Contacts of the strand formed by residues 64 - 71 (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 ASP 64 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63F VAL* 1.3 71.5 - - - +
65F GLY* 1.3 57.5 + - - +
81F SER* 3.7 2.1 - - - -
82F ASP* 2.9 31.9 + - + +
113F VAL 2.8 16.6 - - - +
114F LYS* 2.9 21.4 - - - -
115F VAL* 3.0 14.5 + - - +
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Residues in contact with GLY 65 (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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63F VAL* 3.0 9.5 + - - -
64F ASP* 1.3 75.0 - - - +
66F THR* 1.3 64.4 + - - -
79F ILE* 4.2 2.0 - - - -
80F GLU 2.8 15.5 - - - -
81F SER* 3.5 3.1 - - - -
82F ASP* 3.2 16.3 - - - +
112F ARG* 3.1 7.6 - - - +
113F VAL* 2.8 25.7 + - - +
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Residues in contact with THR 66 (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* 1.3 72.9 - - - -
67F ILE* 1.3 66.1 + - - +
68F GLY* 3.0 5.0 + - - -
79F ILE* 3.4 5.2 - - - +
80F GLU* 2.5 33.7 + - - +
82F ASP* 3.7 9.0 + - - -
110F GLY 3.3 16.4 - - - +
111F GLN 3.1 23.6 - - - +
112F ARG* 3.5 12.1 - - + +
113F VAL 4.8 0.4 - - - +
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Residues in contact with ILE 67 (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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66F THR* 1.3 69.7 - - - +
68F GLY* 1.3 71.7 + - - +
69F LYS 3.0 18.4 - - - +
70F ILE* 3.0 38.6 - - + -
77F PHE* 4.2 8.3 - - + -
78F SER 3.2 7.4 - - - +
79F ILE* 3.4 14.0 - - + +
107F ALA* 5.0 6.7 - - + -
108F GLU 3.9 11.9 - - - +
109F GLU* 3.6 12.5 - - - +
110F GLY* 3.9 6.2 - - - +
111F GLN* 2.8 32.5 + - + +
113F VAL* 4.1 16.3 - - + +
119F VAL* 5.5 9.4 - - + -
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Residues in contact with GLY 68 (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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66F THR 3.0 7.9 + - - -
67F ILE* 1.3 76.9 - - - +
69F LYS* 1.3 60.8 + - - -
78F SER* 2.8 19.3 + - - -
79F ILE* 3.6 2.2 - - - +
80F GLU* 5.2 1.6 - - - -
109F GLU* 3.4 18.9 - - - +
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Residues in contact with LYS 69 (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* 3.0 8.6 - - - +
68F GLY* 1.3 76.9 - - - -
70F ILE* 1.3 59.0 + - - +
71F PHE* 4.2 6.2 - - - -
77F PHE* 3.3 2.0 - - - -
78F SER* 2.7 35.8 + - - -
109F GLU* 3.4 9.6 - - - -
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Residues in contact with ILE 70 (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* 3.0 25.8 - - + -
69F LYS* 1.3 71.0 - - - +
71F PHE* 1.3 70.5 + - - +
72F GLU* 3.1 2.6 + - - -
74F ASN* 4.4 5.6 - - + -
76F ALA 3.6 12.3 - - - +
77F PHE* 4.0 7.2 - - + -
105F ARG* 2.9 49.3 + - - +
107F ALA* 4.0 6.5 - - + +
108F GLU 3.7 6.3 - - - -
109F GLU* 3.1 54.5 - - + +
119F VAL* 5.6 6.5 - - + +
120F ILE* 4.5 7.4 - - + -
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Residues in contact with PHE 71 (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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69F LYS* 5.2 4.0 - - - -
70F ILE* 1.3 73.0 - - - +
72F GLU* 1.3 59.3 - - - +
73F THR* 3.0 13.0 - - + +
74F ASN* 2.6 29.2 + - - +
75F HIS* 3.8 8.3 - - + -
76F ALA* 3.0 36.9 + - + +
77F PHE* 5.2 3.4 - - - -
78F SER* 6.3 0.9 - - - -
88F PHE* 3.8 13.9 - + - -
90F HIS* 4.2 1.3 - + - -
105F ARG* 3.0 8.5 + - - -
474G ILE* 3.7 37.0 - - + -
475G GLU* 4.4 11.0 - - + -
477G THR* 4.1 5.6 - - - -
478G GLU* 3.2 45.1 - - + -
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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