Contacts of the helix formed by residues 121 - 135 (chain E) in PDB entry 6FF7
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 ASN 121 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119E HIS 3.6 2.6 + - - -
120E ILE* 1.3 77.3 - - - +
122E ASP* 1.3 60.4 + - - +
123E PHE* 4.5 5.2 - - + +
124E MET* 5.0 10.8 - - + +
125E PHE* 3.3 22.6 + - - +
86F PHE* 5.3 2.2 - - - +
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Residues in contact with ASP 122 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120E ILE 3.7 1.7 + - - +
121E ASN* 1.3 74.6 - - - +
123E PHE* 1.3 61.1 + - - +
125E PHE* 3.4 4.2 - - - +
126E GLU* 2.9 32.3 + - - +
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Residues in contact with PHE 123 (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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43A LYS 5.3 9.2 - - - +
44A ARG* 5.5 8.7 - - - +
121E ASN* 3.5 3.2 - - + +
122E ASP* 1.3 79.7 - - - +
124E MET* 1.3 59.1 + - - +
126E GLU* 3.4 4.7 + - - +
127E GLN* 2.9 29.4 + - - +
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Residues in contact with MET 124 (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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121E ASN* 4.7 11.2 + - + +
123E PHE* 1.3 76.0 - - - +
125E PHE* 1.3 59.1 + - - +
127E GLN* 3.6 7.7 - - - +
128E GLN* 2.9 32.1 + - - +
285F GLU 5.9 2.7 - - - +
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Residues in contact with PHE 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E ILE* 5.6 4.3 - - + -
121E ASN 3.3 23.1 + - - +
122E ASP* 3.4 7.4 + - - +
124E MET* 1.3 78.2 - - - +
126E GLU* 1.3 57.5 + - - +
128E GLN* 3.5 3.0 + - - +
129E ARG* 2.9 28.9 + - - +
33P TYR* 5.0 3.3 - - - +
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Residues in contact with GLU 126 (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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216 U 5.9 3.1 - - - +
122E ASP 2.9 17.0 + - - +
123E PHE* 4.0 3.4 - - - +
125E PHE* 1.3 76.0 - - - +
127E GLN* 1.3 57.2 + - - +
129E ARG* 3.5 7.8 - - - +
130E ARG* 2.9 29.6 + - - +
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Residues in contact with GLN 127 (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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123E PHE 2.9 18.6 + - - +
124E MET* 3.6 9.9 - - - +
125E PHE 3.2 0.2 - - - -
126E GLU* 1.3 76.8 - - - +
128E GLN* 1.3 57.7 + - - +
130E ARG* 3.3 6.2 + - - +
131E THR* 2.9 26.9 + - - -
166E THR* 5.9 6.5 - - - -
167E VAL* 5.3 4.2 + - - +
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Residues in contact with GLN 128 (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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124E MET 2.9 17.2 + - - +
125E PHE* 4.2 2.5 - - - +
127E GLN* 1.3 72.8 - - - +
129E ARG* 1.3 60.5 + - - +
131E THR* 3.5 9.7 - - - -
132E PHE* 3.0 29.3 + - - +
138E ALA* 4.1 19.5 - - + +
139E LEU 5.5 2.2 - - - +
33P TYR* 5.4 0.9 - - - -
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Residues in contact with ARG 129 (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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125E PHE 2.9 18.8 + - - +
126E GLU* 3.5 10.8 - - - +
128E GLN* 1.3 77.8 - - - +
130E ARG* 1.3 56.5 + - - +
132E PHE* 3.4 4.8 + - - +
133E ALA* 2.9 28.6 + - - +
33P TYR* 3.7 33.6 - - + +
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Residues in contact with ARG 130 (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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216 U 4.5 30.8 - - + +
126E GLU 2.9 17.1 + - - +
127E GLN* 3.8 5.4 - - - +
129E ARG* 1.3 72.7 - - - +
131E THR* 1.3 60.2 + - - +
133E ALA* 3.7 8.8 - - - +
134E THR* 2.9 31.9 + - - -
167E VAL* 4.7 12.4 - - + +
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Residues in contact with THR 131 (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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127E GLN 2.9 17.6 + - - -
128E GLN* 3.5 11.4 - - - -
129E ARG 3.2 0.2 - - - -
130E ARG* 1.3 77.0 - - - +
132E PHE* 1.3 56.1 + - - +
134E THR* 4.9 2.0 - - - -
135E TYR* 2.9 30.7 + - - +
136E GLY 3.3 3.5 + - - -
137E TYR 4.0 12.9 - - - +
138E ALA* 5.8 0.2 - - - -
165E LEU 5.2 4.5 - - - -
166E THR* 5.2 7.6 - - - -
167E VAL* 4.9 13.9 - - - +
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Residues in contact with PHE 132 (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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128E GLN 3.0 16.5 + - - +
129E ARG* 3.9 5.2 - - - +
131E THR* 1.3 75.2 - - - +
133E ALA* 1.3 64.3 + - - +
136E GLY* 3.2 23.8 + - - +
137E TYR* 3.8 15.2 + - - +
138E ALA* 4.3 9.9 - - + -
31P ASN* 5.7 9.9 - - + -
33P TYR* 6.1 2.2 - - + -
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Residues in contact with ALA 133 (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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216 U 5.6 9.0 - - - +
129E ARG 2.9 17.9 + - - +
130E ARG* 3.7 9.6 - - - +
131E THR 3.3 0.4 - - - -
132E PHE* 1.3 79.4 - - - +
134E THR* 1.3 61.2 + - - +
61P VAL* 4.9 16.2 - - + +
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Residues in contact with THR 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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216 U 4.8 11.7 - - - -
130E ARG 2.9 16.1 + - - -
131E THR* 4.1 2.7 - - - -
133E ALA* 1.3 79.5 - - - +
135E TYR* 1.3 62.7 + - - +
167E VAL* 5.5 5.2 - - - -
125Q LYS 5.3 6.3 - - - -
126Q LEU 5.8 0.2 - - - -
127Q GLU* 5.2 20.8 - - - +
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Residues in contact with TYR 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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131E THR* 2.9 11.5 + - - +
134E THR* 1.3 77.1 - - - +
136E GLY* 1.3 63.9 + - - +
137E TYR* 3.6 3.3 - - + +
155E SER* 4.5 3.5 - - - -
158E GLU* 4.1 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