Contacts of the strand formed by residues 116 - 119 (chain C) in PDB entry 3GUT
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 LEU 116 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C GLY 5.0 0.9 - - - -
45C SER* 3.3 7.0 + - - -
46C ILE* 2.7 50.0 + - + +
59C PRO* 4.3 15.0 - - + -
74C ILE* 4.8 15.5 - - + -
90C LEU* 4.7 14.8 - - + -
95C CYS* 4.7 3.1 - - - -
100C TYR* 4.1 34.5 - - + -
113C PHE* 3.5 39.0 + - + +
114C GLN 3.7 1.8 - - - -
115C ASN* 1.3 81.7 - - - +
117C GLY* 1.3 59.0 + - - +
159C LEU* 5.0 10.3 - - + -
161C PHE* 5.6 0.9 - - + -
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Residues in contact with GLY 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ALA* 4.8 6.7 - - - -
44C GLY 4.6 10.8 - - - -
45C SER* 5.1 0.2 - - - -
46C ILE* 4.0 2.2 - - - -
90C LEU* 3.2 6.2 - - - +
91C VAL* 2.4 55.4 + - - +
116C LEU* 1.3 75.4 - - - +
118C ILE* 1.3 65.1 + - - -
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Residues in contact with ILE 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C PHE* 3.0 54.6 - - + -
35C ARG 3.6 15.9 + - - -
43C ALA* 4.0 12.6 - - - +
46C ILE* 3.5 35.6 - - + +
76C LEU* 4.4 8.5 - - + -
88C HIS* 4.5 9.4 - - + -
89C GLU 3.6 2.2 - - - +
90C LEU* 3.7 26.2 - - + -
91C VAL* 4.7 0.9 - - - -
116C LEU* 5.3 0.7 - - + -
117C GLY* 1.3 73.2 - - - +
119C GLN* 1.3 66.4 + - - +
120C CYS 4.5 0.2 - - - +
157C VAL* 4.6 11.2 - - + -
159C LEU* 4.8 8.7 - - + -
183C ILE* 5.2 4.9 - - + -
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Residues in contact with GLN 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ARG* 3.1 14.4 - - + +
36C TYR 4.0 3.3 + - - +
37C LYS* 3.4 58.7 + - - +
40C GLY 5.6 2.0 + - - -
41C ARG 5.0 9.3 + - - -
43C ALA* 5.9 0.2 - - - -
88C HIS* 3.7 1.2 - - - +
89C GLU* 2.7 57.2 + - + +
91C VAL* 4.0 28.1 - - + +
118C ILE* 1.3 76.0 - - - +
120C CYS* 1.3 63.2 + - - +
121C VAL* 4.9 0.9 - - - +
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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