Contacts of the strand formed by residues 146 - 153 (chain A) in PDB entry 3QPV
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 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ASN* 3.6 25.1 + - - +
33A SER* 4.3 19.3 - - - +
34A PRO 3.0 6.2 + - - +
35A THR* 3.6 20.4 - - + +
36A VAL* 2.9 26.3 + - - +
144A ASP 4.1 0.8 + - - -
145A PHE* 1.3 79.8 - - - +
147A ALA* 1.3 60.6 + - - +
227A GLN* 3.5 34.5 + - - +
228A ASP* 2.9 39.7 + - - +
231A GLN* 4.6 2.9 - - - +
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Residues in contact with ALA 147 (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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35A THR* 4.8 0.4 - - - -
36A VAL* 3.4 8.5 - - + +
38A VAL* 5.2 5.2 - - + -
136A ILE* 5.9 1.1 - - + -
137A LEU* 4.0 27.4 - - + -
140A ALA* 4.1 15.5 - - + -
145A PHE 3.9 0.2 + - - -
146A LYS* 1.3 79.1 - - - +
148A PHE* 1.3 60.9 + - - +
149A PHE* 4.4 10.0 - - + -
210A SER* 4.0 8.1 + - - +
227A GLN* 3.5 19.1 + - - +
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Residues in contact with PHE 148 (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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35A THR* 4.3 12.1 - - + -
36A VAL 3.0 7.0 + - - +
37A ILE* 3.4 16.0 - - + +
38A VAL* 2.9 24.7 + - - +
147A ALA* 1.3 75.1 - - - +
149A PHE* 1.3 63.4 + - - +
150A ILE* 3.7 30.5 - - + -
210A SER* 3.3 12.8 - - - -
211A LEU* 3.8 19.1 - - - -
212A ILE* 3.8 20.4 - - + -
223A VAL* 6.1 0.4 - - + -
224A ASN 5.3 1.1 - - - -
226A VAL* 5.5 4.7 - - + -
231A GLN* 3.3 46.7 - - + +
234A ILE* 4.0 15.7 - - + -
235A VAL* 4.0 19.1 - - + -
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Residues in contact with PHE 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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38A VAL* 3.4 43.7 - - + +
40A VAL* 4.1 4.3 - - + -
133A ARG* 3.8 37.2 - - + -
136A ILE* 5.3 1.6 - - + -
137A LEU* 3.5 31.0 - - + -
147A ALA* 4.4 11.4 - - + -
148A PHE* 1.3 75.8 - - - +
150A ILE* 1.3 64.6 + - - +
151A GLU 4.2 0.4 - - - -
200A LEU* 3.7 21.1 - - + -
209A LEU* 3.5 33.7 - - + -
210A SER 2.7 19.2 + - - -
211A LEU* 3.0 8.5 - - + +
212A ILE* 2.9 26.7 + - - +
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Residues in contact with ILE 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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37A ILE* 3.6 24.7 - - + -
38A VAL 2.9 8.3 + - - -
39A MET* 3.3 32.6 - - + +
40A VAL* 2.7 29.7 + - - +
50A ILE* 4.5 7.2 - - + -
54A LEU* 3.9 17.7 - - + -
148A PHE* 3.7 22.0 - - + -
149A PHE* 1.3 76.5 - - - +
151A GLU* 1.3 57.6 + - - +
212A ILE* 3.4 15.5 - - + -
214A VAL* 4.3 13.0 - - + -
234A ILE* 4.1 1.3 - - + -
238A LEU* 3.8 25.8 - - + -
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Residues in contact with GLU 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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40A VAL* 3.2 22.5 - - + +
149A PHE 4.2 0.4 - - - -
150A ILE* 1.3 75.8 - - - +
152A SER* 1.3 59.7 + - - +
153A VAL* 3.9 11.4 + - + -
197A TYR* 2.5 29.5 + - - +
199A PRO* 3.2 16.5 - - - +
200A LEU* 2.9 42.7 + - + +
212A ILE 3.0 8.6 + - - +
213A LYS* 3.0 25.8 + - - +
214A VAL* 2.7 36.6 + - - +
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Residues in contact with SER 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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39A MET* 5.9 1.3 - - - +
40A VAL 3.0 14.0 + - - +
41A GLY* 4.1 6.9 - - - -
42A LEU 4.8 0.2 + - - -
45A ARG* 2.5 50.0 + - - +
47A LYS* 4.4 8.5 - - - +
50A ILE* 4.7 12.7 - - - +
150A ILE 4.2 0.6 + - - -
151A GLU* 1.3 73.5 - - - +
153A VAL* 1.3 63.2 + - - +
197A TYR* 4.4 1.4 + - - -
214A VAL* 3.4 6.0 + - - -
700A ADP 3.5 21.5 + - - -
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Residues in contact with VAL 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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151A GLU* 3.9 17.0 - - + -
152A SER* 1.3 76.9 + - - +
154A CYS* 1.3 66.2 + - - +
155A ASP* 4.2 18.8 - - - +
197A TYR* 3.9 20.9 - - + +
199A PRO* 5.4 1.8 - - + -
213A LYS* 4.1 20.9 - - + +
214A VAL 2.8 13.8 + - - +
215A ILE* 3.5 13.1 - - + -
216A ASP* 3.0 27.4 + - - +
217A VAL 4.7 0.5 + - - -
700A ADP 5.4 0.5 + - - -
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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