Contacts of the helix formed by residues 182 - 196 (chain A) in PDB entry 5X6E
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 HIS 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A GLN* 3.9 2.7 - - - +
180A ILE* 3.5 5.1 - - + +
181A ALA* 1.3 92.0 + - + +
183A SER* 1.3 63.5 + - - +
184A SER 3.3 4.6 + - - +
185A ALA* 3.5 1.4 + - + -
186A VAL* 3.2 24.7 + - - +
18C G 3.9 19.1 - - + -
19C T 2.8 62.9 + - + -
20C T 3.7 39.2 - - + +
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Residues in contact with SER 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A MET* 3.6 18.2 - - - +
172A GLN* 3.5 30.1 + - - +
182A HIS* 1.3 68.8 - - - +
184A SER* 1.3 59.4 + - - +
186A VAL* 3.4 10.3 + - - +
187A SER* 2.9 29.3 + - - -
7D C 5.6 0.5 - - - +
8D A 4.5 8.7 + - - -
9D T 3.7 14.9 - - - +
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Residues in contact with SER 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A HIS* 4.1 0.6 - - - +
183A SER* 1.3 77.3 - - - +
185A ALA* 1.3 58.1 + - - +
187A SER* 3.1 6.8 + - - -
188A ARG* 2.9 26.4 + - - +
19C T 2.8 26.6 + - - -
20C T 2.8 33.9 + - - -
21C A 4.3 2.7 - - - -
9D T 4.3 11.3 + - - +
10D T 3.8 15.3 + - - +
11D A 3.5 6.4 + - - -
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Residues in contact with ALA 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ILE* 3.7 22.2 - - + -
182A HIS 3.5 2.0 + - - +
183A SER 3.5 0.2 - - - -
184A SER* 1.3 80.6 + - - +
186A VAL* 1.3 58.1 + - - +
188A ARG* 3.1 18.7 - - - +
189A ILE* 2.9 38.0 + - + +
17C T 4.2 15.9 - - + +
18C G 4.9 0.4 - - - +
19C T 3.7 22.1 - - + +
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Residues in contact with VAL 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ILE* 4.7 8.7 - - + -
171A MET* 3.1 34.8 - - + +
172A GLN* 5.2 0.4 - - - -
174A LEU* 4.0 17.7 - - + -
175A GLY* 3.5 27.6 - - - +
180A ILE* 3.7 18.6 - - + -
182A HIS 3.2 18.4 - - - +
183A SER* 3.6 7.0 - - - +
184A SER 3.2 0.8 - - - -
185A ALA* 1.3 77.7 - - - +
187A SER* 1.3 56.9 + - - +
189A ILE* 3.4 3.3 + - - +
190A ILE* 2.8 30.2 + - + +
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Residues in contact with SER 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A MET* 3.5 17.5 - - - +
183A SER 2.9 14.8 + - - -
184A SER 3.4 9.0 - - - -
186A VAL* 1.3 72.9 - - - +
188A ARG* 1.3 53.4 + - - +
190A ILE* 3.2 1.2 + - - +
191A SER* 2.5 49.5 + - - -
9D T 3.6 41.5 + - - +
10D T 3.9 13.1 - - - +
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Residues in contact with ARG 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A SER* 2.9 13.3 + - - +
185A ALA* 3.1 15.6 - - - +
187A SER* 1.3 73.7 - - - +
189A ILE* 1.3 67.9 + - + +
191A SER* 3.1 8.0 + - - -
192A LYS* 3.0 42.0 + - + +
17C T 3.0 45.0 - - - +
18C G 2.8 48.2 + - - -
19C T 3.0 13.2 + - - -
10D T 4.9 3.9 - - + +
11D A 4.8 0.8 + - - +
12D A 2.9 19.0 - - - +
13D C 4.5 1.8 - - - +
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Residues in contact with ILE 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A LYS* 5.4 1.8 - - + -
140A LEU* 3.9 29.8 - - + +
143A ILE* 3.8 37.2 - - + -
180A ILE* 4.3 12.3 - - + -
185A ALA* 2.9 31.1 + - + +
186A VAL* 3.9 3.4 - - - +
188A ARG* 1.3 81.7 - - + +
190A ILE* 1.3 66.1 + - - +
192A LYS* 3.3 15.6 + - - +
193A LEU* 3.1 24.9 + - + +
17C T 4.3 37.0 - - + +
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Residues in contact with ILE 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ILE* 4.1 21.5 - - + -
147A LEU* 4.8 1.6 - - + -
171A MET* 3.4 25.4 - - + -
174A LEU* 3.8 25.6 - - + -
186A VAL* 2.8 23.7 + - + +
187A SER* 3.4 8.5 - - - +
189A ILE* 1.3 73.3 - - - +
191A SER* 1.3 61.9 + - - +
193A LEU* 3.3 15.6 - - + +
194A LYS* 3.1 21.3 + - - +
199A ILE* 4.0 16.7 - - + +
201A TYR* 6.4 0.9 - - + -
206A PHE* 4.3 17.0 - - + -
9D T 4.0 10.8 - - - +
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Residues in contact with SER 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A SER* 2.5 32.5 + - - -
188A ARG* 3.3 8.5 - - - -
190A ILE* 1.3 74.2 - - - +
192A LYS* 1.3 60.6 + - - +
193A LEU 3.0 2.0 - - - -
194A LYS* 2.7 58.0 + - - +
195A GLN* 3.5 3.2 + - - +
9D T 5.3 0.9 + - - -
10D T 3.1 19.1 + - - -
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Residues in contact with LYS 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LEU* 4.0 30.5 - - + +
188A ARG* 3.0 27.9 + - + +
189A ILE* 3.3 13.8 + - + +
191A SER* 1.3 75.1 - - - +
193A LEU* 1.3 57.6 + - + +
195A GLN* 3.7 8.1 + - - +
196A GLU* 2.8 28.8 - - - +
16C A 4.4 25.1 + - - +
17C T 4.5 11.7 + - + -
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Residues in contact with LEU 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LEU* 4.8 7.4 - - + -
143A ILE* 4.4 7.6 - - + -
144A CYS* 4.6 10.5 - - - -
147A LEU* 3.7 30.5 - - + -
189A ILE* 3.1 20.7 + - + +
190A ILE* 3.3 21.1 - - + +
191A SER 3.0 0.2 - - - -
192A LYS* 1.3 72.7 - - + +
194A LYS* 1.3 51.7 + - - +
195A GLN 2.7 7.7 + - - -
196A GLU* 2.6 32.3 + - - +
198A VAL* 3.0 33.3 - - + +
199A ILE* 3.5 20.9 - - + -
213A TYR* 4.4 18.8 - - + +
214A LEU* 5.8 0.2 - - + -
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Residues in contact with LYS 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ILE* 3.1 9.1 + - + +
191A SER* 2.7 39.9 + - - +
193A LEU* 1.3 74.3 - - - +
195A GLN* 1.3 89.0 + - - +
196A GLU 3.5 4.3 - - - +
197A LYS* 5.2 0.9 - - - -
199A ILE* 3.8 20.8 - - + +
10D T 3.2 38.2 + - - -
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Residues in contact with GLN 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A SER 3.5 7.3 + - - +
192A LYS* 4.0 5.6 - - - +
193A LEU 2.7 5.9 + - - -
194A LYS* 1.3 104.2 - - + +
196A GLU* 1.3 75.0 + - - +
197A LYS* 3.5 2.3 + - - +
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Residues in contact with GLU 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LYS 2.8 21.5 - - - +
193A LEU 2.6 20.1 + - - +
194A LYS 3.5 4.9 - - - +
195A GLN* 1.3 80.7 - - - +
197A LYS* 1.3 54.9 + - - +
198A VAL* 2.6 30.1 + - + -
199A ILE 4.0 1.0 + - - -
213A TYR* 4.7 20.0 + - + -
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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