W ILE* 1.3 77.8 - - - +
180W LYS* 1.4 62.1 + - - +
181W ASN* 3.7 14.1 - - - +
182W LYS* 2.8 42.8 + - - +
183W LEU* 3.3 14.8 - - - +
184W ASP* 5.4 0.2 + - - -
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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