Contacts of the helix formed by residues 162 - 174 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151D ILE* 5.2 0.5 - - - +
154D VAL* 4.1 17.7 - - - +
158D GLY 3.4 13.7 - - - -
159D LEU 4.2 1.0 + - - -
160D LEU 3.8 1.6 - - - -
161D TYR* 1.3 77.9 - - - +
163D SER* 1.3 59.8 + - - +
164D GLN* 3.3 9.2 + - - +
165D VAL* 3.1 34.2 + - - +
166D ASN* 2.8 38.8 + - - +
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Residues in contact with SER 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D TYR* 5.6 0.3 - - - -
161D TYR 4.3 0.4 + - - -
162D SER* 1.3 73.0 + - - +
164D GLN* 1.3 63.0 + - - +
166D ASN* 3.4 11.8 + - - +
167D SER* 3.0 29.7 + - - -
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Residues in contact with GLN 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D VAL* 6.0 0.8 - - - +
151D ILE* 3.8 34.8 - - + +
152D HIS 4.9 5.4 + - - +
162D SER* 3.2 7.5 + - - +
163D SER* 1.3 77.3 - - - +
165D VAL* 1.3 65.8 + - + +
167D SER* 3.3 7.7 + - - -
168D LEU* 3.1 36.0 + - + +
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Residues in contact with VAL 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D LEU* 3.9 17.9 - - + -
128D ILE* 4.4 7.4 - - + -
151D ILE* 3.7 27.1 - - + -
154D VAL* 5.0 0.2 - - + -
159D LEU* 3.4 35.7 - - + +
162D SER* 3.1 25.3 + - - +
164D GLN* 1.3 75.6 - - - +
166D ASN* 1.3 60.5 + - - +
168D LEU* 3.0 10.1 + - - +
169D ILE* 2.8 44.8 + - + +
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Residues in contact with ASN 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D GLY 5.0 4.2 + - - -
22D ILE* 4.0 23.2 - - - +
25D TYR* 3.0 55.2 - - + +
160D LEU 4.9 2.3 + - - +
161D TYR* 5.2 2.2 - - - +
162D SER 2.8 34.4 + - - +
163D SER* 3.5 10.0 - - - +
164D GLN 3.3 0.2 - - - -
165D VAL* 1.3 77.8 - - - +
167D SER* 1.3 62.1 + - - +
169D ILE* 3.2 9.0 + - - +
170D LYS 3.0 18.2 + - - -
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Residues in contact with SER 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D TYR* 3.7 14.0 + - - -
163D SER* 3.0 17.0 + - - -
164D GLN* 3.6 10.6 - - - -
165D VAL 3.2 0.2 - - - -
166D ASN* 1.3 75.6 - - - +
168D LEU* 1.3 63.7 + - - +
170D LYS* 3.4 5.9 + - - +
171D GLU* 3.2 28.2 + - - +
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Residues in contact with LEU 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D THR* 4.6 5.1 - - + +
128D ILE* 3.3 33.1 - - + +
147D ARG* 3.8 28.4 + - - +
149D VAL* 3.8 31.0 - - + -
151D ILE* 4.0 18.8 - - + -
164D GLN* 3.1 27.0 + - + +
165D VAL* 3.0 4.5 + - - +
167D SER* 1.3 74.6 - - - +
169D ILE* 1.3 60.9 + - - +
171D GLU* 3.3 12.4 + - - +
172D GLY* 2.8 26.9 + - - -
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Residues in contact with ILE 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ILE* 3.7 38.6 - - + -
25D TYR* 5.5 0.4 - - + -
26D LEU* 4.3 14.1 - - + -
74D VAL* 4.3 15.3 - - + -
100D VAL* 4.2 13.1 - - + +
102D LEU* 4.0 22.0 - - + -
128D ILE* 4.5 0.7 - - + -
165D VAL* 2.8 31.9 + - + +
166D ASN* 3.5 11.4 - - - +
168D LEU* 1.3 75.6 - - - +
170D LYS* 1.3 64.9 + - - +
172D GLY* 3.2 1.4 + - - -
173D LEU* 2.9 45.1 + - + +
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Residues in contact with LYS 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D TYR* 3.6 28.7 - - + +
26D LEU* 5.0 0.7 - - - -
29D GLN* 2.8 34.0 + - + +
31D TRP* 4.1 18.2 - - + -
166D ASN 3.0 6.4 + - - +
167D SER* 3.4 11.2 - - - +
168D LEU 3.2 0.2 - - - -
169D ILE* 1.3 78.6 - - - +
171D GLU* 1.3 63.3 + - + +
173D LEU* 3.2 2.8 + - - +
174D ASN* 3.0 46.1 + - - +
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Residues in contact with GLU 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C GLY* 6.6 0.2 - - - -
180C THR* 3.8 28.4 - - + +
147D ARG* 2.8 38.5 + - - +
167D SER* 3.2 18.5 + - - +
168D LEU* 3.6 15.5 - - - +
170D LYS* 1.3 79.2 - - + +
172D GLY* 1.3 59.4 + - - +
174D ASN* 3.0 10.6 + - - +
175D GLY 3.4 0.3 + - - -
176D GLY* 2.7 29.6 + - - -
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Residues in contact with GLY 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ASN* 3.6 21.0 - - - +
99D VAL 5.2 0.7 - - - +
100D VAL* 3.8 15.8 - - - +
124D LEU 5.7 0.2 - - - +
126D THR* 3.5 23.7 + - - -
147D ARG* 5.0 0.4 - - - +
168D LEU 2.8 15.7 + - - -
169D ILE 3.6 4.0 - - - -
171D GLU* 1.3 77.1 - - - +
173D LEU* 1.3 59.2 + - - +
174D ASN 3.7 0.2 + - - -
175D GLY 4.3 0.7 + - - -
176D GLY 4.5 0.2 - - - -
177D GLY* 4.1 11.7 + - - -
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Residues in contact with LEU 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D HIS* 5.0 3.5 - - - -
6D VAL* 4.3 7.9 - - + -
26D LEU* 4.1 17.7 - - + -
31D TRP* 3.8 33.6 - - + +
72D ASP* 3.6 37.1 - - + +
73D ILE 4.8 0.9 - - - +
74D VAL* 4.4 11.7 - - + -
98D ASN* 3.5 23.8 + - + +
100D VAL* 4.1 15.3 - - + -
169D ILE* 2.9 35.7 + - + +
170D LYS 3.9 1.1 - - - +
172D GLY* 1.3 78.1 - - - +
174D ASN* 1.3 64.6 + - - +
175D GLY 3.6 0.9 - - - -
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Residues in contact with ASN 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C LYS* 2.8 25.5 + - - +
179C ASN 3.4 2.9 - - - +
180C THR* 3.5 18.0 + - - +
3D HIS* 3.5 24.6 + - - -
31D TRP* 3.8 16.0 - - - -
170D LYS* 3.0 33.1 + - - +
171D GLU* 3.0 7.0 + - - +
173D LEU* 1.3 84.5 - - - +
175D GLY* 1.3 57.2 + - - +
176D GLY 3.5 1.8 - - - -
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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