Contacts of the strand formed by residues 146 - 149 (chain A) in PDB entry 2G4C
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 ARG 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A LEU* 4.1 17.2 - - - +
139A LEU 4.7 1.2 + - - -
141A GLY* 2.7 33.7 + - - +
142A ASP* 4.3 5.5 + - - +
144A ALA 2.5 31.3 + - - +
145A PHE* 1.3 74.1 - - - +
147A LEU* 1.3 62.8 + - - +
148A VAL* 3.6 9.2 + - + +
174A VAL* 4.6 6.7 - - + -
175A LEU* 3.1 46.9 + - + +
178A SER* 3.6 30.2 + - - -
179A GLY 3.2 16.8 - - - -
146C ARG 3.6 0.3 - - - +
147C LEU* 3.7 2.8 - - - -
148C VAL* 3.0 34.8 + - + +
150C ALA* 3.6 19.1 - - + +
153C LEU* 5.1 2.5 - - + -
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Residues in contact with LEU 147 (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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133A HIS* 3.6 24.7 - - + -
145A PHE 4.8 2.0 - - - +
146A ARG* 1.3 73.6 - - - +
148A VAL* 1.3 62.8 + - - +
149A SER 4.0 1.6 + - - -
178A SER* 3.7 13.3 + - - -
179A GLY 3.2 13.4 + - - +
180A LYS* 4.0 13.7 - - - +
181A LEU* 3.8 13.5 - - + -
145C PHE* 4.6 10.8 - - + -
146C ARG 4.0 3.1 - - - -
147C LEU* 3.0 35.7 - - + -
181C LEU* 3.8 19.1 - - + -
231C ILE* 3.2 35.5 - - + +
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Residues in contact with VAL 148 (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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146A ARG* 3.9 11.9 - - + +
147A LEU* 1.3 75.0 - - - +
149A SER* 1.3 56.0 + - - +
150A ALA* 2.7 18.5 + - - -
152A THR* 4.0 13.7 - - - +
153A LEU* 4.1 19.3 - - + -
170A PHE* 5.3 2.0 - - + -
174A VAL* 4.3 25.8 - - + -
178A SER* 4.5 7.2 - - - +
145C PHE* 3.9 2.0 - - - -
146C ARG* 3.0 25.0 + - + +
148C VAL* 3.0 42.4 - - + -
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Residues in contact with SER 149 (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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147A LEU 4.0 1.2 + - - -
148A VAL* 1.3 69.0 - - - +
150A ALA* 1.3 51.8 + - - +
151A GLU* 3.1 5.9 + - - +
152A THR* 2.4 57.4 + - - +
144C ALA 3.9 2.9 + - - -
145C PHE* 3.5 32.5 - - - -
217C PRO* 4.8 3.8 - - - +
229C LYS* 3.7 33.1 + - - +
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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