Contacts of the helix formed by residues 133 - 141 (chain E) in PDB entry 2GJ6
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 SER 133 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126D TYR* 3.8 22.0 - - - +
127D GLN 3.6 23.6 + - - -
128D LEU* 3.4 10.0 - - - +
131E GLU 4.4 0.4 - - - -
132E PRO* 1.3 74.7 - - - +
134E GLU* 1.3 60.4 + - - +
135E ALA* 3.3 19.4 + - - +
136E GLU* 3.1 28.7 + - - +
137E ILE* 3.1 16.9 + - - +
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Residues in contact with GLU 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E PRO 4.6 5.8 - - - +
133E SER* 1.3 72.9 + - - +
135E ALA* 1.3 58.0 + - - +
137E ILE* 3.7 14.3 - - + +
138E SER* 3.1 29.6 + - - -
244E ARG* 3.4 38.7 + - - +
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Residues in contact with ALA 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D TYR* 4.0 5.3 - - + -
203D PHE* 6.0 0.3 - - - -
205D PRO* 4.0 35.2 - - + +
133E SER* 3.3 11.8 + - - +
134E GLU* 1.3 78.3 - - - +
136E GLU* 1.3 60.2 + - - +
138E SER* 4.1 5.1 - - - -
139E HIS* 3.3 25.5 + - - +
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Residues in contact with GLU 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D TYR* 3.6 35.9 - - + +
128D LEU* 5.4 0.5 - - - +
140D LEU* 4.9 2.2 - - - +
142D THR* 4.8 0.7 - - - +
132E PRO* 4.3 0.7 - - - +
133E SER* 3.1 31.0 + - - +
135E ALA* 1.3 75.5 - - - +
137E ILE* 1.3 56.6 + - - +
140E THR* 2.5 50.8 + - + +
142E LYS 3.4 11.5 - - - +
143E ALA* 3.8 1.7 - - - -
144E THR* 2.4 50.4 + - - +
197E ARG* 3.4 17.5 + - - -
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Residues in contact with ILE 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E PRO* 4.2 9.9 - - + +
133E SER 3.1 13.7 + - - +
134E GLU* 3.7 17.5 - - + +
136E GLU* 1.3 76.0 - - - +
138E SER* 1.3 61.1 + - - +
141E GLN* 3.3 24.3 + - - +
142E LYS 3.8 17.0 - - - +
143E ALA* 4.3 9.9 - - + -
200E ALA* 3.9 12.2 - - + +
203E TRP* 3.7 32.1 - - + +
204E GLN* 3.5 28.5 - - + +
244E ARG* 6.2 1.1 - - - +
246E ASP* 6.0 0.4 - - - +
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Residues in contact with SER 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E GLU 3.1 19.1 + - - -
135E ALA* 4.3 5.4 - - - -
137E ILE* 1.3 78.9 - - - +
139E HIS* 1.3 60.2 + - - +
141E GLN* 4.9 3.0 + - - +
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Residues in contact with HIS 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D ASP* 3.5 30.1 + - - +
124D ALA* 5.4 1.6 - - + -
126D TYR* 3.8 20.0 - - + +
203D PHE* 4.4 44.8 - + + +
135E ALA 3.3 17.8 + - - +
136E GLU 3.3 2.5 + - - +
138E SER* 1.3 80.3 - - - +
140E THR* 1.3 62.4 + - + +
141E GLN* 3.8 2.7 + - - +
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Residues in contact with THR 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D ASP* 4.9 7.2 - - - +
126D TYR* 3.5 25.4 - - - +
143D ASP* 3.7 19.7 - - - +
173D PHE* 6.5 0.4 - - - -
136E GLU* 2.5 33.7 + - + +
139E HIS* 1.3 83.1 - - + +
141E GLN* 1.3 66.3 + - - +
142E LYS* 2.9 47.4 + - - +
197E ARG* 4.1 8.9 + - - +
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Residues in contact with GLN 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E ILE 3.3 18.4 + - - +
138E SER 5.6 3.1 - - - +
139E HIS 5.6 1.9 + - - +
140E THR* 1.3 80.7 + - - +
142E LYS* 1.3 64.6 + - - +
199E SER* 3.9 6.9 - - - -
200E ALA* 3.3 23.5 + - + +
201E THR* 5.7 1.0 - - - +
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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