Contacts of the helix formed by residues 162 - 174 (chain F) in PDB entry 2QXU
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 SER 162 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151F ILE* 5.1 0.9 - - - +
154F VAL* 4.0 17.9 - - - +
158F GLY 3.3 15.0 - - - -
159F LEU 4.5 1.0 + - - -
160F LEU 3.7 1.8 - - - -
161F TYR* 1.3 76.1 - - - +
163F SER* 1.3 59.9 + - - +
164F GLN* 3.3 8.3 + - - +
165F VAL* 3.1 35.0 + - - +
166F ASN* 2.9 38.8 + - - +
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Residues in contact with SER 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F TYR* 5.6 0.3 - - - -
161F TYR 4.3 0.6 + - - -
162F SER* 1.3 71.6 + - - +
164F GLN* 1.3 62.8 + - - +
166F ASN* 3.3 11.5 + - - +
167F SER* 3.1 26.2 + - - -
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Residues in contact with GLN 164 (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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149F VAL* 5.9 0.8 - - - +
151F ILE* 3.6 42.2 - - + +
152F HIS 4.7 6.8 + - - +
162F SER* 3.3 7.7 + - - +
163F SER* 1.3 79.5 - - - +
165F VAL* 1.3 63.1 - - - +
167F SER* 3.3 9.3 + - - +
168F LEU* 3.2 29.0 + - + +
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Residues in contact with VAL 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F LEU* 3.8 16.4 - - + -
128F ILE* 4.3 6.1 - - + -
151F ILE* 3.5 27.1 - - + -
154F VAL* 5.2 0.4 - - + -
159F LEU* 3.3 33.9 - - + +
162F SER* 3.1 30.0 + - - +
164F GLN* 1.3 75.4 - - - +
166F ASN* 1.3 60.0 + - - +
168F LEU* 3.0 10.8 + - - +
169F ILE* 2.8 44.7 + - + +
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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
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21F GLY 4.9 4.0 + - - -
22F ILE* 3.8 24.8 + - - +
25F TYR* 3.1 56.1 - - + +
160F LEU 4.8 1.6 - - - +
161F TYR* 5.2 2.4 - - - +
162F SER 2.9 34.8 + - - +
163F SER* 3.6 9.6 - - - +
165F VAL* 1.3 77.7 - - - +
167F SER* 1.3 62.4 + - - +
169F ILE* 3.2 9.5 + - - +
170F LYS 3.0 18.4 + - - -
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Residues in contact with SER 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F TYR* 3.7 14.8 + - - -
163F SER* 3.1 15.6 + - - -
164F GLN* 3.6 10.7 - - - -
166F ASN* 1.3 76.2 - - - +
168F LEU* 1.3 62.6 + - - +
170F LYS* 3.3 5.9 + - - +
171F GLU* 3.1 30.3 + - - +
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Residues in contact with LEU 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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126F THR* 4.7 8.0 - - + +
128F ILE* 3.4 28.3 - - + -
147F ARG* 3.7 28.0 + - - +
149F VAL* 3.8 29.8 - - + -
151F ILE* 4.0 18.4 - - + -
164F GLN* 3.2 21.7 + - + +
165F VAL* 3.0 9.5 + - - +
167F SER* 1.3 76.5 - - - +
169F ILE* 1.3 64.9 + - - +
171F GLU* 3.3 14.1 + - - +
172F GLY* 3.0 19.6 + - - -
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Residues in contact with ILE 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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22F ILE* 3.5 43.1 - - + -
26F LEU* 4.4 10.3 - - + -
74F VAL* 4.1 16.2 - - + -
100F VAL* 4.2 13.8 - - + +
102F LEU* 4.1 15.7 - - + -
128F ILE* 4.5 0.4 - - + -
165F VAL* 2.8 34.7 + - + +
166F ASN* 3.2 13.0 + - - +
168F LEU* 1.3 75.6 - - - +
170F LYS* 1.3 58.8 + - - +
172F GLY* 3.2 1.7 + - - -
173F LEU* 2.9 51.6 + - + +
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Residues in contact with LYS 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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25F TYR* 3.5 29.1 - - + +
26F LEU* 4.9 1.6 - - - -
29F GLN* 2.6 36.6 + - + +
31F TRP* 3.8 20.0 - - + -
166F ASN 3.0 6.9 + - - +
167F SER* 3.4 10.5 - - - +
169F ILE* 1.3 77.8 - - - +
171F GLU* 1.3 64.2 + - + +
173F LEU* 3.3 2.5 + - - +
174F ASN* 3.0 47.3 + - - +
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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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180E THR* 3.7 31.5 + - + +
147F ARG* 2.8 40.7 + - - +
167F SER* 3.1 19.6 + - - +
168F LEU* 3.5 16.9 - - - +
169F ILE 3.3 0.2 - - - -
170F LYS* 1.3 76.2 - - + +
172F GLY* 1.3 55.0 + - - +
174F ASN* 3.2 12.9 + - - +
175F GLY 3.5 0.2 + - - -
176F GLY* 2.7 29.3 + - - -
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Residues in contact with GLY 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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98F ASN* 3.3 17.6 - - - +
100F VAL* 3.9 13.0 - - - -
126F THR* 3.9 21.3 - - - -
147F ARG* 5.1 0.6 - - - +
168F LEU 3.0 13.6 + - - -
169F ILE 3.2 2.7 + - - -
171F GLU* 1.3 78.3 - - - +
173F LEU* 1.3 60.9 + - - +
175F GLY* 3.1 12.5 + - - -
176F GLY* 3.7 5.8 + - - -
177F GLY* 4.4 2.0 + - - -
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Residues in contact with LEU 173 (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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3F HIS* 4.7 5.4 - - - +
6F VAL* 4.2 7.9 - - + -
26F LEU* 3.7 36.3 - - + -
31F TRP* 3.6 28.5 - - + +
72F ASP* 3.6 32.7 - - + +
73F ILE 4.6 3.8 - - - +
74F VAL* 4.1 17.9 - - + -
98F ASN* 3.1 20.2 + - + +
100F VAL* 4.4 10.3 - - + -
169F ILE* 2.9 31.7 + - + +
170F LYS 4.0 0.2 - - - +
172F GLY* 1.3 75.9 - - - +
174F ASN* 1.3 61.1 + - - +
175F GLY 3.1 1.1 - - - -
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Residues in contact with ASN 174 (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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122E LYS* 3.0 26.5 + - - +
180E THR 5.5 3.4 - - - +
181E ASN 5.3 2.9 - - - +
3F HIS* 3.3 27.8 + - - -
31F TRP* 3.7 16.3 - - - -
98F ASN* 4.7 0.4 - - - -
170F LYS* 3.0 35.3 + - - +
171F GLU* 3.8 5.4 - - - +
172F GLY 3.1 0.6 - - - -
173F LEU* 1.3 76.9 - - - +
175F GLY* 1.3 57.2 + - - +
176F GLY 3.5 1.1 - - - -
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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