Contacts of the helix formed by residues 203 - 220 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191K ASP* 3.8 16.2 - - - -
192K ASP* 5.5 0.9 - - - -
201K ASP* 2.6 25.6 + - - +
202K ALA* 1.3 77.4 - - - +
204K VAL* 1.3 68.0 + - - +
205K HIS* 3.8 11.9 + - - +
206K ALA* 2.6 27.4 + - - +
207K MET* 3.2 8.5 + - - -
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Residues in contact with VAL 204 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135K LEU 4.8 9.2 - - - +
136K THR* 5.4 6.2 + - - -
189K LEU* 3.6 24.1 - - + +
190K MET* 3.2 20.0 - - - +
191K ASP* 2.9 46.3 + - - +
202K ALA 3.5 3.3 + - - -
203K SER* 1.3 70.7 - - - +
205K HIS* 1.3 63.9 + - - +
207K MET* 4.1 7.6 - - - -
208K ALA* 3.2 22.8 + - + +
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Residues in contact with HIS 205 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9K VAL* 6.3 0.6 - - - +
132K TYR* 3.2 34.4 + - - -
136K THR* 5.5 3.8 - - - -
203K SER* 2.7 15.3 + - - +
204K VAL* 1.3 77.8 - - - +
206K ALA* 1.3 68.4 + - + +
208K ALA* 4.9 1.3 - - - -
209K GLU* 3.2 43.2 + - - +
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Residues in contact with ALA 206 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200K HIS* 5.2 3.6 - - + +
201K ASP* 3.5 32.1 - - - +
203K SER* 2.6 21.2 + - - +
205K HIS* 1.3 82.4 + - - +
207K MET* 1.3 68.1 + - - +
209K GLU* 2.7 20.0 + - - +
210K ASP* 2.8 23.2 + - - +
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Residues in contact with MET 207 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31K VAL* 4.4 14.1 - - + +
35K VAL* 4.7 1.6 - - + -
189K LEU* 4.3 27.1 - - + -
190K MET 4.5 7.4 - - - +
193K LEU* 4.1 14.6 - - + -
194K VAL* 3.3 47.1 - - + +
196K TYR* 3.8 21.3 + - + +
202K ALA* 3.6 28.5 - - + +
203K SER 3.2 6.9 + - - +
204K VAL* 4.0 11.9 - - - +
206K ALA* 1.3 76.4 - - - +
208K ALA* 1.3 64.4 + - - +
210K ASP* 3.0 3.3 + - - +
211K VAL* 2.8 28.6 + - - +
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Residues in contact with ALA 208 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132K TYR* 3.8 16.6 - - + +
135K LEU* 3.9 28.7 - - + -
136K THR* 4.4 4.9 - - - +
189K LEU* 4.0 4.6 - - + +
204K VAL* 3.2 16.8 + - + +
205K HIS 3.7 3.6 - - - +
206K ALA 3.2 0.4 - - - -
207K MET* 1.3 76.7 - - - +
209K GLU* 1.3 66.2 + - - +
211K VAL* 3.3 9.8 - - - +
212K SER* 2.8 30.6 + - - -
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Residues in contact with GLU 209 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9K VAL* 4.0 19.7 - - + +
10K PRO* 5.2 3.5 - - - +
11K PHE* 3.1 42.3 - - + -
24K GLN* 3.6 17.3 + - - +
132K TYR* 3.6 14.6 - - + -
205K HIS* 3.2 34.6 + - - +
206K ALA* 2.7 15.9 + - - +
208K ALA* 1.3 74.6 - - - +
210K ASP* 1.3 64.4 + - - +
212K SER* 4.6 0.2 - - - -
213K ALA* 3.3 5.4 + - - +
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Residues in contact with ASP 210 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K GLN* 2.7 43.4 + - + +
27K ARG* 3.2 30.5 + - - -
28K GLY* 4.2 13.9 - - - +
196K TYR* 3.2 22.9 + - - +
200K HIS* 4.8 1.6 - - - -
206K ALA* 2.8 22.6 + - - +
207K MET 3.0 6.2 + - - +
209K GLU* 1.3 73.9 - - - +
211K VAL* 1.3 55.1 + - - +
212K SER 2.6 5.2 + - - -
213K ALA* 2.6 28.6 + - - +
214K PHE* 2.8 9.8 + - - +
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Residues in contact with VAL 211 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28K GLY* 3.8 13.6 - - - +
31K VAL* 3.8 30.0 - - + +
32K TYR* 3.9 16.4 - - + +
36K CYS* 3.9 14.6 - - - -
135K LEU* 3.6 24.7 - - + -
189K LEU* 6.0 0.2 - - + -
207K MET 2.8 16.6 + - - +
208K ALA* 3.3 11.2 - - - +
210K ASP* 1.3 73.0 - - - +
212K SER* 1.3 61.4 + - - +
214K PHE* 3.3 1.6 - - + +
215K LEU* 2.8 39.2 + - + +
301K HEM 4.0 13.0 - - + -
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Residues in contact with SER 212 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K PHE* 3.8 17.3 - - - -
104K ALA* 5.3 0.3 - - - +
128K PRO* 3.6 14.8 + - - +
131K ILE* 3.8 11.7 - - - +
132K TYR* 3.5 25.5 + - - +
135K LEU* 4.5 0.3 - - - +
208K ALA 2.8 18.4 + - - -
209K GLU 3.6 5.2 - - - -
210K ASP 2.6 4.2 + - - -
211K VAL* 1.3 76.1 - - - +
213K ALA* 1.3 53.1 + - - -
215K LEU* 2.6 30.2 + - - +
216K MET* 2.7 18.2 + - - +
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Residues in contact with ALA 213 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K PHE* 4.2 4.4 - - + -
13K PHE* 3.8 27.8 - - + -
20K PHE* 3.8 2.1 - - + -
24K GLN* 3.7 28.3 - - + +
25K LEU* 3.2 15.8 - - + +
209K GLU 3.3 9.5 + - - +
210K ASP 2.6 12.3 + - - +
212K SER* 1.3 75.2 - - - +
214K PHE* 1.3 61.8 + - - +
216K MET* 3.1 4.2 + - - +
217K TRP 3.0 17.2 + - - -
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Residues in contact with PHE 214 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25K LEU* 3.6 27.3 - - + +
28K GLY* 3.8 20.4 - - - -
29K LEU* 3.8 30.1 - - + -
32K TYR* 3.5 24.5 - - + -
42K MET* 3.0 40.6 - - + -
50K LEU* 4.6 5.6 - - + -
56K PRO* 4.8 2.7 - - + -
89K PHE* 5.0 2.0 - + - -
210K ASP 2.8 6.3 + - - -
211K VAL* 3.3 10.3 - - + +
213K ALA* 1.3 74.6 - - - +
215K LEU* 1.3 64.8 - - + +
217K TRP* 2.8 41.6 + + - +
218K ALA* 2.7 32.9 + - + -
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Residues in contact with LEU 215 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32K TYR* 5.1 2.9 - - + -
36K CYS* 5.6 0.2 - - - -
42K MET* 4.2 19.1 - - + -
100K LEU* 3.8 53.9 - - + +
101K SER 4.8 0.7 - - - +
103K MET* 5.5 0.7 - - + -
104K ALA* 3.8 6.6 + - - +
131K ILE* 4.4 27.8 - - + -
211K VAL* 2.8 20.0 + - + +
212K SER* 2.6 15.4 + - - +
214K PHE* 1.3 82.0 - - + +
216K MET* 1.3 58.6 + - - +
218K ALA* 3.5 5.0 - - + +
219K ALA* 3.1 23.4 + - - +
301K HEM 4.0 20.2 - - + -
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Residues in contact with MET 216 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431J BGL 4.0 22.9 - - - +
13K PHE* 3.6 35.9 - - + -
20K PHE* 4.0 9.6 - - + -
104K ALA* 3.7 30.2 - - + +
105K LYS* 5.3 4.3 - - + -
128K PRO* 4.4 14.8 - - + -
212K SER 2.7 13.8 + - - +
213K ALA 3.3 9.4 - - - +
214K PHE 2.9 0.2 + - - -
215K LEU* 1.3 72.2 - - - +
217K TRP* 1.3 64.9 + - - +
219K ALA* 3.2 2.9 + - - -
220K GLU* 2.9 31.9 + - + +
223K LEU* 4.4 11.7 - - + -
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Residues in contact with TRP 217 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85J ARG* 6.3 0.4 - - - -
20K PHE* 3.3 30.2 - + + -
25K LEU* 3.9 12.3 - - + -
45K VAL* 4.6 9.6 - - + -
49K SER* 3.5 48.0 - - - -
50K LEU* 4.2 10.1 - - + -
52K GLU* 5.8 0.9 + - + -
53K PRO 5.8 0.2 + - - -
54K GLY 3.9 8.4 + - - -
55K GLY* 3.5 22.3 - - - +
56K PRO* 3.6 22.0 - - + -
213K ALA 3.0 7.0 + - - +
214K PHE* 2.8 40.1 + + - +
216K MET* 1.3 74.2 - - - +
218K ALA* 1.3 90.5 + - + +
220K GLU 2.9 1.4 + - - +
221K PRO* 2.8 61.7 + - + +
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Residues in contact with ALA 218 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85J ARG* 2.8 31.2 + - - -
42K MET* 3.9 26.7 - - - -
45K VAL* 3.9 8.3 - - + +
101K SER 3.9 4.7 - - - +
214K PHE* 2.7 18.5 + - + +
215K LEU* 3.5 18.6 - - + +
217K TRP* 1.3 92.8 - - + +
219K ALA* 1.3 57.5 + - - +
221K PRO* 3.7 0.3 - - - +
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Residues in contact with ALA 219 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81J GLU* 4.4 2.1 - - - +
85J ARG* 3.7 5.3 + - - +
101K SER 3.1 21.1 - - - +
102K LEU* 3.7 35.7 - - + +
104K ALA* 4.6 6.1 - - + -
105K LYS* 3.8 20.3 + - + -
215K LEU 3.1 12.8 + - - +
216K MET 3.8 2.7 - - - +
217K TRP 3.0 0.8 - - - -
218K ALA* 1.3 75.9 - - - +
220K GLU* 1.3 59.2 + - - +
221K PRO* 3.2 12.1 - - - +
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Residues in contact with GLU 220 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84J MET* 5.1 2.9 - - - +
91J PHE* 5.6 2.1 - - - +
95J TYR* 2.7 27.5 + - - -
272J ASN* 4.2 2.5 + - - +
20K PHE* 4.1 4.9 - - - -
105K LYS* 3.5 32.1 + - + +
216K MET* 2.9 21.4 + - + +
217K TRP 2.9 10.0 + - - -
219K ALA* 1.3 72.2 - - - +
221K PRO* 1.3 65.2 - - - +
222K LYS* 3.2 9.5 + - - +
223K LEU* 3.0 34.7 + - + +
226K ARG* 2.3 34.5 + - - +
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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
------------------------------------------------------------
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