Contacts of the helix formed by residues 19 - 33 (chain B) in PDB entry 3KHE
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 GLN 19 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B SER* 1.3 87.8 + - - +
20B LYS* 1.3 65.8 + - - +
21B LEU* 3.0 7.6 + - - -
22B ALA* 2.9 29.8 + - + +
23B GLN* 3.0 13.2 + - - +
158B THR 5.2 0.2 - - - +
161B GLN* 3.9 34.3 - - + +
162B VAL* 3.4 17.5 - - + +
165B GLU* 2.9 42.4 + - - +
182B MET* 3.1 32.9 - - - +
186B ILE* 4.9 0.7 - - + -
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Residues in contact with LYS 20 (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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18B SER 3.8 7.3 + - - -
19B GLN* 1.3 79.8 - - - +
21B LEU* 1.3 60.0 + - - +
23B GLN* 3.6 11.0 - - - +
24B ALA* 2.9 30.7 + - - +
145B LEU* 4.1 6.7 - - + -
149B PHE* 3.8 28.2 - - + -
154B VAL* 5.7 0.7 - - + -
158B THR* 3.7 36.4 + - + +
161B GLN* 3.1 26.8 + - - +
162B VAL* 4.5 2.4 - - - +
200B GOL 3.1 41.2 + - - +
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Residues in contact with LEU 21 (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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19B GLN* 3.0 7.8 + - - +
20B LYS* 1.3 75.7 - - - +
22B ALA* 1.3 65.4 + - - +
24B ALA* 3.4 1.6 + - - +
25B ALA* 3.0 24.6 + - - +
132B PHE* 4.0 26.2 - - + -
140B ILE* 4.1 22.2 - - + -
145B LEU* 3.8 24.0 - - + +
148B LEU* 4.8 1.1 - - + -
159B TRP* 5.0 1.1 - - + -
162B VAL* 3.8 27.4 - - + +
174B VAL* 4.1 23.3 - - + -
179B PHE* 4.2 6.7 - - + -
182B MET* 3.7 24.7 - - + -
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Residues in contact with ALA 22 (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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18B SER* 3.5 16.4 - - - +
19B GLN* 2.9 25.2 + - - +
21B LEU* 1.3 76.9 - - - +
23B GLN* 1.3 62.1 + - - +
25B ALA* 3.4 1.7 + - - +
26B MET* 3.1 28.0 + - - +
182B MET* 3.7 16.0 - - + +
183B MET* 3.9 12.0 - - - +
186B ILE* 3.9 15.7 - - + -
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Residues in contact with GLN 23 (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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17B SER* 5.5 3.8 - - - -
18B SER* 3.6 19.6 + - - +
19B GLN 3.0 14.5 + - - +
20B LYS* 3.6 14.5 - - - +
21B LEU 3.3 0.2 - - - -
22B ALA* 1.3 74.3 - - - +
24B ALA* 1.3 66.3 + - - +
26B MET* 3.3 6.3 + - - +
27B LEU* 3.2 23.7 + - + +
98B PHE* 3.8 56.7 + - + +
149B PHE* 4.0 22.9 - - - -
200B GOL 4.0 21.3 + - - -
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Residues in contact with ALA 24 (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 LYS 2.9 16.5 + - - +
21B LEU* 3.8 4.3 - - - +
23B GLN* 1.3 79.6 - - - +
25B ALA* 1.3 55.5 + - - +
27B LEU* 3.5 5.8 + - - +
28B PHE* 3.0 32.4 + - - +
132B PHE* 3.6 4.9 - - + -
148B LEU* 3.9 29.4 - - + -
149B PHE* 4.0 16.1 - - + -
196B GOL 5.0 0.5 + - - -
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Residues in contact with ALA 25 (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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21B LEU 3.0 17.8 + - - +
22B ALA 3.5 4.5 - - - +
24B ALA* 1.3 76.1 - - - +
26B MET* 1.3 66.9 + - - +
28B PHE* 3.8 1.0 - - - +
29B MET* 3.1 34.0 + - + +
128B ALA* 4.8 1.5 - - - +
132B PHE* 3.6 12.5 - - + -
179B PHE* 3.7 30.5 - - + -
183B MET* 3.9 15.9 - - + -
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Residues in contact with MET 26 (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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15B PHE* 3.4 30.5 - - + -
22B ALA 3.1 16.1 + - - +
23B GLN* 3.9 4.9 - - - +
25B ALA* 1.3 76.9 - - - +
27B LEU* 1.3 57.7 + - - +
29B MET* 3.4 9.8 + - + +
30B GLY* 2.8 29.6 + - - -
98B PHE* 5.0 2.2 - - + -
111B THR* 3.7 23.0 - - + +
116B LYS* 3.5 24.2 - - - -
119B LEU* 4.3 7.6 - - + +
183B MET* 3.6 19.1 - - + -
186B ILE* 4.4 7.6 - - - -
187B CYS* 3.8 24.0 - - - -
199B GOL 4.3 15.0 - - - -
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Residues in contact with LEU 27 (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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23B GLN* 3.2 16.1 + - + +
24B ALA* 4.1 5.2 - - - +
26B MET* 1.3 81.2 - - - +
28B PHE* 1.3 51.8 + - - +
31B SER* 2.7 59.2 + - - +
98B PHE* 3.8 41.3 - - + -
99B ASP* 6.6 0.4 - - + -
107B SER 4.2 6.1 - - - +
108B GLU* 4.4 6.7 - - + -
111B THR* 3.6 15.0 - - + +
196B GOL 3.3 33.9 - - - +
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Residues in contact with PHE 28 (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 ALA 3.0 19.8 + - - +
25B ALA 3.8 2.2 - - - +
27B LEU* 1.3 75.0 - - - +
29B MET* 1.3 58.3 + - - +
32B LYS* 2.9 47.8 + - + +
33B LEU* 3.6 33.8 + - + -
128B ALA* 4.1 27.8 - - + -
131B GLN* 3.9 30.1 - - + -
132B PHE* 4.1 17.5 - + + -
196B GOL 3.3 17.7 + - - +
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Residues in contact with MET 29 (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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25B ALA* 3.1 32.2 + - + +
26B MET* 3.7 10.5 - - - +
28B PHE* 1.3 75.8 - - - +
30B GLY* 1.3 58.3 + - - +
33B LEU* 3.1 31.6 + - + +
34B THR* 3.3 13.2 + - - +
119B LEU* 3.8 20.9 - - + +
120B LEU* 4.0 14.1 - - + -
124B ARG* 3.9 36.6 - - + +
125B LEU* 3.8 26.2 - - + -
128B ALA* 4.0 11.4 - - + -
183B MET* 3.8 20.2 - - + -
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Residues in contact with GLY 30 (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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26B MET 2.8 17.1 + - - -
27B LEU 3.6 0.2 - - - -
29B MET* 1.3 77.3 - - - +
31B SER* 1.3 57.0 - - - +
34B THR* 2.8 23.3 + - - +
107B SER* 4.8 1.2 + - - -
110B VAL* 3.8 15.9 - - - +
111B THR* 3.6 19.5 - - - -
119B LEU* 3.8 14.1 - - - -
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Residues in contact with SER 31 (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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27B LEU* 2.7 37.3 + - - +
30B GLY* 1.3 76.8 - - - +
32B LYS* 1.3 64.3 + - - +
34B THR* 4.6 2.8 + - - +
107B SER* 3.3 22.7 + - - -
111B THR* 3.9 0.5 + - - -
196B GOL 2.8 44.1 + - - -
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Residues in contact with LYS 32 (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 PHE* 2.9 38.3 + - + +
31B SER* 1.3 84.6 + - - +
33B LEU* 1.3 72.9 + - + +
34B THR 3.5 6.3 + - - +
196B GOL 3.7 30.0 - - - -
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Residues in contact with LEU 33 (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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54A ASP* 5.5 5.2 - - + +
28B PHE* 3.9 37.2 - - + +
29B MET* 3.1 16.2 + - - +
32B LYS* 1.3 89.6 - - + +
34B THR* 1.3 61.3 + - - +
35B THR* 4.0 4.0 + - - +
124B ARG* 3.2 47.2 + - + +
127B ALA* 3.3 33.7 - - + -
128B ALA 4.2 0.4 - - - +
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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