Contacts of the helix formed by residues 203 - 220 (chain B) in PDB entry 2QJK
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 203 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B ASP* 3.8 16.6 - - - +
192B ASP* 5.2 1.1 + - - -
201B ASP* 2.5 27.3 + - - +
202B ALA* 1.3 77.3 - - - +
204B VAL* 1.3 67.6 + - - +
205B HIS* 3.9 11.9 + - - +
206B ALA* 2.6 26.7 + - - +
207B MET* 3.1 9.2 + - - -
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Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B LEU 4.8 7.6 - - - +
136B THR* 5.4 5.8 - - - +
189B LEU* 3.4 26.1 - - + +
190B MET* 3.2 19.3 - - - +
191B ASP* 2.9 47.9 - - - +
202B ALA 3.4 3.3 + - - -
203B SER* 1.3 69.8 - - - +
205B HIS* 1.3 63.5 + - - +
207B MET* 4.5 8.5 - - - -
208B ALA* 3.2 23.2 + - + +
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Residues in contact with HIS 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 6.3 0.8 - - - +
132B TYR* 3.1 34.9 + - - +
136B THR* 5.4 3.4 - - - -
203B SER* 2.8 11.4 + - - +
204B VAL* 1.3 81.0 - - - +
206B ALA* 1.3 68.9 + - + +
208B ALA* 4.9 1.3 - - - -
209B GLU* 3.2 43.0 + - - +
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Residues in contact with ALA 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B HIS* 5.2 3.6 - - + +
201B ASP* 3.5 32.8 - - - +
203B SER* 2.6 21.6 + - - +
205B HIS* 1.3 80.3 + - + +
207B MET* 1.3 69.0 + - - +
209B GLU* 2.7 19.7 + - - +
210B ASP* 2.8 22.7 + - - +
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Residues in contact with MET 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B VAL* 4.4 21.1 - - + +
35B VAL* 4.7 4.0 - - + -
189B LEU* 4.7 15.0 - - + -
190B MET 4.6 6.5 - - - +
193B LEU* 4.2 15.9 - - + -
194B VAL* 3.3 46.2 - - + +
196B TYR* 4.2 19.7 + - + +
202B ALA* 3.5 30.5 - - + +
203B SER 3.1 7.2 + - - +
204B VAL* 4.0 11.9 - - - +
206B ALA* 1.3 77.4 - - - +
208B ALA* 1.3 55.7 + - - +
210B ASP* 2.9 3.6 + - - +
211B VAL* 2.8 37.1 + - - +
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Residues in contact with ALA 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B TYR* 3.8 17.0 - - + +
135B LEU* 3.8 19.3 - - + -
136B THR* 4.4 4.5 - - - +
189B LEU* 3.8 14.7 - - + +
204B VAL* 3.2 16.1 + - + +
205B HIS 3.7 4.0 - - - +
206B ALA 3.1 0.4 - - - -
207B MET* 1.3 78.2 - - - +
209B GLU* 1.3 65.5 + - - +
211B VAL* 3.3 9.1 - - - +
212B SER* 2.8 30.4 + - - -
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Residues in contact with GLU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 4.0 19.8 - - + +
10B PRO* 5.1 4.3 - - - +
11B PHE* 3.1 41.4 - - + -
24B GLN* 3.6 16.9 + - - +
132B TYR* 3.5 13.9 - - + -
205B HIS* 3.2 34.1 + - - +
206B ALA* 2.7 15.8 + - - +
208B ALA* 1.3 76.9 - - - +
210B ASP* 1.3 64.2 + - - +
212B SER* 4.6 0.2 - - - -
213B ALA* 3.3 6.2 + - - +
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Residues in contact with ASP 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLN* 2.8 42.9 + - + +
27B ARG* 3.2 31.0 + - - -
28B GLY* 4.2 13.5 - - - +
196B TYR* 3.2 24.3 + - - +
200B HIS* 4.7 1.4 - - - -
206B ALA* 2.8 26.7 + - - +
207B MET 2.9 6.0 + - - +
209B GLU* 1.3 69.9 - - - +
211B VAL* 1.3 55.2 + - - +
212B SER 2.6 5.3 + - - -
213B ALA* 2.6 27.9 + - - +
214B PHE 2.8 9.5 + - - -
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Residues in contact with VAL 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B GLY* 3.8 14.6 - - - +
31B VAL* 3.8 31.6 - - + +
32B TYR* 4.0 16.2 - - + +
36B CYS* 4.0 14.1 - - - -
135B LEU* 3.6 25.8 - - + -
189B LEU* 6.0 0.2 - - + -
207B MET 2.8 16.2 + - - +
208B ALA* 3.3 12.6 - - - +
210B ASP* 1.3 72.3 - - - +
212B SER* 1.3 61.8 + - - +
214B PHE* 3.4 2.0 - - + +
215B LEU* 2.8 38.8 + - + +
301B HEM 4.2 8.7 - - + -
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Residues in contact with SER 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B PHE* 3.8 17.0 - - - -
104B ALA* 5.4 0.2 - - - +
128B PRO* 3.8 14.7 - - - +
131B ILE* 3.8 11.5 - - - +
132B TYR* 3.5 25.3 + - - +
135B LEU* 4.4 0.2 - - - +
208B ALA 2.8 18.7 + - - -
209B GLU 3.5 5.6 - - - -
210B ASP 2.6 4.4 + - - -
211B VAL* 1.3 75.2 - - - +
213B ALA* 1.3 54.5 + - - -
215B LEU* 2.6 29.8 + - - +
216B MET* 2.6 18.8 + - - +
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Residues in contact with ALA 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B PHE* 4.3 4.3 - - + -
13B PHE* 3.8 28.0 - - + -
20B PHE* 3.9 2.0 - - + -
24B GLN* 3.8 28.9 - - + +
25B LEU* 3.3 13.9 - - + +
209B GLU 3.3 9.0 + - - +
210B ASP 2.6 12.4 + - - +
212B SER* 1.3 75.3 - - - +
214B PHE* 1.3 62.5 + - - +
216B MET* 3.1 4.0 + - - +
217B TRP 3.0 17.8 + - - -
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Residues in contact with PHE 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 3.6 27.7 - - + +
28B GLY* 3.8 20.9 - - - -
29B LEU* 3.8 30.5 - - + -
32B TYR* 3.6 30.5 - + + -
42B MET* 3.2 38.1 - - + -
50B LEU* 4.7 3.1 - - + -
56B PRO* 4.8 2.7 - - + -
89B PHE* 5.0 2.2 - + - -
210B ASP 2.8 6.1 + - - -
211B VAL* 3.4 10.1 - - + +
213B ALA* 1.3 76.5 - - - +
215B LEU* 1.3 59.6 + - + +
217B TRP* 2.8 39.3 + + - +
218B ALA* 2.7 32.6 + - + -
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Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B TYR* 5.1 3.6 - - + -
36B CYS* 5.6 0.4 - - - -
42B MET* 4.0 19.3 - - - -
100B LEU* 3.8 55.2 - - + +
103B MET* 5.5 0.9 - - + -
104B ALA* 4.0 6.1 + - + +
131B ILE* 4.4 28.0 - - + -
211B VAL* 2.8 20.0 + - + +
212B SER* 2.6 15.4 + - - +
214B PHE* 1.3 83.6 - - + +
216B MET* 1.3 58.9 + - - -
218B ALA* 3.6 4.5 - - + +
219B ALA* 3.1 22.9 + - - +
301B HEM 4.1 18.6 - - + -
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Residues in contact with MET 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A BGL 3.8 26.5 - - - +
13B PHE* 3.5 40.8 - - + -
20B PHE* 4.0 9.4 - - + -
104B ALA* 3.8 28.0 - - + +
105B LYS* 5.9 3.6 - - + -
128B PRO* 4.4 15.3 - - + -
212B SER 2.6 14.6 + - - +
213B ALA* 3.3 10.1 - - - +
214B PHE 3.0 0.2 - - - -
215B LEU* 1.3 72.5 - - - +
217B TRP* 1.3 59.2 + - - +
219B ALA* 3.2 3.4 + - - +
220B GLU* 2.9 37.3 + - + +
223B LEU* 4.5 8.7 - - + -
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Residues in contact with TRP 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE* 3.4 27.3 - + + -
25B LEU* 3.9 11.7 - - + -
45B VAL* 4.7 9.6 - - + -
49B SER* 3.5 47.6 - - - -
50B LEU* 4.2 9.6 - - + -
52B GLU* 5.4 1.6 - - + -
53B PRO 5.8 0.4 + - - -
54B GLY 3.9 7.8 - - - -
55B GLY* 3.5 22.8 - - - +
56B PRO* 3.6 22.7 - - + -
213B ALA 3.0 7.7 + - - +
214B PHE* 2.8 38.7 + + - +
216B MET* 1.3 73.4 - - - +
218B ALA* 1.3 91.7 + - + +
219B ALA 2.8 0.9 + - - -
220B GLU 2.9 0.8 + - - +
221B PRO* 2.8 61.4 + - + +
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Residues in contact with ALA 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ARG* 2.9 29.5 + - - -
42B MET* 3.9 31.2 - - + -
45B VAL* 4.0 8.6 - - + +
101B SER 3.9 5.2 - - - +
214B PHE* 2.7 17.3 + - + +
215B LEU* 3.6 16.8 - - + +
217B TRP* 1.3 91.1 - - + +
219B ALA* 1.3 58.0 + - - +
221B PRO* 3.7 0.2 - - - +
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Residues in contact with ALA 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A GLU* 4.5 2.6 - - - +
85A ARG* 3.7 7.9 + - - +
101B SER 3.1 20.0 - - - +
102B LEU* 3.7 26.8 - - + +
103B MET 4.6 0.4 - - - +
104B ALA* 4.7 7.6 - - + +
105B LYS* 3.8 22.0 + - + +
215B LEU 3.1 13.6 + - - +
216B MET* 3.8 2.9 - - - +
217B TRP 2.8 1.0 + - - -
218B ALA* 1.3 80.4 - - - +
220B GLU* 1.3 58.7 + - + +
221B PRO* 3.3 9.2 - - - +
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Residues in contact with GLU 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A MET* 5.0 3.1 - - - +
91A PHE* 5.6 2.9 - - - +
95A TYR* 2.7 27.5 + - - -
272A ASN* 4.3 2.2 + - - +
20B PHE* 4.0 5.5 - - - -
105B LYS* 3.6 29.6 + - + -
216B MET* 2.9 22.4 + - + +
217B TRP 2.9 9.8 + - - -
219B ALA* 1.3 71.7 - - + +
221B PRO* 1.3 64.1 - - - +
222B LYS* 3.2 8.7 + - - +
223B LEU* 3.0 34.3 + - + +
226B ARG* 2.4 34.7 + - - +
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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