Contacts of the helix formed by residues 155 - 172 (chain F) in PDB entry 1QZH
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 155 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154F THR* 1.3 78.7 + - - +
156F ASP* 1.3 64.8 + - - -
157F LYS 4.3 0.2 - - - -
158F GLU* 2.7 20.5 + - - +
159F GLU* 3.3 20.3 + - - +
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Residues in contact with ASP 156 (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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155F GLY* 1.3 71.0 - - - -
157F LYS* 1.3 66.7 + - - +
159F GLU* 3.6 15.2 - - - +
160F GLN* 2.9 42.2 + - - +
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Residues in contact with LYS 157 (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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5F VAL 5.9 2.2 - - - +
6F ILE* 5.9 1.2 - - - +
22F ILE* 4.2 14.6 - - + +
23F GLY* 4.5 12.6 - - - +
155F GLY* 3.2 0.4 - - - -
156F ASP* 1.3 81.5 - - - +
158F GLU* 1.3 72.3 + - - +
160F GLN* 3.3 7.3 + - - +
161F PHE* 3.3 17.5 + - - +
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Residues in contact with GLU 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F ILE* 4.0 25.2 - - + +
23F GLY* 4.3 7.3 - - - -
46F PHE* 3.6 22.1 - - + -
106F LEU* 4.6 7.4 - - + +
132F TRP* 4.1 7.6 - - + -
154F THR* 3.3 33.9 - - + +
155F GLY* 2.7 32.4 + - - +
157F LYS* 1.3 78.7 + - - +
159F GLU* 1.3 60.3 + - - +
160F GLN 3.2 0.2 - - - -
161F PHE* 3.7 3.8 - - - -
162F ALA* 2.9 30.1 + - - +
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Residues in contact with GLU 159 (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 TRP* 3.4 25.1 + - - +
135F PHE* 3.6 28.4 - - - -
154F THR* 5.3 1.6 + - - -
155F GLY 3.3 19.4 + - - +
156F ASP* 3.4 19.7 - - - +
157F LYS 3.2 0.6 - - - -
158F GLU* 1.3 78.4 - - - +
160F GLN* 1.3 61.0 + - - +
162F ALA* 3.4 3.3 + - - +
163F LEU* 3.1 39.0 + - + +
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Residues in contact with GLN 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F VAL* 3.7 38.9 - - - +
6F ILE* 4.8 8.6 + - + +
156F ASP* 2.9 36.7 + - - +
157F LYS* 3.5 5.6 - - - +
159F GLU* 1.3 75.2 - - - +
161F PHE* 1.3 65.0 + - - +
163F LEU* 3.1 23.2 + - - +
164F LEU* 2.9 38.4 + - + +
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Residues in contact with PHE 161 (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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6F ILE* 4.0 22.4 - - + +
11F LEU* 4.1 22.4 - - + -
14F LEU* 4.6 8.7 - - + -
15F LEU* 4.5 11.2 - - + -
20F TYR* 3.5 35.4 - + - -
22F ILE* 3.2 31.2 - - + -
46F PHE* 3.5 22.9 - + + -
157F LYS 3.3 9.7 + - - +
158F GLU* 3.7 7.6 - - - +
159F GLU 3.4 0.2 - - - -
160F GLN* 1.3 79.2 - - - +
162F ALA* 1.3 57.0 + - - +
164F LEU* 3.4 5.8 + - - +
165F LEU* 3.0 60.4 + - + +
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Residues in contact with ALA 162 (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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46F PHE* 4.2 6.5 - - + -
104F PRO* 3.7 18.1 - - + +
132F TRP* 3.7 37.0 - - + -
135F PHE* 4.2 4.5 - - + -
158F GLU 2.9 18.1 + - - +
159F GLU 3.5 5.8 - - - +
161F PHE* 1.3 77.7 - - - +
163F LEU* 1.3 63.2 + - - +
165F LEU* 3.5 2.0 + - - +
166F ASN* 3.0 25.3 + - - +
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Residues in contact with LEU 163 (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 PHE* 3.6 44.1 - - + +
159F GLU* 3.1 30.0 + - + +
160F GLN* 3.2 30.5 - - - +
162F ALA* 1.3 74.4 - - - +
164F LEU* 1.3 71.1 + - + +
166F ASN* 3.2 3.8 + - - +
167F LYS* 2.8 24.6 + - - +
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Residues in contact with LEU 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F ILE* 3.3 48.9 - - + +
7F ASP* 3.3 26.0 - - - +
8F SER* 4.6 3.4 - - - +
11F LEU* 3.4 23.6 - - + -
160F GLN* 2.9 32.6 + - + +
161F PHE* 3.6 8.1 - - - +
163F LEU* 1.3 78.9 - - + +
165F LEU* 1.3 55.9 + - - +
167F LYS* 2.8 14.0 + - + +
168F ILE* 2.8 40.2 + - + +
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Residues in contact with LEU 165 (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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11F LEU* 4.2 10.5 - - + -
15F LEU* 5.1 0.7 - - + -
46F PHE* 3.8 25.6 - - + +
47F GLY* 3.8 15.0 - - - +
48F ILE* 3.8 16.2 - - + +
72F TRP* 4.4 2.4 - - + -
73F ASP* 4.4 10.1 - - + -
74F PRO* 3.5 33.2 - - + -
104F PRO* 5.4 0.2 - - + -
161F PHE* 3.0 51.5 + - + +
162F ALA* 3.8 4.5 - - - +
164F LEU* 1.3 75.8 - - - +
166F ASN* 1.3 57.8 + - - +
168F ILE* 3.4 3.5 + - - +
169F TRP* 2.9 31.2 + - - +
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Residues in contact with ASN 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F ILE* 3.7 7.3 - - - +
102F GLY 3.1 20.0 + - - -
104F PRO* 4.0 7.2 - - + +
134F ASP* 2.9 26.5 + - - +
135F PHE* 3.5 27.5 - - + +
136F SER* 3.1 27.4 + - - -
162F ALA 3.0 19.0 + - - +
163F LEU 3.7 2.7 - - - +
165F LEU* 1.3 75.5 - - - +
167F LYS* 1.3 59.5 + - - +
169F TRP* 3.7 6.7 - - - +
170F ASP* 3.0 25.6 + - - +
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Residues in contact with LYS 167 (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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8F SER* 5.7 10.8 - - - -
136F SER* 6.0 0.2 - - - -
163F LEU 2.8 14.3 + - - +
164F LEU* 2.8 15.8 + - + +
166F ASN* 1.3 76.2 + - - +
168F ILE* 1.3 69.3 + - + +
170F ASP* 3.0 16.2 + - - +
171F GLU* 3.1 40.5 + - + +
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Residues in contact with ILE 168 (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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8F SER* 4.7 23.1 - - - +
11F LEU* 3.4 46.2 - - + -
12F ASN* 5.2 4.3 - - - +
72F TRP* 4.4 2.5 - - + -
74F PRO* 4.1 17.0 - - + -
164F LEU* 2.8 19.7 + - + +
165F LEU* 3.9 3.8 - - - +
167F LYS* 1.3 75.2 - - + +
169F TRP* 1.3 61.2 + - - +
171F GLU* 3.6 16.1 + - - +
172F GLN* 3.3 47.0 + - + +
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Residues in contact with TRP 169 (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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48F ILE* 3.8 21.0 - - + +
50F LYS* 4.3 19.7 - - + +
72F TRP* 3.5 41.7 - + + -
101F VAL* 3.7 26.9 - - + -
102F GLY* 3.5 30.3 - - - -
134F ASP* 4.1 13.0 - - - -
136F SER* 4.3 7.2 - - - -
165F LEU 2.9 19.7 + - - +
166F ASN* 3.7 10.1 - - - +
168F ILE* 1.3 75.6 - - - +
170F ASP* 1.3 75.4 + - - +
171F GLU 3.4 0.3 + - - -
172F GLN* 3.5 8.2 + - - -
173F THR* 2.9 48.7 + - + +
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Residues in contact with ASP 170 (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 SER* 3.4 34.5 + - - +
166F ASN 3.0 19.7 + - - +
167F LYS* 3.4 7.0 - - - +
169F TRP* 1.3 83.2 - - - +
171F GLU* 1.3 66.7 + - - +
173F THR* 3.2 7.8 + - - -
174F ASN* 3.1 29.6 + - - +
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Residues in contact with GLU 171 (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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167F LYS* 3.1 40.9 + - + +
168F ILE* 3.9 18.3 - - - +
170F ASP* 1.3 76.1 - - + +
172F GLN* 1.3 59.1 + - + +
173F THR 2.9 10.7 + - - -
174F ASN* 3.2 16.9 + - - +
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Residues in contact with GLN 172 (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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72F TRP* 3.8 19.1 - - + -
74F PRO* 5.0 7.3 + - - +
76F CYS 4.6 3.5 - - - +
78F THR* 3.6 35.9 + - - -
168F ILE* 3.3 38.7 + - + +
169F TRP* 4.1 4.5 - - - +
170F ASP 3.4 0.4 - - - -
171F GLU* 1.3 78.5 - - + +
173F THR* 1.3 65.2 + - + +
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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
------------------------------------------------------------
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