Contacts of the strand formed by residues 37 - 44 (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 GLU 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A PHE* 1.3 75.1 - - - +
38A PHE* 1.3 58.0 + - - +
39A THR* 5.8 1.6 - - - +
96A ARG* 3.4 27.8 - - + +
98A THR* 6.1 0.2 - - - +
143A ASP* 4.7 17.3 - - + +
147A HIS* 3.5 9.2 - - + -
288A GLN* 2.5 27.8 + - - -
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Residues in contact with PHE 38 (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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36A PHE 4.2 0.4 + - - +
37A GLU* 1.3 74.7 - - - +
39A THR* 1.3 76.9 + - - +
40A LEU* 4.1 9.0 - - + -
95A LEU* 5.0 5.2 - - + -
96A ARG 2.9 9.5 + - - +
97A LEU* 3.5 13.3 - - + +
98A THR* 2.8 26.0 + - - +
147A HIS* 3.5 24.5 - - + -
148A CYS* 3.8 17.7 - - + -
280A LEU* 4.0 19.3 - - + -
284A MET* 3.6 56.5 - - + -
287A LEU* 3.9 14.4 - - + -
288A GLN* 3.8 20.2 - - + +
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Residues in contact with THR 39 (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 GLU* 5.8 1.7 - - - +
38A PHE* 1.3 76.9 + - - +
40A LEU* 1.3 61.5 + - - +
98A THR* 3.3 17.5 + - + +
100A VAL* 3.7 27.1 - - + -
121A TYR* 5.5 0.9 - - - +
143A ASP 4.7 2.8 + - - -
144A ASN* 4.3 17.2 + - - +
145A ARG 3.4 17.8 + - - +
146A VAL* 3.9 22.2 - - + -
147A HIS* 2.9 36.6 + - - +
148A CYS 3.5 5.9 + - - +
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Residues in contact with LEU 40 (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 PHE* 4.1 14.7 - - + -
39A THR* 1.3 73.5 - - - +
41A MET* 1.3 66.5 + - - +
42A VAL* 4.4 3.6 - - + -
54A ILE* 4.3 14.4 - - + -
58A PHE* 4.5 21.1 - - + -
97A LEU* 4.4 5.2 - - + -
98A THR 2.8 11.9 + - - +
99A VAL* 3.3 12.2 - - + +
100A VAL 2.8 29.5 + - - +
148A CYS* 3.5 19.3 - - + +
150A PHE* 3.6 53.4 - - + -
280A LEU* 4.6 5.6 - - + -
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Residues in contact with MET 41 (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* 1.3 78.3 - - - +
42A VAL* 1.3 64.3 + - - +
43A VAL* 3.8 18.4 - - + -
81A ILE* 5.1 2.0 - - + -
100A VAL* 3.3 25.1 - - + +
102A THR* 4.4 6.3 - - + -
118A ILE* 3.7 27.8 - - + +
121A TYR* 4.0 21.3 - - + -
122A ILE* 3.9 29.6 - - + -
146A VAL* 3.6 22.7 - - + +
148A CYS 2.8 9.2 + - - +
149A CYS* 3.2 12.5 - - - -
150A PHE 2.8 26.9 + - - -
167A PHE* 5.1 0.7 - - - -
171A ILE* 5.8 0.2 - - - -
175A VAL* 6.0 0.2 - - - -
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Residues in contact with VAL 42 (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* 4.4 6.3 - - + -
41A MET* 1.3 78.5 - - - +
43A VAL* 1.3 65.1 + - - +
50A LYS* 4.0 23.7 - - + -
54A ILE* 3.6 32.1 - - + -
99A VAL* 4.0 18.2 - - + -
100A VAL 2.9 7.7 + - - +
101A ASP* 3.5 19.0 - - - +
102A THR* 2.9 26.0 + - - +
150A PHE* 3.7 6.1 - - + -
152A PHE* 3.8 22.9 - - + -
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Residues in contact with VAL 43 (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* 3.8 13.2 - - + -
42A VAL* 1.3 82.0 - - - +
44A GLY* 1.3 61.2 + - - +
50A LYS* 4.1 5.2 - - - +
102A THR* 3.6 14.6 - - + +
105A TYR* 3.6 41.5 - - + -
118A ILE* 4.5 1.1 - - + -
149A CYS* 3.8 14.6 - - - -
150A PHE 3.0 8.2 + - - +
151A TYR* 3.4 18.5 - - + -
152A PHE* 2.9 25.6 + - - -
167A PHE* 3.7 24.7 - - + -
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Residues in contact with GLY 44 (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* 1.3 81.3 - - - +
45A GLU* 1.3 69.9 + - - +
46A SER 3.4 1.2 + - - -
50A LYS* 3.2 21.7 + - - +
102A THR* 4.7 1.0 + - - +
105A TYR* 3.6 24.2 - - - +
151A TYR* 4.6 2.2 - - - -
152A PHE* 3.9 14.1 - - - -
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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