Contacts of the helix formed by residues 218 - 237 (chain I) in PDB entry 6AHU
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 LYS 218 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A A 4.2 20.7 + - - +
24A G 3.0 26.9 + - - -
4I PHE* 3.7 30.9 - - + -
201I TYR* 5.0 12.0 + - + -
204I ALA* 4.3 23.8 + - + +
215I SER 3.3 13.6 + - - +
216I ASP 3.2 0.6 - - - -
217I ALA* 1.3 77.6 - - - +
219I ALA* 1.3 62.9 + - - +
221I VAL* 3.4 20.4 - - - +
222I SER* 3.6 10.2 + - - -
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Residues in contact with ALA 219 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215I SER 4.0 1.5 + - - +
216I ASP* 3.0 33.1 + - - +
218I LYS* 1.3 77.6 - - + +
220I ALA* 1.3 58.7 + - - +
221I VAL 3.2 1.8 - - - -
222I SER* 4.5 2.0 - - - -
223I THR* 2.8 46.6 + - + +
224I ASN* 2.9 16.0 + - - +
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Residues in contact with ALA 220 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185I VAL 3.4 27.1 - - - +
186I ILE* 3.7 9.2 - - - +
187I ILE* 4.3 19.1 + - + -
207I GLY* 6.2 0.2 - - - -
212I LEU* 5.0 12.3 - - + -
216I ASP* 3.1 9.6 + - - +
217I ALA* 3.5 17.0 - - + +
218I LYS 3.2 1.4 - - - -
219I ALA* 1.3 77.7 - - - +
221I VAL* 1.3 56.9 + - - +
224I ASN* 3.8 8.1 - - - +
225I CYS* 3.4 15.0 - - - -
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Residues in contact with VAL 221 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I PHE* 3.7 25.4 - - + -
5I ALA* 3.9 12.7 + - + +
6I ASP* 3.6 13.2 + - - +
7I LEU* 3.8 34.1 - - + -
30I TYR* 5.6 0.4 - - + -
187I ILE* 5.6 0.4 - - + -
200I PRO* 4.7 4.0 - - + +
203I VAL* 3.9 31.0 - - + -
204I ALA* 5.4 2.7 - - - +
217I ALA 4.2 2.0 + - - +
218I LYS* 3.4 20.2 - - + +
220I ALA* 1.3 77.0 - - - +
222I SER* 1.3 58.9 + - - +
225I CYS* 3.4 21.9 - - - +
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Residues in contact with SER 222 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2I ALA* 5.0 3.1 - - - -
3I VAL 3.2 28.3 + - - +
4I PHE* 3.6 28.4 - - - +
6I ASP* 4.9 1.6 - - - +
218I LYS* 3.6 16.4 + - - -
219I ALA* 4.5 2.2 - - - -
221I VAL* 1.3 82.1 - - - +
223I THR* 1.3 68.3 + - - +
224I ASN 3.7 0.2 - - - -
225I CYS* 4.1 1.4 - - - +
226I ARG* 3.3 21.7 + - - +
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Residues in contact with THR 223 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219I ALA* 2.8 35.1 + - + +
222I SER* 1.3 75.3 + - - +
224I ASN* 1.3 67.7 + - - +
225I CYS 3.2 0.2 - - - -
226I ARG* 3.1 18.0 + - - +
227I ALA* 3.3 11.1 + - - +
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Residues in contact with ASN 224 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182I GLY 5.4 1.4 + - - -
183I LYS 3.2 21.2 + - - +
184I ASN* 3.5 17.8 - - + +
185I VAL* 3.4 25.9 + - - +
186I ILE* 3.6 23.9 - - + +
216I ASP* 4.6 11.3 + - - -
219I ALA* 2.9 19.5 + - - +
220I ALA* 3.8 6.9 - - - +
223I THR* 1.3 81.1 - - - +
225I CYS* 1.3 61.4 + - - +
227I ALA* 3.6 15.6 + - - +
228I ALA* 3.8 8.1 + - - +
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Residues in contact with CYS 225 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I ASP* 3.2 40.7 - - + +
7I LEU* 4.2 8.7 - - - -
76I ARG* 4.8 4.9 + - - -
186I ILE* 3.7 19.1 - - - -
220I ALA 3.4 17.7 - - - -
221I VAL* 3.4 26.5 - - - +
222I SER 4.0 1.9 + - - +
223I THR 3.2 0.8 - - - -
224I ASN* 1.3 75.7 - - - +
226I ARG* 1.3 63.3 + - - +
227I ALA 3.3 0.2 - - - -
228I ALA* 3.6 17.4 + - - +
229I LEU* 4.3 3.5 + - - +
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Residues in contact with ARG 226 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I ALA 5.6 5.9 - - - +
3I VAL* 5.3 19.8 - - + +
6I ASP* 4.9 8.3 + - - +
222I SER 3.3 18.4 + - - +
223I THR* 3.1 10.4 + - - +
225I CYS* 1.3 78.9 - - - +
227I ALA* 1.3 62.7 + - - +
228I ALA 3.2 1.1 + - - -
229I LEU* 3.6 6.1 + - - +
230I LEU* 3.3 42.5 + - - +
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Residues in contact with ALA 227 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149I GLY 5.7 1.2 - - - +
184I ASN* 6.2 3.6 - - + -
223I THR 3.3 8.4 + - - +
224I ASN* 3.9 12.6 - - - +
225I CYS 3.3 0.8 - - - -
226I ARG* 1.3 79.4 - - - +
228I ALA* 1.3 58.0 + - - +
229I LEU 3.5 0.2 - - - -
230I LEU* 3.9 13.0 - - + -
231I HIS* 3.1 30.9 + - + +
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Residues in contact with ALA 228 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76I ARG* 3.9 20.4 - - - +
102I VAL* 3.7 9.3 - - + +
123I ASP* 4.9 2.5 - - - +
124I LEU* 3.8 30.1 - - + -
151I ALA* 6.1 1.3 - - + -
186I ILE* 6.1 1.6 - - + -
224I ASN 3.8 6.1 + - - +
225I CYS* 3.6 14.7 + - - +
226I ARG 3.2 1.0 - - - -
227I ALA* 1.3 78.0 - - - +
229I LEU* 1.3 57.8 + - - +
231I HIS* 4.5 1.2 - - - +
232I GLY* 3.0 25.5 + - - -
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Residues in contact with LEU 229 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I VAL* 5.8 6.7 - - + -
72I LYS* 5.4 14.4 - - + +
74I LEU* 3.8 37.0 - - + -
76I ARG* 4.6 4.6 - - - +
101I ASP* 3.6 26.0 - - - +
102I VAL* 4.5 6.5 - - + -
225I CYS 4.3 2.6 + - - +
226I ARG* 3.6 8.0 + - - +
227I ALA 3.5 0.2 - - - -
228I ALA* 1.3 77.4 - - - +
230I LEU* 1.3 63.1 + - - +
232I GLY* 5.0 0.2 - - - -
233I GLU* 3.2 33.0 + - + +
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Residues in contact with LEU 230 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226I ARG* 3.3 40.2 + - - +
227I ALA* 4.2 9.4 - - + -
228I ALA 3.3 0.6 - - - -
229I LEU* 1.3 80.1 - - - +
231I HIS* 1.3 59.5 + - - +
233I GLU* 4.0 16.8 + - - +
234I THR* 4.4 11.4 - - - +
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Residues in contact with HIS 231 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122I VAL 5.1 5.8 - - - -
123I ASP* 3.6 20.7 + - + +
148I ARG* 3.9 27.6 + - + +
149I GLY* 4.7 18.7 + - - +
150I LEU* 6.2 0.4 - - - -
227I ALA* 3.1 19.3 + - + +
228I ALA* 4.5 1.3 - - - +
230I LEU* 1.3 75.0 - - - +
232I GLY* 1.3 60.4 + - - +
233I GLU 3.3 0.7 - - - -
234I THR* 3.2 22.3 + - - -
235I ARG* 3.8 9.1 + - + +
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Residues in contact with GLY 232 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101I ASP* 2.9 25.2 - - - +
102I VAL* 4.8 1.6 - - - -
123I ASP* 3.6 25.3 + - - -
228I ALA 3.0 17.0 + - - -
229I LEU* 4.0 0.9 - - - -
230I LEU 3.5 0.2 - - - -
231I HIS* 1.3 76.8 + - - +
233I GLU* 1.3 62.6 + - - +
234I THR 3.4 0.2 - - - -
235I ARG* 3.5 4.6 + - - +
236I LYS 3.4 12.6 + - - -
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Residues in contact with GLU 233 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101I ASP* 3.9 13.0 + - - +
229I LEU* 3.2 24.3 + - + +
230I LEU* 4.3 13.5 - - - +
231I HIS 3.3 0.8 - - - -
232I GLY* 1.3 77.9 - - - +
234I THR* 1.3 64.3 + - + +
236I LYS* 3.4 4.1 + - + +
237I THR* 3.3 29.9 + - + +
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Residues in contact with THR 234 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230I LEU 4.4 10.9 + - - +
231I HIS* 3.2 19.4 + - - -
233I GLU* 1.3 76.6 - - + +
235I ARG* 1.3 60.2 + - - +
237I THR* 3.0 29.1 - - - +
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Residues in contact with ARG 235 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90I LEU 5.6 1.6 + - - -
94I SER* 4.2 21.7 + - - -
99I LEU 5.8 1.2 + - - -
100I TYR 5.1 1.6 + - - -
101I ASP 5.2 3.7 + - - +
103I VAL* 3.5 32.3 - - - +
121I ASP* 2.5 45.6 + - - +
122I VAL* 4.5 1.1 - - - +
123I ASP* 3.6 24.6 + - - -
231I HIS* 4.2 11.7 - - + +
232I GLY* 3.5 10.4 + - - +
233I GLU 3.2 0.6 - - - -
234I THR* 1.3 82.3 + - - +
236I LYS* 1.3 66.3 + - - +
237I THR 4.5 1.7 - - - +
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Residues in contact with LYS 236 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98I ARG* 3.3 42.6 + - + +
99I LEU* 3.4 42.7 - - - +
100I TYR 3.7 1.0 - - - +
101I ASP* 3.4 44.3 + - - +
232I GLY 3.4 3.6 + - - +
233I GLU* 3.9 5.8 - - - +
234I THR 3.4 0.4 - - - -
235I ARG* 1.3 85.1 - - - +
237I THR* 1.3 66.2 + - + +
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Residues in contact with THR 237 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98I ARG* 6.1 2.2 - - - -
233I GLU* 3.3 23.5 + - + +
234I THR* 3.0 22.0 + - - +
235I ARG 4.5 2.0 - - - +
236I LYS* 1.3 86.1 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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