Contacts of the strand formed by residues 152 - 158 (chain F) in PDB entry 5GAG
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 152 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2305A U 3.2 15.7 - - - -
36F LEU* 4.4 13.9 - - + -
37F ASN 3.9 7.4 - - - +
38F MET* 3.6 29.2 - - + -
57F LEU* 5.0 2.2 - - + -
60F ILE* 3.6 22.0 - - + -
131F GLY* 3.5 1.0 - - - -
132F VAL* 2.9 49.2 + - + -
135F GLN* 4.8 6.3 - - + -
138F PHE* 4.3 13.2 - - + -
150F ARG 3.8 0.9 + - - +
151F GLY* 1.3 74.7 - - - +
153F ASP* 1.3 88.2 + - - +
154F ILE* 3.7 21.3 - - + -
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Residues in contact with ASP 153 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2304A G 3.1 53.3 + - - +
2305A U 3.6 21.9 - - + +
2313A C 3.4 18.2 - - - +
36F LEU* 3.2 9.4 - - - -
37F ASN* 2.9 52.6 + - + +
130F MET 4.2 0.4 - - - -
131F GLY* 4.3 1.7 - - - -
152F LEU* 1.3 77.6 - - - +
154F ILE* 1.3 62.0 + - - +
155F THR* 4.1 5.7 + - - +
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Residues in contact with ILE 154 (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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2304A G 5.9 0.4 - - - -
34F ILE* 5.1 0.9 - - + -
35F THR 3.8 1.6 - - - -
36F LEU* 3.6 13.9 - - + -
99F PHE* 3.5 32.5 - - + -
103F LEU* 3.9 21.1 - - + -
128F TYR 3.6 2.1 - - - +
129F SER* 3.7 0.4 - - - -
130F MET* 2.9 63.0 + - + +
132F VAL* 3.8 22.4 - - + -
138F PHE* 4.5 6.5 - - + -
152F LEU* 3.7 13.0 - - + -
153F ASP* 1.3 74.6 - - - +
155F THR* 1.3 62.7 + - - +
156F ILE* 4.4 16.8 - - + -
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Residues in contact with THR 155 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2313A C 3.4 25.1 + - - -
2314A A 3.4 41.9 + - - +
34F ILE* 3.3 6.2 - - - +
35F THR* 2.9 42.4 + - - +
127F ASN* 5.6 0.2 - - + -
128F TYR 3.5 5.6 - - - +
129F SER* 4.0 17.0 + - - +
153F ASP* 4.8 5.4 + - - +
154F ILE* 1.3 77.2 + - - +
156F ILE* 1.3 66.7 + - - +
157F THR* 4.1 5.5 + - - +
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Residues in contact with ILE 156 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31F VAL* 3.5 33.0 - - + -
33F LYS 3.7 1.8 - - - -
34F ILE* 3.9 20.6 - - + -
100F PHE* 4.6 10.1 - - + -
103F LEU* 5.5 0.9 - - + -
127F ASN* 3.6 2.6 - - - -
128F TYR* 2.9 64.2 + - + +
154F ILE* 4.4 17.9 - - + +
155F THR* 1.3 78.1 - - - +
157F THR* 1.3 61.4 + - - +
158F THR* 3.8 8.9 + - - +
170F LEU* 4.7 12.1 - - + -
175F PHE* 4.2 20.9 - - + -
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Residues in contact with THR 157 (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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2314A A 3.1 34.2 + - - +
2315A G 4.0 18.2 - - - +
31F VAL* 3.8 2.1 - - - +
32F GLU* 3.0 40.4 + - - +
33F LYS* 2.9 37.5 + - + +
35F THR* 5.5 0.3 + - - -
127F ASN* 3.3 15.7 - - - +
155F THR* 4.1 2.1 - - - +
156F ILE* 1.3 74.2 - - - +
158F THR* 1.3 66.7 + - - +
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Residues in contact with THR 158 (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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29F PRO* 3.9 1.3 - - + -
30F ARG 3.5 16.4 + - - +
31F VAL* 4.2 5.2 - - - +
32F GLU* 4.3 2.4 - - - +
125F ARG 4.9 0.2 - - - +
126F GLY 3.3 15.5 + - - +
127F ASN* 3.3 15.8 + - - +
156F ILE* 3.8 16.0 + - - +
157F THR* 1.3 81.1 + - - +
159F THR* 1.3 65.4 + - - +
160F ALA* 3.2 27.9 + - + +
166F GLY* 4.7 5.0 + - - -
169F LEU* 3.6 25.5 - - + +
170F LEU* 6.1 1.9 - - - +
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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