Contacts of the strand formed by residues 148 - 153 (chain A) in PDB entry 6UPQ
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 CYS 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A PHE* 3.8 19.1 - - + -
39A THR 3.5 1.4 + - - -
40A LEU* 3.5 9.4 - - + -
41A MET 2.8 30.7 + - - -
146A VAL* 3.4 7.0 + - - +
147A HIS* 1.3 80.9 - - - +
149A CYS* 1.3 58.1 + - - +
150A PHE* 3.8 21.1 - - - -
175A VAL* 3.9 5.1 - - - +
176A ASN 3.4 9.4 - - - -
178A VAL* 3.5 30.5 - - - -
279A MET* 5.9 0.2 - - - -
280A LEU* 4.8 2.0 - - - -
287A LEU* 4.3 15.3 - - + -
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Residues in contact with CYS 149 (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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41A MET* 3.2 18.2 - - + -
43A VAL* 3.8 29.6 - - - -
148A CYS* 1.3 73.4 - - - +
150A PHE* 1.3 73.7 + - - +
151A TYR* 3.4 5.6 + - - -
167A PHE* 4.3 3.4 - - - -
171A ILE* 4.1 18.4 - - + -
175A VAL* 3.8 24.9 - - + -
176A ASN 2.8 9.4 + - - +
177A ILE* 3.6 3.9 - - - +
178A VAL 2.8 27.1 + - - -
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Residues in contact with PHE 150 (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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40A LEU* 3.6 30.7 - - + +
41A MET 2.8 12.0 + - - +
42A VAL* 3.7 2.8 - - + -
43A VAL 3.0 27.0 + - - +
53A LEU* 5.0 0.4 - - + -
54A ILE* 4.2 12.1 - - + -
57A LEU* 3.8 25.6 - - + -
148A CYS* 3.8 13.0 - - - -
149A CYS* 1.3 71.5 - - - +
151A TYR* 1.3 58.8 + - - +
152A PHE* 3.6 26.0 + + + -
178A VAL* 3.4 30.3 - - + +
180A VAL* 4.4 4.7 - - + -
276A LEU* 3.7 26.0 - - + -
279A MET* 4.9 1.6 - - + -
280A LEU* 4.2 23.6 - - + -
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Residues in contact with TYR 151 (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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43A VAL* 3.4 20.2 - - + -
44A GLY* 4.9 0.4 - - - -
45A GLU* 5.5 0.7 + - - +
105A TYR* 2.7 36.8 + + - -
149A CYS* 3.4 6.0 + - - +
150A PHE* 1.3 71.5 - - - +
152A PHE* 1.3 75.8 + - - +
153A ILE* 3.6 14.5 + - + +
163A LEU* 4.7 0.3 - - - +
164A ASP* 2.5 50.0 + - + -
167A PHE* 3.5 31.4 - + + -
168A MET* 4.3 14.1 - - + -
171A ILE* 6.3 0.2 - - + -
177A ILE* 4.5 17.0 - - + -
178A VAL 3.0 10.8 + - - +
179A PRO* 3.4 4.7 - - + +
180A VAL* 2.8 26.4 + - - -
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Residues in contact with PHE 152 (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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42A VAL* 3.8 15.9 - - + -
43A VAL 2.9 8.7 + - - +
44A GLY* 3.9 7.5 - - - -
45A GLU 4.6 0.5 + - - -
48A LEU* 3.7 19.3 - - + +
49A GLY 5.0 1.1 - - - -
50A LYS* 3.5 47.3 - - + -
53A LEU* 3.4 40.6 - - + -
54A ILE* 4.8 2.5 - - + -
150A PHE* 3.6 34.8 - + + -
151A TYR* 1.3 83.5 - - - +
153A ILE* 1.3 61.0 + - - +
154A SER 4.1 0.2 + - - -
164A ASP* 5.0 0.9 - - - +
180A VAL* 3.3 21.5 - - + -
182A ALA* 3.9 20.0 - - + -
239A VAL* 4.7 2.9 - - + -
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Residues in contact with ILE 153 (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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48A LEU* 4.2 1.6 - - - -
151A TYR* 3.9 21.1 - - + +
152A PHE* 1.3 74.8 - - - +
154A SER* 1.3 77.8 + - - +
155A PRO* 3.5 0.5 - - - +
159A GLY 4.9 7.6 - - - +
160A LEU* 3.6 33.4 - - + -
164A ASP* 4.5 8.7 - - - +
168A MET* 5.0 2.2 - - + -
179A PRO* 3.8 27.4 - - + -
180A VAL 2.7 18.7 + - - +
181A ILE* 3.7 4.8 - - + -
182A ALA* 3.1 23.6 + - - +
195A LEU* 5.6 0.2 - - + -
199A ILE* 3.9 33.0 - - + -
236A PRO* 5.3 0.4 - - + -
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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