Contacts of the strand formed by residues 154 - 159 (chain A) in PDB entry 2UVQ
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 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A PHE* 4.1 18.8 - - + -
25A LEU 3.4 2.3 + - - +
26A ILE* 3.4 24.4 - - + +
27A GLY 3.0 25.6 + - - +
152A PHE* 3.9 0.9 - - - +
153A HIS* 1.3 82.2 - - - +
155A ARG* 1.3 70.7 + - - +
156A LEU* 4.2 17.0 - - + -
207A ASP* 3.8 17.9 - - + +
208A VAL* 4.6 9.2 - - + -
223A ILE* 4.1 24.9 - - + -
226A HIS* 4.8 12.6 - - + +
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Residues in contact with ARG 155 (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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27A GLY 3.5 3.6 - - - -
143A PHE* 3.7 28.9 - - + -
149A ARG* 3.3 39.4 + - - +
150A ASP* 4.4 7.9 + - - +
152A PHE* 3.8 18.8 + - + +
154A LEU* 1.3 80.1 - - - +
156A LEU* 1.3 64.2 + - - +
205A TYR* 2.9 43.4 + - - +
206A ALA* 3.7 1.2 - - - -
207A ASP* 2.7 57.4 + - - +
208A VAL 3.2 9.4 + - - +
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Residues in contact with LEU 156 (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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26A ILE* 3.8 26.5 - - + -
27A GLY 2.7 11.9 + - - +
28A VAL* 3.3 19.2 - - + -
29A SER 2.8 24.8 + - - -
39A VAL* 6.5 0.9 - - + -
43A ILE* 5.8 3.6 - - + -
136A LEU* 6.0 0.7 - - + -
143A PHE* 3.3 7.6 - - - -
154A LEU* 4.2 9.9 - - + -
155A ARG* 1.3 77.4 - - - +
157A PHE* 1.3 61.0 + - - +
206A ALA* 4.7 0.2 - - - -
208A VAL* 3.5 36.6 - - + +
210A ILE* 4.1 18.6 - - + -
223A ILE* 3.7 35.7 - - + -
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Residues in contact with PHE 157 (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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29A SER* 4.0 9.4 - - - -
30A GLY* 3.7 27.1 - - - -
31A GLY 4.7 2.2 - - - -
143A PHE* 4.6 5.2 - + - -
156A LEU* 1.3 74.3 - - - +
158A VAL* 1.3 77.4 + - - +
159A ASP* 3.3 16.1 + - + -
195A PHE* 5.4 2.7 - + - -
199A CYS* 4.3 17.3 - - - -
200A LEU* 4.8 10.1 - - + -
202A THR* 4.4 3.4 - - - -
203A LYS* 3.6 58.1 - - + -
206A ALA* 3.5 20.2 - - + -
208A VAL 3.2 6.7 + - - -
209A ILE* 3.4 8.8 - - + +
210A ILE* 2.8 27.7 + - - +
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Residues in contact with VAL 158 (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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28A VAL* 4.0 19.1 - - + -
29A SER 3.2 16.8 + - - +
30A GLY* 3.6 9.7 - - - -
31A GLY 4.3 0.5 + - - -
34A SER* 3.1 50.1 - - - +
35A GLY* 4.2 4.9 - - - +
36A LYS* 4.3 12.1 - - - +
39A VAL* 4.7 8.7 - - + -
157A PHE* 1.3 76.0 - - - +
159A ASP* 1.3 60.8 + - - +
160A THR* 3.5 0.6 + - - +
210A ILE* 3.4 22.0 - - + +
212A ARG 4.0 10.3 - - - +
213A GLY* 4.1 11.2 - - - -
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Residues in contact with ASP 159 (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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157A PHE* 3.3 15.4 + - + -
158A VAL* 1.3 70.6 - - - +
160A THR* 1.3 64.0 + - - +
161A ASP* 5.0 7.9 - - - +
200A LEU* 5.3 3.5 - - - +
203A LYS* 3.1 31.2 + - - +
209A ILE* 3.6 23.8 - - + +
210A ILE 2.9 8.8 + - - +
211A PRO* 3.5 6.5 - - + +
212A ARG 3.1 24.1 + - - -
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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