Contacts of the helix formed by residues 151 - 161 (chain W) 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 LYS 151 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149W LYS* 3.0 10.8 + - + +
150W VAL* 1.3 74.5 - - - +
152W LEU* 1.3 65.8 + - - +
153W LYS* 3.3 6.7 - - + +
154W GLU* 3.0 21.6 + - + +
155W ARG* 3.1 11.7 + - - +
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Residues in contact with LEU 152 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150W VAL 4.3 0.2 + - - -
151W LYS* 1.3 70.2 - - - +
153W LYS* 1.3 67.9 + - - +
155W ARG* 2.9 10.7 + - - +
156W GLN* 2.9 24.6 + - - +
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Residues in contact with LYS 153 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151W LYS* 3.3 5.8 - - + +
152W LEU* 1.3 79.4 - - - +
154W GLU* 1.3 57.7 + - - +
156W GLN* 3.4 7.0 + - - +
157W GLU* 3.0 29.0 + - - +
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Residues in contact with GLU 154 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133W LEU* 5.3 4.3 - - + +
136W ILE* 5.1 9.8 - - + +
150W VAL* 5.5 3.1 - - + -
151W LYS* 3.0 20.7 + - + +
153W LYS* 1.3 73.8 - - - +
155W ARG* 1.3 59.4 + - - +
157W GLU* 3.3 7.7 + - - +
158W ALA* 2.9 32.3 + - - +
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Residues in contact with ARG 155 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136W ILE* 5.3 6.7 - - + +
151W LYS 3.1 9.9 + - - +
152W LEU* 2.9 13.1 + - - +
154W GLU* 1.3 77.1 - - - +
156W GLN* 1.3 63.3 + - - +
158W ALA* 3.1 8.3 + - - +
159W GLU* 2.9 21.4 + - - +
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Residues in contact with GLN 156 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152W LEU 2.9 12.2 + - - +
153W LYS* 3.7 10.1 - - - +
155W ARG* 1.3 76.5 - - - +
157W GLU* 1.3 53.5 + - - +
159W GLU* 2.7 29.3 + - - +
160W LYS* 3.0 11.8 + - - +
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Residues in contact with GLU 157 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133W LEU* 5.3 3.9 - - + +
153W LYS 3.0 17.3 + - - +
154W GLU* 3.7 7.9 - - - +
156W GLN* 1.3 76.5 - - - +
158W ALA* 1.3 60.8 + - - +
160W LYS* 3.5 6.7 + - - +
161W MET* 3.4 23.7 + - - +
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Residues in contact with ALA 158 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133W LEU* 3.6 39.5 - - + +
136W ILE* 4.5 2.5 - - + -
137W TYR* 3.8 27.2 - - + +
154W GLU 2.9 17.6 + - - +
155W ARG* 3.5 7.4 - - - +
157W GLU* 1.3 75.2 - - - +
159W GLU* 1.3 57.9 + - - +
161W MET* 2.5 23.1 - - - +
162W PHE* 4.0 1.7 - - - +
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Residues in contact with GLU 159 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155W ARG 2.9 10.4 + - - +
156W GLN* 2.7 16.0 + - - +
158W ALA* 1.3 77.0 - - - +
160W LYS* 1.3 67.4 + - - +
163W LYS* 3.0 24.9 + - - +
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Residues in contact with LYS 160 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156W GLN 3.0 10.5 + - - +
157W GLU* 3.5 8.9 + - - +
159W GLU* 1.3 80.1 - - - +
161W MET* 1.3 67.6 + - - +
162W PHE 3.1 0.3 + - - -
163W LYS* 2.8 16.4 + - - +
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Residues in contact with MET 161 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133W LEU* 5.8 5.2 - - + -
157W GLU 3.4 12.4 + - - +
158W ALA* 2.5 31.6 - - - +
160W LYS* 1.3 79.8 - - - +
162W PHE* 1.3 60.1 + - - +
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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