Contacts of the strand formed by residues 136 - 142 (chain F) in PDB entry 1GLE
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 136 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26F LEU* 3.8 28.3 - - + -
52F ILE* 2.9 37.7 + - - +
54F PRO* 3.8 1.6 - - - +
59F MET* 4.9 0.2 - - - -
89F VAL* 4.0 16.2 - - + -
90F HIS 3.4 14.6 - - - +
91F PHE* 3.7 19.8 - - + -
92F GLY 3.2 6.6 + - - -
134F THR 2.7 17.0 + - - -
135F LEU* 1.3 76.1 + - - +
137F PRO* 1.3 63.6 - - - +
138F VAL* 3.4 10.3 + - + +
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Residues in contact with PRO 137 (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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33F ILE* 5.6 2.0 - - + -
36F VAL* 3.8 24.2 - - + -
41F PHE* 3.8 45.5 - - + -
50F ILE 3.5 8.3 - - - +
51F ALA* 4.0 3.1 - - + -
88F PHE* 3.6 2.9 - - + +
89F VAL* 3.6 0.9 - - - +
90F HIS 3.0 33.2 + - - +
92F GLY 4.6 2.9 - - - +
93F ILE* 4.8 1.6 - - + -
135F LEU* 3.0 17.0 - - + +
136F THR* 1.3 89.2 - - - +
138F VAL* 1.3 62.0 - - - +
139F VAL* 4.0 5.4 - - + -
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Residues in contact with VAL 138 (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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22F ILE* 5.0 6.7 - - + -
25F PRO* 3.9 27.8 - - + -
26F LEU* 5.2 1.1 - - + -
49F GLY* 3.2 2.8 - - - -
50F ILE* 2.7 51.8 + - + +
52F ILE* 4.3 13.5 - - + -
62F PRO* 5.6 1.3 - - + -
87F LEU* 4.8 16.2 - - + -
88F PHE 3.5 3.6 - - - +
89F VAL* 4.0 19.3 - - + -
136F THR* 3.4 12.1 - - + +
137F PRO* 1.3 79.7 - - - +
139F VAL* 1.3 59.3 - - - +
163F VAL* 5.0 6.7 - - + -
164F ILE* 4.4 4.0 - - + +
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Residues in contact with VAL 139 (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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33F ILE* 3.4 34.3 - - + -
41F PHE* 4.3 18.8 - - + -
46F VAL* 5.0 8.5 - - + +
47F GLY 4.0 6.5 - - - +
48F ASP 3.1 13.0 - - - +
86F GLU 3.6 1.0 - - - +
87F LEU* 3.6 5.9 - - - +
88F PHE* 2.8 62.5 + - + +
137F PRO* 4.6 1.1 - - + -
138F VAL* 1.3 82.4 - - - +
140F ILE* 1.3 68.2 + - - +
141F SER* 4.8 0.7 - - - +
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Residues in contact with ILE 140 (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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22F ILE* 4.1 9.6 - - + -
47F GLY* 3.3 4.2 - - - -
48F ASP 2.5 32.3 + - - +
85F VAL* 4.0 12.6 - - + -
86F GLU 3.1 5.6 - - - +
87F LEU* 3.5 17.9 - - + -
139F VAL* 1.3 71.5 - - - +
141F SER* 1.3 63.3 + - - +
142F ASN* 3.4 26.2 - - - +
143F MET* 3.8 3.6 - - - +
146F ILE* 3.5 25.6 - - + -
149F LEU* 3.0 31.4 - - + -
164F ILE* 4.1 14.1 - - + -
166F ILE* 4.0 16.8 - - + -
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Residues in contact with SER 141 (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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46F VAL* 3.7 23.6 - - - +
47F GLY* 4.6 1.4 - - - -
86F GLU* 3.1 27.9 + - - +
87F LEU 5.3 0.3 - - - -
88F PHE* 4.9 10.3 - - - +
139F VAL* 3.9 1.5 - - - -
140F ILE* 1.3 71.7 - - - +
142F ASN* 1.3 59.2 + - - +
143F MET* 2.9 15.4 + - - +
144F ASP* 4.8 1.7 - - - +
474G ILE* 4.7 19.4 - - - +
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Residues in contact with ASN 142 (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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84F GLY 3.1 23.2 - - - +
85F VAL* 4.4 1.6 - - - +
86F GLU* 3.6 34.4 + - - +
140F ILE* 3.4 18.6 - - - +
141F SER* 1.3 76.6 + - - +
143F MET* 1.4 50.1 + - - +
144F ASP* 2.6 29.5 + - - +
145F GLU* 3.0 22.6 + - + +
146F ILE* 3.9 11.3 - - - +
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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