Contacts of the strand formed by residues 117 - 121 (chain C) in PDB entry 3DGG
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 THR 117 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115C ALA 4.8 2.6 + - - -
116C PRO* 1.3 71.1 + - - +
118C VAL* 1.3 65.5 + - - +
119C SER* 4.1 8.1 + - - +
138C PHE* 3.4 4.0 - - - +
140C ASN* 2.9 43.0 + - + +
141C ASN* 5.5 2.6 - - - +
143D THR* 5.0 8.7 - - - +
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Residues in contact with VAL 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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116C PRO* 3.9 10.7 + - + +
117C THR* 1.3 77.0 - - - +
119C SER* 1.3 69.2 + - - +
137C CYS* 3.7 15.5 - - - -
138C PHE 3.2 2.7 - - - -
139C LEU* 3.2 33.7 - - + -
197C CYS* 4.0 8.7 - - - +
199C ALA* 4.1 10.8 - - + -
208C ILE* 3.7 28.4 - - + +
210C LYS* 3.5 42.9 - - + +
134D SER* 4.8 0.2 + - - -
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Residues in contact with SER 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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117C THR* 4.7 6.2 + - - +
118C VAL* 1.3 80.4 + - - +
120C ILE* 1.3 61.4 + - - +
121C PHE* 3.7 25.4 - - - -
136C VAL 3.9 0.5 - - - +
137C CYS* 3.3 5.4 - - - -
138C PHE* 2.9 35.8 + - - +
210C LYS* 4.7 0.9 - - - -
134D SER* 3.7 9.4 - - - -
143D THR* 3.6 26.8 + - - +
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Residues in contact with ILE 120 (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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119C SER* 1.3 72.4 - - - +
121C PHE* 1.3 69.2 + - - +
122C PRO 4.3 0.2 - - - -
135C VAL* 4.4 4.9 - - + -
136C VAL 3.6 7.9 - - - +
151C TRP* 4.1 11.4 - - + -
195C TYR 3.7 18.8 - - - +
197C CYS* 4.0 20.2 - - - +
210C LYS* 3.6 24.7 - - + +
211C SER 4.0 11.2 - - - +
212C PHE* 3.7 27.8 - - + -
133D GLY* 3.4 7.1 + - - -
134D SER* 3.0 49.0 + - - +
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Residues in contact with PHE 121 (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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119C SER* 3.7 24.5 - - - -
120C ILE* 1.3 79.5 - - - +
122C PRO* 1.3 71.9 - - + +
134C SER 4.3 0.3 - - - +
135C VAL* 3.6 6.8 - - - +
136C VAL* 2.9 42.2 + - + +
138C PHE* 3.4 33.4 - + - -
212C PHE* 4.2 3.6 - - - -
130D LEU* 3.5 40.2 - - + +
131D ALA 3.3 29.6 - - - +
132D PRO* 3.9 5.4 - - + -
134D SER* 5.7 0.2 - - - -
143D THR 3.3 32.1 - - - -
144D LEU* 4.0 7.9 - - - -
145D GLY 4.2 0.4 - - - -
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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