Contacts of the strand formed by residues 75 - 82 (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 HIS 75 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59F MET* 4.8 2.8 - - - +
71F PHE* 3.8 7.4 + + - +
73F THR* 3.3 26.9 + - + +
74F ASN* 1.3 75.7 - - - +
76F ALA* 1.3 64.7 + - + +
90F HIS* 2.7 24.0 + + - -
91F PHE* 2.9 35.6 + - + +
95F THR* 3.8 13.9 - - - -
96F VAL* 3.1 24.5 - - + -
103F PHE* 3.8 32.3 - - + -
120F ILE* 4.5 3.4 - - - -
169F ZN 2.0 33.0 - - - -
478G GLU* 2.6 15.3 + - - -
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Residues in contact with ALA 76 (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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59F MET* 5.3 1.3 - - - -
70F ILE* 3.6 6.6 - - - +
71F PHE* 3.0 39.0 + - + +
74F ASN 3.5 0.6 - - - -
75F HIS* 1.3 89.3 + - + +
77F PHE* 1.3 68.6 + - - +
88F PHE* 4.3 3.6 - - + -
89F VAL 3.0 20.2 - - - +
90F HIS* 3.6 25.8 - - + -
120F ILE* 4.3 2.2 - - - +
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Residues in contact with PHE 77 (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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25F PRO* 5.4 0.9 - - + -
59F MET* 3.3 35.0 - - + -
60F VAL 4.7 4.5 - - - -
61F ALA* 5.2 0.4 - - - -
62F PRO* 4.6 14.1 - - + -
67F ILE* 4.3 7.4 - - + -
69F LYS 3.3 14.8 - - - +
70F ILE* 4.0 15.7 - - + -
71F PHE* 4.7 3.1 - - - +
76F ALA* 1.3 81.6 - - - +
78F SER* 1.3 73.5 + - - +
79F ILE* 3.1 26.0 - - + -
87F LEU 3.8 0.2 - - - +
88F PHE* 3.7 7.3 - - - -
89F VAL* 2.7 51.3 + - + -
119F VAL* 3.8 37.9 - - + -
120F ILE* 4.9 2.7 - - + -
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Residues in contact with SER 78 (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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67F ILE* 3.2 8.3 - - - +
68F GLY* 2.8 18.7 + - - -
69F LYS* 2.7 28.5 + - - -
71F PHE* 5.9 1.1 - - - -
77F PHE* 1.3 76.8 - - - +
79F ILE* 1.3 72.0 + - - +
86F GLU* 6.3 2.0 - - - -
87F LEU 2.9 11.7 - - - -
88F PHE* 4.4 9.4 - - - +
474G ILE* 5.2 13.0 - - - -
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Residues in contact with ILE 79 (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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61F ALA* 5.0 0.7 - - + -
62F PRO* 4.6 13.7 - - + -
63F VAL* 3.5 39.9 - - + +
65F GLY* 4.2 1.1 - - - +
66F THR 3.3 25.1 - - - +
67F ILE* 3.4 13.0 - - + +
68F GLY* 3.6 2.5 - - - +
77F PHE* 3.1 28.5 - - + -
78F SER* 1.3 85.7 - - - +
80F GLU* 1.3 64.4 - - - +
81F SER 3.9 0.7 + - - -
85F VAL 3.4 2.8 - - - +
86F GLU* 3.6 3.7 - - - -
87F LEU* 2.6 44.6 + - + +
113F VAL* 4.8 7.2 - - + -
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Residues in contact with GLU 80 (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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65F GLY* 2.8 2.1 - - - -
66F THR* 2.5 45.8 + - - +
68F GLY* 4.6 2.2 - - - +
79F ILE* 1.3 76.5 - - - +
81F SER* 1.3 66.1 + - - +
82F ASP* 4.2 0.2 - - - +
84F GLY* 5.3 6.7 - - - -
85F VAL 3.3 6.5 - - - +
86F GLU* 3.6 33.1 - - + +
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Residues in contact with SER 81 (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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20F ILE* 6.4 0.4 - - - -
63F VAL* 3.2 35.8 - - - +
64F ASP 4.1 0.9 - - - -
65F GLY* 3.5 1.1 - - - -
79F ILE 3.9 1.4 + - - -
80F GLU* 1.3 78.2 - - - +
82F ASP* 1.3 59.8 + - - +
83F SER* 2.8 20.7 + - - -
84F GLY* 2.8 22.0 + - - -
85F VAL* 2.7 39.4 + - - +
87F LEU* 4.9 0.2 - - - -
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Residues in contact with ASP 82 (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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64F ASP* 2.9 33.1 + - + +
65F GLY* 3.2 14.6 + - - +
66F THR* 3.7 11.1 + - - -
81F SER* 1.3 72.6 - - - +
83F SER* 1.3 54.1 + - - +
84F GLY 3.4 2.6 + - - -
112F ARG* 5.3 4.7 - - - +
113F VAL 5.2 0.2 - - - +
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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