Contacts of the helix formed by residues 126 - 137 (chain J) in PDB entry 2FFX
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 ASP 126 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11J ASN* 3.4 20.6 + - - +
12J TYR* 3.7 11.4 - - - -
13J SER 4.9 0.7 + - - +
16J VAL* 4.7 7.1 - - + +
76J ARG* 3.2 25.3 + - - -
121J GLY* 2.9 24.0 + - - +
122J SER* 4.9 1.0 - - - +
124J ARG* 4.4 7.0 - - + +
125J THR* 1.3 73.6 - - - +
127J PRO* 1.3 63.0 - - - +
128J HIS* 3.2 5.0 + - - +
129J LEU* 2.9 31.0 + - + +
130J CYS* 3.2 16.9 + - - +
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Residues in contact with PRO 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J ASN* 4.0 9.0 - - - +
125J THR* 3.3 12.6 - - - +
126J ASP* 1.3 83.1 - - - +
128J HIS* 1.3 61.1 + - + +
130J CYS* 3.4 8.3 + - + +
131J ASP* 2.9 30.0 + - - +
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Residues in contact with HIS 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72J MET* 4.7 16.2 - - + +
75J GLN* 5.1 9.4 - - + -
76J ARG* 3.7 35.9 + - - +
126J ASP* 3.2 7.0 + - - +
127J PRO* 1.3 82.3 - - + +
129J LEU* 1.3 64.9 + - - +
131J ASP* 3.3 13.6 + - - +
132J PHE* 2.9 29.5 + + + +
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Residues in contact with LEU 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J TYR* 5.2 1.1 - - + -
16J VAL* 3.6 31.2 - - + -
72J MET* 3.7 32.3 - - + -
76J ARG* 4.1 2.0 - - - +
117J LEU* 3.7 30.5 - - + +
118J HIS* 5.3 0.4 - - - -
121J GLY* 3.7 26.2 - - - -
126J ASP* 2.9 26.4 + - - +
128J HIS* 1.3 78.0 + - - +
130J CYS* 1.3 65.8 + - - +
132J PHE* 3.2 9.6 + - + +
133J LEU* 3.0 30.4 + - + +
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Residues in contact with CYS 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118J HIS* 3.2 22.8 - - + +
121J GLY* 5.9 1.3 - - - -
122J SER* 6.0 4.0 - - - +
126J ASP 3.2 10.2 + - - +
127J PRO* 3.6 12.3 - - + +
129J LEU* 1.3 81.1 - - - +
131J ASP* 1.3 62.3 + - - +
133J LEU* 3.2 3.6 + - - +
134J GLU* 3.0 35.2 + - - +
193J CD 2.6 30.7 - - - -
201J CD 4.2 1.1 - - - -
202J CD 2.6 28.9 - - - -
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Residues in contact with ASP 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J PRO 2.9 17.3 + - - +
128J HIS* 3.6 13.3 + - - +
129J LEU 3.3 0.2 - - - -
130J CYS* 1.3 77.0 - - - +
132J PHE* 1.3 58.0 + - - +
134J GLU* 3.4 11.3 + - - +
135J THR* 2.8 49.2 + - - -
191J CD 3.8 14.2 - - - -
202J CD 4.0 0.6 - - - -
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Residues in contact with PHE 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68J ARG* 3.7 39.9 - - + -
69J LEU* 3.7 11.4 - - + -
72J MET* 3.6 46.7 - - + -
75J GLN* 5.6 2.0 - - - -
128J HIS* 2.9 28.1 + + + +
129J LEU* 3.2 7.4 + - + +
131J ASP* 1.3 79.4 + - - +
133J LEU* 1.3 75.3 + - + +
135J THR* 4.7 2.5 - - - -
136J HIS* 3.1 38.2 + + - +
137J PHE* 3.5 29.1 - + - -
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Residues in contact with LEU 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69J LEU* 4.9 2.0 - - + -
114J LEU* 4.1 20.9 - - + +
117J LEU* 4.0 27.4 - - + -
118J HIS* 3.7 39.7 - - + +
129J LEU* 3.0 23.4 + - + +
130J CYS* 3.7 6.5 - - - +
132J PHE* 1.3 100.2 - - + +
134J GLU* 1.3 58.1 + - - +
137J PHE* 2.9 21.9 + - + +
138J LEU* 2.9 36.6 + - + -
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Residues in contact with GLU 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118J HIS* 4.4 5.8 + - + -
130J CYS* 3.0 28.4 + - - +
131J ASP* 3.8 8.5 - - - +
133J LEU* 1.3 77.2 - - - +
135J THR* 1.3 63.6 + - - +
137J PHE 4.5 0.2 + - - -
138J LEU* 4.0 24.0 + - + +
139J ASP* 4.5 17.5 + - - +
202J CD 2.3 29.9 - - - -
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Residues in contact with THR 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131J ASP* 2.8 37.3 + - - -
132J PHE* 4.0 3.1 - - - -
134J GLU* 1.3 80.7 - - - +
136J HIS* 1.3 85.3 + - + +
139J ASP* 6.2 0.2 - - - +
140J GLU* 5.7 0.7 - - - +
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Residues in contact with HIS 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68J ARG* 3.2 50.3 + - - +
132J PHE* 3.1 30.2 + + - +
135J THR* 1.3 98.3 + - + +
137J PHE* 1.3 71.7 + - + +
140J GLU* 4.2 19.3 - - - +
194J CD 2.3 31.0 - - - -
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Residues in contact with PHE 137 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J TYR* 3.4 34.5 - + - -
65J GLY* 3.5 23.3 - - - -
68J ARG* 3.4 28.5 - - + -
69J LEU* 3.8 15.3 - - + -
114J LEU* 3.8 24.7 - - + -
132J PHE* 3.5 38.4 - + - -
133J LEU* 2.9 18.1 + - + +
134J GLU 4.5 0.4 + - - -
135J THR 3.8 1.2 - - - -
136J HIS* 1.3 88.1 - - + +
138J LEU* 1.3 67.0 + - + +
139J ASP 3.5 1.5 - - - +
140J GLU* 3.2 6.9 + - - +
141J GLU* 3.0 25.9 + - + +
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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