Contacts of the helix formed by residues 162 - 174 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151C ILE* 5.2 0.3 - - - +
154C VAL* 4.1 16.4 - - - +
158C GLY 3.4 14.1 - - - -
159C LEU 4.4 1.0 + - - -
160C LEU 3.8 1.4 - - - -
161C TYR* 1.3 77.7 - - - +
163C SER* 1.3 59.1 + - - +
164C GLN* 3.2 11.4 + - - +
165C VAL* 3.1 33.4 + - - +
166C ASN* 2.8 40.3 + - - +
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Residues in contact with SER 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C TYR* 5.6 0.4 - - - -
162C SER* 1.3 73.4 + - - +
164C GLN* 1.3 64.4 + - - +
166C ASN* 3.7 11.5 - - - +
167C SER* 3.1 27.9 + - - -
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Residues in contact with GLN 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C ILE* 3.7 42.2 - - + +
152C HIS 4.6 7.8 + - - +
162C SER* 3.2 8.4 + - - +
163C SER* 1.3 83.8 + - - +
165C VAL* 1.3 62.9 + - - +
167C SER* 3.4 7.4 + - - -
168C LEU* 3.2 27.7 + - + +
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Residues in contact with VAL 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C LEU* 3.8 26.7 - - + -
128C ILE* 4.4 6.3 - - + -
151C ILE* 3.6 27.8 - - + -
154C VAL* 4.7 0.4 - - + -
159C LEU* 3.3 34.8 - - + +
162C SER* 3.1 24.6 + - - +
164C GLN* 1.3 74.6 - - - +
166C ASN* 1.3 61.9 + - - +
168C LEU* 2.9 10.6 + - - +
169C ILE* 2.8 35.1 + - + +
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Residues in contact with ASN 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C GLY 5.2 3.3 + - - -
22C ILE* 4.0 23.0 - - - +
25C TYR* 3.1 56.4 - - + +
160C LEU 4.9 1.7 - - - +
161C TYR* 5.2 1.6 - - - +
162C SER 2.8 38.0 + - - +
163C SER* 3.7 8.8 - - - +
165C VAL* 1.3 77.9 - - - +
167C SER* 1.3 63.4 + - - +
169C ILE* 3.1 9.7 + - - +
170C LYS 2.9 18.4 + - - -
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Residues in contact with SER 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C TYR* 3.6 14.7 + - - -
163C SER 3.1 18.1 + - - -
164C GLN* 3.6 7.0 - - - -
165C VAL 3.2 0.2 - - - -
166C ASN* 1.3 76.0 - - - +
168C LEU* 1.3 64.5 + - - +
170C LYS* 3.3 6.8 + - - +
171C GLU* 3.2 28.5 + - - +
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Residues in contact with LEU 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C THR* 4.8 8.1 - - + +
128C ILE* 3.5 28.9 - - + +
147C ARG* 3.7 29.6 + - - +
149C VAL* 3.9 28.3 - - + -
151C ILE* 3.9 19.7 - - + -
164C GLN* 3.2 18.6 + - + +
165C VAL* 2.9 9.4 + - - +
167C SER* 1.3 75.7 - - - +
169C ILE* 1.3 66.9 + - - +
171C GLU* 3.3 13.3 + - - +
172C GLY* 3.0 19.4 + - - -
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Residues in contact with ILE 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ILE* 3.8 40.4 - - + -
25C TYR* 5.3 0.7 - - + -
26C LEU* 4.4 9.6 - - + -
74C VAL* 4.1 17.0 - - + -
100C VAL* 4.2 14.4 - - + +
102C LEU* 4.0 17.5 - - + -
128C ILE* 4.4 0.7 - - + -
165C VAL* 2.8 34.7 + - + +
166C ASN* 3.1 13.4 + - - +
168C LEU* 1.3 75.6 - - - +
170C LYS* 1.3 58.9 + - - +
172C GLY* 3.3 1.4 + - - -
173C LEU* 2.9 49.4 + - + +
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Residues in contact with LYS 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C TYR* 3.5 30.2 + - + +
26C LEU* 4.9 1.3 - - - -
29C GLN* 3.6 25.2 + - + +
31C TRP* 3.7 28.3 - - + -
166C ASN 2.9 6.2 + - - +
167C SER* 3.4 11.7 - - - +
169C ILE* 1.3 78.0 - - - +
171C GLU* 1.3 67.5 + - - +
173C LEU* 3.3 2.5 + - - +
174C ASN* 3.1 39.9 + - - +
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Residues in contact with GLU 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C ARG* 2.8 36.9 + - - +
167C SER* 3.2 18.0 + - - +
168C LEU* 3.3 15.4 + - - +
170C LYS* 1.3 80.6 - - + +
172C GLY* 1.3 55.6 - - - +
174C ASN* 3.0 14.1 + - - +
175C GLY 3.4 0.3 + - - -
176C GLY* 2.7 29.3 + - - -
178D GLN* 4.8 0.2 - - - +
180D THR* 3.7 36.7 + - + +
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Residues in contact with GLY 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C ASN* 3.4 17.2 - - - +
100C VAL* 3.9 19.5 - - - -
126C THR* 3.9 16.4 - - - -
147C ARG* 5.1 0.8 - - - +
168C LEU 3.0 13.6 + - - -
169C ILE 3.3 3.1 + - - -
171C GLU* 1.3 78.0 - - - +
173C LEU* 1.3 60.3 + - - +
175C GLY 3.2 10.0 + - - -
176C GLY* 3.6 6.7 + - - -
177C GLY* 4.3 3.3 + - - -
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Residues in contact with LEU 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C HIS* 4.8 4.5 - - - -
6C VAL* 4.3 6.5 - - + -
26C LEU* 3.8 31.0 - - + -
31C TRP* 3.6 26.5 + - + +
72C ASP* 3.5 39.2 - - + +
73C ILE 4.7 2.5 - - - +
74C VAL* 4.2 18.4 - - + -
98C ASN* 3.3 18.3 + - + +
100C VAL* 4.6 7.4 - - + -
169C ILE* 2.9 38.1 + - + +
170C LYS 3.9 0.2 - - - +
172C GLY* 1.3 77.2 - - - +
174C ASN* 1.3 61.2 + - - +
175C GLY 3.2 1.6 - - - -
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Residues in contact with ASN 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C HIS* 3.1 31.4 + - - -
31C TRP* 3.8 13.6 - - - -
98C ASN* 4.7 0.2 - - - -
170C LYS* 3.1 32.2 + - - +
171C GLU* 3.0 7.9 + - - +
173C LEU* 1.3 76.3 - - - +
175C GLY* 1.3 60.9 + - - +
176C GLY 3.5 1.1 - - - -
122D LYS* 3.2 29.0 + - - +
179D ASN 4.9 0.7 - - - +
180D THR* 5.3 9.3 + - - +
181D ASN* 5.3 0.7 - - - +
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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