Contacts of the helix formed by residues 162 - 175 (chain Q) in PDB entry 2AK4
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 162 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158Q ALA 3.1 14.1 + - - -
159Q TYR 3.1 4.0 + - - -
161Q GLU* 1.3 80.2 - - - +
163Q LEU* 1.3 65.3 + - - -
164Q CYS 3.3 1.6 - - - -
165Q VAL* 3.2 5.5 + - - +
166Q GLU* 3.2 17.8 + - - +
28T THR* 3.3 27.6 + - - -
29T THR* 3.7 8.5 - - - -
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Residues in contact with LEU 163 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62Q ARG* 3.7 25.6 - - - +
158Q ALA 4.1 2.4 + - - -
159Q TYR* 3.3 19.0 + - + -
162Q GLY* 1.3 69.4 - - - -
164Q CYS* 1.3 64.2 + - - +
166Q GLU* 3.9 10.3 - - + -
167Q TRP* 3.0 49.3 + - + +
1S LEU* 3.8 8.5 - - + +
4S PRO* 3.8 12.6 - - + -
28T ASP* 4.4 18.4 - - - +
29T THR* 5.4 0.6 - - + +
96T TYR* 3.5 32.1 + - + +
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Residues in contact with CYS 164 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5Q MET* 3.4 26.8 - - - +
100Q GLY* 4.0 8.1 - - - -
101Q CYS* 2.1 56.0 - - + -
159Q TYR* 3.0 39.3 + - + +
160Q LEU* 3.9 6.1 - - - +
163Q LEU* 1.3 75.2 - - - +
165Q VAL* 1.3 57.2 + - - +
168Q LEU* 3.0 31.0 + - - +
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Residues in contact with VAL 165 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101Q CYS* 4.2 4.9 - - - -
103Q LEU* 3.9 21.3 - - + +
107Q GLY 4.8 4.0 - - - +
108Q ARG* 6.0 0.2 - - - -
109Q LEU* 3.8 30.7 - - + +
160Q LEU 3.8 18.2 - - - +
161Q GLU 4.1 10.5 - - - +
162Q GLY 3.2 7.9 + - - +
164Q CYS* 1.3 76.5 - - - +
166Q GLU* 1.3 60.6 + - + +
168Q LEU* 3.3 4.3 + - - +
169Q ARG* 2.9 56.7 + - - +
28T THR* 6.0 0.7 - - - +
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Residues in contact with GLU 166 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162Q GLY 3.2 7.7 + - - +
163Q LEU* 4.1 11.2 - - + +
165Q VAL* 1.3 79.1 - - + +
167Q TRP* 1.3 62.8 + - + +
169Q ARG* 2.8 40.8 + - - +
170Q ARG* 3.1 26.6 + - - +
27T ARG 5.7 2.8 - - - +
28T THR* 3.7 32.3 - - - +
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Residues in contact with TRP 167 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5Q MET* 4.5 1.8 - - + -
55Q GLU* 3.9 7.6 - - - -
59Q TYR* 3.5 31.4 - + - -
62Q ARG* 4.1 18.9 - - - +
163Q LEU* 3.0 48.2 + - + +
164Q CYS 4.3 1.1 - - - +
166Q GLU* 1.3 76.9 - - + +
168Q LEU* 1.3 60.7 + - - +
170Q ARG* 3.2 45.4 + - - +
171Q TYR* 2.8 54.8 + + + -
1007Q IOD 4.3 11.4 - - + -
1S LEU* 3.5 45.8 - - + +
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Residues in contact with LEU 168 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Q HIS 4.0 3.1 - - - +
4Q SER* 3.7 15.9 - - - +
5Q MET* 3.7 36.7 - - + +
28Q VAL* 3.8 32.1 - - + -
101Q CYS* 4.1 7.0 - - - +
103Q LEU* 3.8 28.7 - - + -
164Q CYS 3.0 20.0 + - - +
165Q VAL 3.6 4.3 - - - +
167Q TRP* 1.3 75.6 - - - +
169Q ARG* 1.3 56.6 + - - +
171Q TYR* 3.2 7.6 + - - +
172Q LEU* 2.9 47.3 + - + +
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Residues in contact with ARG 169 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103Q LEU* 4.0 17.5 - - + -
107Q GLY* 4.2 15.2 + - - -
165Q VAL* 2.9 40.0 + - - +
166Q GLU* 2.8 43.8 + - - +
168Q LEU* 1.3 76.2 - - - +
170Q ARG* 1.3 60.6 + - - +
172Q LEU* 3.4 10.5 + - + +
173Q GLU* 3.1 22.9 + - - +
28T THR* 5.5 4.0 - - - +
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Residues in contact with ARG 170 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54Q GLN* 5.9 1.8 + - - +
55Q GLU* 2.8 42.9 + - - +
166Q GLU 3.1 13.9 + - - +
167Q TRP* 3.2 39.5 + - - +
169Q ARG* 1.3 74.5 - - - +
171Q TYR* 1.3 61.6 + - - +
173Q GLU* 3.3 6.2 + - - +
174Q ASN* 2.9 44.6 + - - +
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Residues in contact with TYR 171 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Q MET* 3.6 22.9 - - - -
28Q VAL* 4.0 16.4 - - + -
33Q PHE* 3.9 9.9 - + - -
51Q TRP* 3.7 21.4 - + + -
52Q ILE* 3.4 25.6 - - + -
55Q GLU* 4.0 11.2 - - - -
59Q TYR* 2.5 28.8 + - - -
167Q TRP* 2.8 46.5 + + - -
168Q LEU* 3.6 5.4 - - - +
170Q ARG* 1.3 73.9 - - - +
172Q LEU* 1.3 54.1 + - - +
174Q ASN* 3.2 5.2 + - - +
175Q GLY 2.8 31.5 + - - -
179Q LEU* 3.5 9.2 - - + +
1S LEU 2.7 27.1 + - - -
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Residues in contact with LEU 172 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Q HIS* 3.5 55.4 - - + +
28Q VAL* 4.1 17.3 - - + -
103Q LEU* 4.1 12.3 - - + -
168Q LEU* 2.9 37.0 + - + +
169Q ARG* 3.6 8.5 - - + +
171Q TYR* 1.3 76.8 - - - +
173Q GLU* 1.3 53.7 + - - +
176Q LYS* 3.2 17.5 - - - -
179Q LEU* 4.1 14.8 - - + -
180Q GLN* 2.7 33.1 + - + +
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Residues in contact with GLU 173 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169Q ARG 3.1 15.3 + - - +
170Q ARG* 3.7 6.3 - - - +
171Q TYR 3.2 0.2 - - - -
172Q LEU* 1.3 75.9 - - - +
174Q ASN* 1.3 70.1 + - - +
175Q GLY 3.2 1.1 + - - -
176Q LYS* 3.4 38.2 - - - +
180Q GLN* 4.5 4.2 + - - +
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Residues in contact with ASN 174 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51Q TRP* 3.8 18.6 + - + +
54Q GLN* 3.8 38.3 + - - +
55Q GLU* 3.9 8.9 + - - -
170Q ARG* 2.9 50.0 + - - +
171Q TYR* 3.9 6.6 - - + +
173Q GLU* 1.3 81.9 - - - +
175Q GLY* 1.3 56.7 + - - +
176Q LYS* 3.5 0.8 + - - +
177Q GLU* 5.4 4.7 - - - +
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Residues in contact with GLY 175 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51Q TRP* 3.8 25.3 - - - +
171Q TYR 2.8 14.4 + - - -
172Q LEU 3.9 2.9 - - - -
174Q ASN* 1.3 76.7 - - - +
176Q LYS* 1.3 54.5 + - - +
177Q GLU* 3.3 4.7 - - - -
178Q THR* 3.1 7.6 + - - -
179Q LEU* 2.7 37.9 + - - +
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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