Contacts of the strand formed by residues 117 - 121 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A ALA 3.7 3.0 + - - -
116A PRO* 1.3 69.4 - - - +
118A VAL* 1.3 64.7 + - - +
119A SER* 3.9 4.4 + - - -
138A PHE 3.5 3.6 - - - +
140A ASN* 2.9 42.0 + - + +
141A ASN* 5.4 3.5 - - - +
143B THR* 5.4 8.1 - - - +
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Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PRO* 3.5 21.0 + - + +
117A THR* 1.3 78.4 - - - +
119A SER* 1.3 64.2 + - - +
137A CYS* 3.9 20.4 - - - -
138A PHE 3.3 9.4 - - - +
139A LEU* 4.4 14.6 - - + -
197A CYS* 3.9 4.9 - - - +
199A ALA* 4.6 2.2 - - + +
208A ILE* 3.6 34.5 - - + +
210A LYS* 3.0 51.0 + - + +
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Residues in contact with SER 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A THR* 3.9 4.9 + - - -
118A VAL* 1.3 78.1 - - - +
120A ILE* 1.3 60.6 + - - +
121A PHE* 3.5 24.7 - - - -
136A VAL 4.0 0.5 - - - +
137A CYS* 3.4 3.5 - - - -
138A PHE* 2.9 45.2 + - - +
140A ASN* 5.5 0.3 + - - -
210A LYS* 4.6 6.3 - - - +
143B THR* 3.8 21.3 + - - +
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Residues in contact with ILE 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A SER* 1.3 76.3 - - - +
121A PHE* 1.3 71.3 + - - +
122A PRO* 4.2 4.8 - - - +
135A VAL* 4.2 4.3 - - + -
136A VAL 3.5 8.5 - - - +
151A TRP* 4.2 12.1 - - + -
195A TYR 3.9 8.7 - - - +
197A CYS* 3.9 24.7 - - - +
210A LYS* 3.7 39.4 - - + +
211A SER 4.2 12.3 - - - +
212A PHE* 3.8 36.3 - - + -
132B PRO* 5.4 4.7 - - - +
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Residues in contact with PHE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A SER* 3.5 23.6 - - - -
120A ILE* 1.3 79.7 - - - +
122A PRO* 1.4 72.8 - - + +
134A SER 4.4 0.2 - - - +
135A VAL* 3.4 6.8 - - - +
136A VAL* 2.8 39.4 + - + +
138A PHE* 3.5 31.2 - + - -
212A PHE* 4.3 4.0 - - - -
130B LEU* 3.6 40.6 - - + -
131B ALA 3.3 27.8 - - - +
132B PRO* 4.0 5.6 - - + -
143B THR* 3.3 32.8 - - + -
144B LEU 4.3 5.8 - - - -
145B GLY 4.2 0.7 - - - -
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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