Contacts of the strand formed by residues 119 - 123 (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 VAL 119 (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 2.8 15.1 + - - +
60F VAL* 3.8 0.9 - - - -
61F ALA* 3.4 24.5 - - + +
67F ILE* 5.5 9.6 - - + -
70F ILE* 5.6 7.8 - - + +
77F PHE* 3.8 41.1 - - + -
105F ARG* 4.4 2.1 - - - +
106F ILE* 3.3 18.8 + - - -
107F ALA* 3.3 17.7 + - + +
113F VAL* 5.5 4.3 - - + -
117F ASP 3.3 16.4 - - - +
118F THR* 1.3 75.5 - - - +
120F ILE* 1.3 72.0 + - + +
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Residues in contact with ILE 120 (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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58F LYS* 3.6 3.1 - - - +
59F MET* 2.7 52.6 + - + +
70F ILE* 4.5 8.1 - - + -
74F ASN* 3.1 46.4 - - + +
75F HIS* 4.1 3.1 - - - +
76F ALA 4.3 15.3 - - - +
77F PHE* 4.9 0.7 - - + -
103F PHE* 4.2 8.5 - - + -
104F LYS 3.4 9.4 - - - +
105F ARG* 5.0 3.4 - - - -
106F ILE* 3.1 8.5 - - - -
118F THR* 4.2 0.2 - - - +
119F VAL* 1.3 97.4 - - + +
121F GLU* 1.3 76.4 + - - +
122F PHE* 4.8 4.5 - - + -
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Residues in contact with GLU 121 (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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57F ASN* 3.8 7.5 - - - +
58F LYS* 4.2 8.5 - - + -
103F PHE* 3.5 0.2 - - - -
104F LYS* 2.7 42.9 + - + +
106F ILE* 2.8 29.8 - - + +
118F THR* 4.0 11.1 - - + +
120F ILE* 1.3 84.2 - - - +
122F PHE* 1.3 63.7 + - - +
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Residues in contact with PHE 122 (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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26F LEU* 4.1 17.9 - - + -
27F SER 5.9 0.7 - - - -
54F PRO* 4.8 7.6 - - + -
56F GLY* 4.1 7.9 - - - -
57F ASN* 3.2 29.9 + - - +
58F LYS* 3.0 44.6 - - - -
59F MET* 3.3 23.8 - - + -
91F PHE* 3.8 21.5 - + - -
102F GLY 3.1 11.4 - - - +
103F PHE* 4.1 14.8 - - + -
104F LYS* 5.3 0.2 - - - -
120F ILE* 4.2 2.0 - - + -
121F GLU* 1.3 83.1 - - - +
123F ASP* 1.3 60.0 + - - +
124F LEU* 3.8 23.6 + - + -
127F LEU* 4.2 5.8 - - + -
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Residues in contact with ASP 123 (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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102F GLY* 3.0 28.1 + - - +
122F PHE* 1.3 73.4 - - - +
124F LEU* 1.3 52.8 + - - +
125F PRO* 2.4 29.9 - - - +
126F LEU* 2.9 32.3 + - + +
127F LEU* 3.1 14.7 + - - +
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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