Contacts of the helix formed by residues 129 - 144 (chain t) 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 ASP 129 (chain t).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124t THR* 4.1 18.2 - - - +
125t GLU 3.0 18.0 + - - +
126t LYS* 3.7 9.2 + - - +
127t GLU 3.6 1.6 - - - -
128t ARG* 1.3 81.3 - - - +
130t ALA* 1.3 62.1 + - - +
131t GLN* 3.2 9.2 - - + +
132t ALA* 3.1 6.7 + - - +
133t ILE* 3.0 23.6 + - - +
182t PRO 5.9 0.4 - - - +
184t ARG* 5.3 12.6 - - + -
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Residues in contact with ALA 130 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128t ARG 3.9 0.4 + - - -
129t ASP* 1.3 72.0 - - - +
131t GLN* 1.3 59.9 + - - +
133t ILE* 3.7 9.7 - - + +
134t PHE* 2.9 28.9 + - - +
180t LYS 5.4 2.4 - - - +
182t PRO* 3.8 34.7 + - + +
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Residues in contact with GLN 131 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129t ASP* 3.2 4.5 - - + +
130t ALA* 1.3 76.8 - - - +
132t ALA* 1.3 56.9 + - - +
134t PHE* 3.4 6.9 + - - +
135t GLU* 2.9 28.1 + - - +
179t ARG* 4.5 25.9 - - + +
180t LYS 5.7 0.4 - - - -
182t PRO 4.0 13.8 + - - +
184t ARG* 4.9 19.5 - - + +
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Residues in contact with ALA 132 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126t LYS 3.4 26.0 - - - +
127t GLU* 4.0 15.0 - - - +
129t ASP* 3.1 9.8 + - + +
131t GLN* 1.3 77.2 - - - +
133t ILE* 1.3 59.6 + - - +
135t GLU* 3.3 8.3 + - - +
136t ARG* 2.9 28.4 + - - +
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Residues in contact with ILE 133 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1855A GLU* 5.9 7.0 - - + -
127t GLU 5.5 0.4 + - - -
128t ARG 5.5 2.2 - - - +
129t ASP 3.0 12.9 + - - +
130t ALA* 3.7 12.6 - - - +
131t GLN 3.3 0.4 - - - -
132t ALA* 1.3 76.4 - - - +
134t PHE* 1.3 56.6 + - - +
136t ARG* 3.3 7.0 + - - +
137t SER* 2.9 29.9 + - - -
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Residues in contact with PHE 134 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130t ALA 2.9 17.8 + - - +
131t GLN* 3.7 7.2 - - - +
132t ALA 3.3 0.2 - - - -
133t ILE* 1.3 75.5 - - - +
135t GLU* 1.3 57.5 + - - +
137t SER* 3.8 6.3 - - - -
138t GLN* 2.9 31.9 + - - +
179t ARG* 5.0 14.4 - - - +
180t LYS 5.3 5.8 - - - +
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Residues in contact with GLU 135 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131t GLN 2.9 17.4 + - - +
132t ALA* 3.6 9.6 - - - +
133t ILE 3.3 0.2 - - - -
134t PHE* 1.3 74.8 - - - +
136t ARG* 1.3 58.9 + - - +
138t GLN* 3.5 5.4 + - - +
139t LYS* 2.9 30.9 + - - +
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Residues in contact with ARG 136 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132t ALA 2.9 16.9 + - - +
133t ILE* 3.3 7.8 + - - +
135t GLU* 1.3 75.4 - - - +
137t SER* 1.3 57.2 + - - +
139t LYS* 3.4 6.2 + - - +
140t ILE* 2.9 31.4 + - - +
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Residues in contact with SER 137 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133t ILE 2.9 17.0 + - - -
134t PHE* 3.8 7.2 - - - -
136t ARG* 1.3 76.8 - - - +
138t GLN* 1.3 56.5 + - - +
140t ILE* 3.5 4.2 + - - +
141t GLN* 2.9 30.3 + - - +
157t ASN* 5.1 21.3 - - - -
158t ASN* 5.8 9.0 - - - +
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Residues in contact with GLN 138 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134t PHE 2.9 18.4 + - - +
135t GLU* 3.8 6.1 - - - +
137t SER* 1.3 75.2 - - - +
139t LYS* 1.3 58.7 + - - +
141t GLN* 3.4 7.7 + - - +
142t GLU* 2.9 27.5 + - - +
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Residues in contact with LYS 139 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135t GLU 2.9 18.8 + - - +
136t ARG* 3.7 7.0 - - - +
138t GLN* 1.3 76.1 - - - +
140t ILE* 1.3 56.6 + - - +
142t GLU* 2.9 10.4 + - - +
143t GLU* 2.9 26.0 + - - +
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Residues in contact with ILE 140 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136t ARG 2.9 17.5 + - - +
137t SER* 4.2 4.0 - - - +
139t LYS* 1.3 75.9 - - - +
141t GLN* 1.3 57.1 + - - +
143t GLU* 4.2 6.7 - - - +
144t LEU* 3.1 30.0 + - - +
158t ASN* 5.8 7.0 - - + -
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Residues in contact with GLN 141 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137t SER 2.9 18.6 + - - +
138t GLN* 3.7 7.4 - - - +
140t ILE* 1.3 75.7 - - - +
142t GLU* 1.3 62.9 + - - +
144t LEU 3.5 15.8 - - - +
145t ARG* 5.1 2.1 - - - +
160t GLN 5.7 9.0 - - - -
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Residues in contact with GLU 142 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138t GLN 2.9 11.8 + - - +
139t LYS* 2.9 13.2 + - - +
141t GLN* 1.3 77.4 - - - +
143t GLU* 1.3 64.4 + - - +
145t ARG* 4.5 8.7 - - - +
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Residues in contact with GLU 143 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139t LYS 2.9 13.5 + - - +
140t ILE* 4.2 6.7 - - - +
141t GLN 3.4 0.4 - - - -
142t GLU* 1.3 78.3 - - - +
144t LEU* 1.3 61.5 + - - +
145t ARG* 2.9 10.7 + - - +
146t GLY 4.9 0.2 + - - -
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Residues in contact with LEU 144 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140t ILE 3.1 13.3 + - - +
141t GLN* 3.5 15.5 - - - +
143t GLU* 1.3 77.1 - - - +
145t ARG* 1.3 57.8 + - - +
147t LYS* 4.5 21.5 - - + +
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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