Contacts of the helix formed by residues 141 - 154 (chain B) 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 GLY 141 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B HIS 3.4 3.4 + - - -
140B HIS* 1.3 72.2 - - - +
142B LYS* 1.3 50.0 + - - -
143B THR 3.5 2.5 - - - -
144B CYS* 3.2 2.6 + - - -
145B PHE* 2.6 31.6 + - - +
312B SER* 3.3 12.4 - - - -
1500B GTP 2.6 52.9 + - - -
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Residues in contact with LYS 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B LEU* 5.6 11.0 - - + -
135B CYS 6.5 0.7 - - - -
136B GLY* 5.9 3.4 - - - -
137B HIS 5.9 2.2 - - - +
140B HIS* 3.2 1.9 + - + +
141B GLY* 1.3 78.4 - - - +
143B THR* 1.3 57.2 + - - +
145B PHE* 3.0 9.2 + - - +
146B VAL* 3.0 27.9 + - - +
204B ASP* 4.9 8.8 - - + +
228B PHE* 4.3 21.8 - - + -
1500B GTP 3.1 11.1 + - - +
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Residues in contact with THR 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LYS* 1.3 75.5 - - - +
144B CYS* 1.3 57.7 + - - +
146B VAL* 4.1 4.7 - - - +
147B ASP* 3.6 15.9 + - - +
166B CYS* 5.0 13.0 - - - -
168B THR* 4.5 23.1 - - - -
169B ASP* 5.4 7.6 - - - -
204B ASP* 4.7 17.0 - - - +
1500B GTP 3.2 29.0 + - - -
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Residues in contact with CYS 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLY* 3.2 11.0 + - - +
142B LYS 3.1 0.6 - - - -
143B THR* 1.3 76.0 - - - +
145B PHE* 1.3 59.3 + - - +
146B VAL 3.3 0.2 - - - -
147B ASP* 3.2 11.1 + - + +
148B CYS* 2.8 26.7 + - - +
166B CYS* 5.8 4.7 - - + +
312B SER* 4.3 16.5 - - - +
1500B GTP 3.4 28.4 + - + +
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Residues in contact with PHE 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B GLY 2.6 19.7 + - - +
142B LYS* 3.0 11.4 + - - +
144B CYS* 1.3 72.6 - - - +
146B VAL* 1.3 59.9 + - - +
148B CYS* 3.1 9.9 + - - +
149B LEU* 3.0 26.3 + - - +
312B SER* 4.3 11.4 - - - -
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B LYS 3.0 14.2 + - - +
143B THR* 4.1 6.7 - - - +
145B PHE* 1.3 75.5 - - - +
147B ASP* 1.3 58.4 + - - +
149B LEU* 3.5 6.1 + - - +
150B ILE* 2.9 30.1 + - - +
168B THR* 5.9 5.6 - - - -
202B ILE* 6.3 3.4 - - + -
204B ASP* 5.1 10.8 - - + -
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Residues in contact with ASP 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B THR 3.6 14.0 + - - +
144B CYS* 3.2 14.5 + - + +
146B VAL* 1.3 76.8 - - - +
148B CYS* 1.3 59.1 + - - +
150B ILE* 3.7 4.7 - - - +
151B GLU* 2.9 30.7 + - - +
165B LEU* 4.3 20.2 - - + +
166B CYS* 5.6 0.7 - - - -
167B TYR 5.9 0.7 - - - +
168B THR* 6.2 2.2 - - - -
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Residues in contact with CYS 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B CYS 2.8 13.3 + - - +
145B PHE* 3.1 13.0 + - - +
147B ASP* 1.3 77.7 - - - +
149B LEU* 1.3 58.1 + - - +
151B GLU* 3.3 5.7 + - - +
152B GLN* 2.9 25.6 + - - +
312B SER* 4.9 6.5 - - - +
315B SER* 3.7 35.4 - - - -
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Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B PHE 3.0 14.6 + - - +
146B VAL* 4.1 5.8 - - - +
148B CYS* 1.3 77.5 - - - +
150B ILE* 1.3 58.3 + - - +
152B GLN* 3.3 10.8 - - + +
153B THR* 2.9 23.4 + - - -
427B PHE* 5.7 8.1 - - + -
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Residues in contact with ILE 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B VAL 2.9 18.4 + - - +
147B ASP* 4.1 4.7 - - - +
149B LEU* 1.3 75.6 - - - +
151B GLU* 1.3 56.1 + - - +
152B GLN 3.3 0.2 - - - -
153B THR* 3.4 8.9 - - - -
154B HIS* 2.6 36.7 + - - +
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Residues in contact with GLU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ASP 2.9 18.1 + - - +
148B CYS* 3.8 6.3 - - - +
150B ILE* 1.3 74.5 - - - +
152B GLN* 1.3 62.9 + - - +
154B HIS* 2.9 24.4 - - - +
157B ILE* 5.3 12.3 - - + -
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Residues in contact with GLN 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B CYS 2.9 14.2 + - - +
149B LEU* 3.3 14.4 - - - +
151B GLU* 1.3 78.7 - - - +
153B THR* 1.3 61.0 + - - +
154B HIS 4.7 0.7 - - - +
426B GLU* 6.1 3.1 - - - -
427B PHE* 5.8 9.6 - - + +
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Residues in contact with THR 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B VAL* 3.3 27.7 - - - +
112B THR* 5.8 0.7 - - - -
149B LEU 2.9 14.5 + - - -
150B ILE* 3.2 12.8 + - - -
152B GLN* 1.3 80.1 - - - +
154B HIS* 1.3 59.9 + - - +
155B PRO* 3.6 2.4 - - - +
188B VAL* 5.2 14.6 - - - -
189B VAL 5.5 5.8 - - - -
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Residues in contact with HIS 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LEU* 6.3 2.5 - - + -
111B VAL* 4.5 8.7 - - + +
150B ILE 2.6 19.2 + - - +
151B GLU* 2.9 24.9 - - - +
152B GLN 4.8 0.7 - - - -
153B THR* 1.3 72.5 - - - +
155B PRO* 1.3 56.9 - - - +
156B GLU* 3.1 24.9 + - + +
157B ILE* 5.1 2.8 - - - +
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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