Contacts of the strand formed by residues 35 - 40 (chain F) 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 THR 35 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34F ALA* 1.3 78.7 - - - +
36F VAL* 1.4 62.1 + - - +
47F VAL 2.9 20.7 + - - -
48F ALA* 3.5 12.1 - - - +
62F LYS* 4.6 1.1 - - - -
73F SER* 2.9 35.2 + - - +
74F ILE 3.7 20.4 - - - +
75F ALA* 4.5 1.6 - - + -
133F LEU* 3.7 2.2 - - + +
160F SER* 3.4 3.6 + - - -
161F ILE* 2.9 56.1 + - + +
195F LEU* 5.4 0.4 - - - -
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Residues in contact with VAL 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F ALA* 5.5 1.8 - - + -
35F THR* 1.4 78.3 + - - +
37F GLY* 1.3 65.0 + - - +
38F LEU* 4.3 11.4 - - + -
45F VAL 3.7 0.5 - - - +
46F LEU* 3.7 3.1 - - - +
47F VAL* 2.9 43.7 + - + +
133F LEU* 4.2 3.1 - - - -
159F MET 4.0 9.6 - - - +
160F SER* 4.0 14.6 - - - +
168F ALA* 4.8 4.5 - - + -
172F LEU* 5.2 10.8 - - + -
191F GLY 5.0 1.6 - - - +
194F ALA* 4.3 20.6 - - + +
195F LEU* 4.4 36.1 - - + +
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Residues in contact with GLY 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F VAL* 1.3 74.5 - - - +
38F LEU* 1.3 60.1 + - - +
45F VAL 3.3 8.3 - - - -
46F LEU* 4.8 7.0 - - - -
133F LEU* 3.9 10.4 - - - +
144F ILE* 3.0 19.6 - - - +
158F ALA* 3.6 1.0 - - - +
159F MET 2.9 40.9 + - - +
172F LEU* 5.6 0.2 - - - +
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Residues in contact with LEU 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F VAL* 4.7 9.2 - - + -
37F GLY* 1.3 75.0 - - - +
39F LYS* 1.3 64.3 + - - +
44F ALA* 4.1 0.2 - - - -
45F VAL* 2.9 58.2 + - + +
47F VAL* 4.4 5.4 - - + -
144F ILE* 4.2 7.1 - - - +
158F ALA* 4.4 13.7 - - + +
172F LEU* 5.6 2.5 - - + -
179F PHE* 3.4 44.6 - - + -
187F LEU* 3.6 32.8 - - + +
191F GLY* 4.3 18.8 - - - -
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Residues in contact with LYS 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F LEU* 1.3 81.5 - - - +
40F SER* 1.4 59.7 + - - +
43F HIS 3.8 5.6 - - - -
44F ALA* 4.1 13.9 - - + -
45F VAL 4.4 0.2 - - - +
142F PRO* 3.2 31.3 + - + +
143F HIS* 4.1 13.6 - - - -
144F ILE* 4.1 21.4 - - + +
155F ASP* 4.7 1.0 + - - -
156F CYS 2.9 29.3 + - - -
157F ARG* 3.6 22.9 + - - +
179F PHE* 3.0 20.6 - - - +
180F MET* 3.1 36.5 - - + +
187F LEU* 4.3 5.2 - - - -
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Residues in contact with SER 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F LYS* 1.4 70.4 - - - +
41F LYS* 1.4 66.1 + - - +
42F THR* 3.1 17.6 + - - +
43F HIS 3.0 13.2 + - - +
142F PRO* 3.0 22.2 - - - +
179F PHE 3.4 14.8 - - - -
180F MET* 3.5 24.4 + - - -
181F GLU 4.1 3.1 + - - -
182F CYS 3.4 15.0 + - - -
183F ASN* 4.4 0.3 - - - -
187F LEU* 3.5 19.1 - - - -
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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