Contacts of the helix formed by residues 131 - 140 (chain F) in PDB entry 6IY6
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 131 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89F LEU* 3.0 24.9 + - + +
90F SER 5.1 1.4 + - - -
91F SER 3.9 5.9 + - - -
92F CYS* 4.1 10.0 - - - +
95F PHE* 3.3 26.8 - - + -
127F THR 2.9 13.1 + - - +
128F LEU* 3.4 18.8 - - - +
129F LYS 3.2 10.3 - - - +
130F GLY* 1.3 78.6 - - - +
132F ALA* 1.3 62.1 + - - +
133F ALA* 2.7 33.6 + - - +
134F TRP* 2.9 12.3 + - + -
135F GLN* 3.7 12.6 + - - +
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Residues in contact with ALA 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F CYS* 6.1 5.2 - - + -
130F GLY 3.9 2.2 + - - +
131F ASN* 1.3 73.4 + - - +
133F ALA* 1.3 56.3 + - - +
134F TRP 3.1 1.8 - - - -
135F GLN* 2.9 33.1 + - - +
136F GLU* 3.1 11.7 + - - +
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Residues in contact with ALA 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F CYS* 4.3 15.2 - - + +
95F PHE* 4.1 25.4 - - + -
131F ASN* 2.7 12.1 + - - +
132F ALA* 1.3 75.1 - - - +
134F TRP* 1.3 55.5 + - - +
136F GLU* 3.5 17.5 + - - +
137F GLN* 3.0 33.0 + - + +
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Residues in contact with TRP 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F PHE* 3.8 17.6 - + + -
99F ILE* 3.7 33.0 - - + -
128F LEU* 3.0 43.5 - - + +
129F LYS* 4.3 2.5 - - - -
131F ASN* 2.9 10.3 + - + +
132F ALA 3.1 0.2 + - - -
133F ALA* 1.3 75.9 - - - +
135F GLN* 1.3 63.5 + - + +
137F GLN* 3.1 13.8 + - - +
138F LEU* 3.1 57.0 + - + +
143F ALA* 3.8 19.5 - - + -
144F PRO* 4.6 0.7 - - + -
147F VAL* 3.5 21.3 - - + -
148F LYS* 4.2 6.7 - - - -
151F PHE* 3.4 48.2 - + + -
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Residues in contact with GLN 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F LYS* 3.2 33.8 + - - +
131F ASN 3.7 13.3 - - - +
132F ALA* 2.9 12.3 + - - +
134F TRP* 1.3 84.6 - - + +
136F GLU* 1.3 56.0 + - - +
138F LEU* 3.6 13.5 + - + +
139F LYS* 3.2 36.5 + - + +
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Residues in contact with GLU 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F ALA 3.1 10.8 + - - +
133F ALA* 3.5 18.2 - - - +
134F TRP 3.2 0.2 - - - -
135F GLN* 1.3 74.3 - - - +
137F GLN* 1.3 59.4 + - + +
139F LYS* 3.4 7.8 + - - +
140F GLN* 3.0 60.7 + - + +
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Residues in contact with GLN 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F PHE* 4.1 23.2 - - - -
96F THR* 4.5 17.2 - - - +
99F ILE* 4.0 20.0 - - - +
133F ALA* 3.0 15.8 + - + +
134F TRP* 3.1 12.0 + - + +
136F GLU* 1.3 76.1 - - + +
138F LEU* 1.3 52.2 + - - +
140F GLN* 3.6 4.4 - - - -
141F LYS 2.8 11.3 + - - -
142F LYS* 2.8 48.5 + - + +
143F ALA* 3.3 24.9 + - + +
144F PRO* 3.7 10.1 - - - +
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Residues in contact with LEU 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F TRP* 3.1 55.2 + - + +
135F GLN* 3.6 14.4 - - + +
137F GLN* 1.3 72.8 - - - +
139F LYS* 1.3 65.5 + - + +
141F LYS* 3.1 21.2 + - - +
143F ALA* 3.8 19.1 - - + -
148F LYS* 4.1 34.1 + - + +
151F PHE* 4.6 12.8 - - + -
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Residues in contact with LYS 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F GLN* 3.2 20.3 + - - +
136F GLU* 3.4 7.6 + - - +
138F LEU* 1.3 78.3 - - + +
140F GLN* 1.3 64.3 + - + +
141F LYS* 3.2 8.7 + - - +
359H GLY 4.4 12.7 - - - +
361H GLU* 3.2 31.9 + - + +
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Residues in contact with GLN 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F GLU* 3.0 52.7 + - + +
137F GLN* 4.2 4.5 - - - +
139F LYS* 1.3 74.5 - - + +
141F LYS* 1.3 69.0 + - - +
142F LYS* 3.4 22.4 + - + +
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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