Contacts of the strand formed by residues 57 - 61 (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 ASN 57 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56F GLY* 1.3 70.4 - - - +
58F LYS* 1.3 70.4 + - + +
121F GLU* 3.8 6.8 - - - +
122F PHE* 3.2 42.3 + - - +
124F LEU* 4.5 3.2 - - - +
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Residues in contact with LYS 58 (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 3.8 5.7 - - - +
26F LEU* 3.8 11.3 - - - +
27F SER 4.9 0.7 + - - -
56F GLY 3.0 11.6 + - - +
57F ASN* 1.3 85.4 - - + +
59F MET* 1.3 59.1 + - - +
60F VAL* 3.5 30.2 - - + +
116F GLY 4.4 5.9 + - - -
118F THR* 3.5 24.4 + - + +
120F ILE 3.6 9.0 - - - +
121F GLU* 4.2 11.7 - - + -
122F PHE* 3.0 18.0 - - - -
158F VAL* 4.9 21.2 - - + +
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Residues in contact with MET 59 (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* 3.0 4.7 - - + +
26F LEU* 3.7 17.7 - - + -
58F LYS* 1.3 71.6 - - - +
60F VAL* 1.3 57.6 + - - +
75F HIS 4.8 3.6 - - - +
77F PHE* 3.3 34.8 - - + -
89F VAL* 3.9 20.2 - - + +
91F PHE* 3.8 34.5 - - - -
103F PHE* 5.5 1.6 - - - -
118F THR* 4.2 0.9 - - - +
119F VAL* 2.8 31.6 + - - +
120F ILE* 2.7 40.2 + - + +
122F PHE* 3.3 21.1 - - + -
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Residues in contact with VAL 60 (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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24F ALA 4.5 2.2 - - - +
25F PRO* 2.4 52.4 + - + +
58F LYS* 3.5 29.4 - - + +
59F MET* 1.3 79.1 - - - +
61F ALA* 1.4 74.4 + - - +
62F PRO* 3.3 1.4 - - - +
77F PHE* 4.7 3.3 - - - -
116F GLY* 3.3 36.8 - - - +
117F ASP 3.6 7.4 - - - +
118F THR* 4.1 2.7 - - - -
119F VAL* 3.8 4.5 - - - -
158F VAL* 3.8 22.7 - - + -
159F GLY* 4.6 0.9 - - - -
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Residues in contact with ALA 61 (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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24F ALA 4.9 0.7 - - - +
25F PRO* 4.8 0.2 - - - +
60F VAL* 1.4 74.1 - - - +
62F PRO* 1.3 69.0 - - + +
63F VAL 3.4 4.5 - - - +
77F PHE* 5.0 2.5 - - - -
79F ILE* 5.0 1.8 - - + -
113F VAL* 3.1 38.6 - - + -
114F LYS 3.1 14.8 - - - +
115F VAL* 3.7 2.8 - - - +
116F GLY 3.1 20.6 + - - +
117F ASP 3.4 5.3 + - - +
119F VAL* 3.4 16.2 - - + +
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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