Contacts of the helix formed by residues 19 - 33 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A SER* 1.3 78.6 - - - +
20A LYS* 1.3 59.1 + - - +
21A LEU* 3.0 7.4 + - - +
22A ALA* 2.9 23.8 + - - +
23A GLN* 2.9 21.5 + - - +
161A GLN* 3.9 39.9 - - + +
162A VAL* 3.4 17.6 - - + +
165A GLU* 2.7 44.1 + - - +
182A MET* 3.2 31.1 - - - +
186A ILE* 4.8 0.4 - - + -
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Residues in contact with LYS 20 (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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18A SER 3.6 6.7 + - - -
19A GLN* 1.3 74.4 - - - +
21A LEU* 1.3 62.7 + - - +
23A GLN* 3.3 30.0 + - - +
24A ALA* 2.8 30.1 + - - +
100A ARG* 3.5 32.2 - - - +
145A LEU* 4.1 14.6 - - + -
149A PHE* 3.2 35.2 - - + -
154A VAL* 6.3 0.7 - - + -
158A THR* 4.3 18.8 - - + +
161A GLN* 5.1 4.5 - - - +
162A VAL* 4.5 1.8 - - - +
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Residues in contact with LEU 21 (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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19A GLN* 3.0 7.6 + - - +
20A LYS* 1.3 79.2 - - - +
22A ALA* 1.3 58.2 + - - +
24A ALA* 3.7 0.6 - - - -
25A ALA* 2.8 30.5 + - - +
132A PHE* 3.9 26.7 - - + -
140A ILE* 4.3 23.3 - - + -
145A LEU* 3.8 22.9 - - + +
148A LEU* 4.7 1.1 - - + -
159A TRP* 4.7 2.5 - - + -
162A VAL* 3.9 32.2 - - + +
174A VAL* 4.1 23.6 - - + -
179A PHE* 4.3 6.7 - - + -
182A MET* 4.0 19.1 - - + -
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Residues in contact with ALA 22 (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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18A SER* 4.5 4.0 - - - -
19A GLN* 2.9 31.0 + - - +
21A LEU* 1.3 76.3 - - - +
23A GLN* 1.3 61.4 + - - +
25A ALA* 3.3 1.9 + - - +
26A MET* 3.0 30.4 + - - +
182A MET* 3.7 10.4 - - + +
183A MET* 3.9 16.8 - - - +
186A ILE* 3.9 22.9 - - + -
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Residues in contact with GLN 23 (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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17A SER* 5.6 3.3 - - - -
18A SER* 4.0 14.1 + - - +
19A GLN 2.9 18.4 + - - +
20A LYS* 3.3 26.5 + - - +
21A LEU 3.2 0.2 - - - -
22A ALA* 1.3 74.6 - - - +
24A ALA* 1.3 63.1 + - - +
26A MET* 3.5 5.1 + - - +
27A LEU* 3.1 25.5 + - + +
98A PHE* 3.9 47.9 + - + +
100A ARG* 3.9 19.8 - - - +
149A PHE* 3.9 15.3 - - - -
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Residues in contact with ALA 24 (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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20A LYS 2.8 21.2 + - - +
21A LEU* 3.9 3.6 - - - +
23A GLN* 1.3 73.0 - - - +
25A ALA* 1.3 61.6 + - - +
27A LEU* 4.0 5.3 - - - +
28A PHE* 3.0 25.3 + - - +
132A PHE* 3.6 4.4 - - + -
148A LEU* 3.7 31.9 - - + -
149A PHE* 3.9 16.8 - - + -
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Residues in contact with ALA 25 (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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21A LEU 2.8 17.9 + - - +
22A ALA 3.5 4.5 - - - +
23A GLN 3.2 0.2 - - - -
24A ALA* 1.3 74.0 - - - +
26A MET* 1.3 66.2 + - - +
28A PHE* 3.3 1.7 + - - +
29A MET* 3.0 39.4 + - + +
128A ALA* 4.7 1.9 - - + +
132A PHE* 3.7 11.8 - - + -
179A PHE* 3.7 30.5 - - + -
183A MET* 4.0 9.0 - - - -
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Residues in contact with MET 26 (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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15A PHE* 3.6 30.5 - - + -
18A SER* 6.4 0.7 - - - -
22A ALA 3.0 16.8 + - - +
23A GLN* 4.2 4.5 - - - +
25A ALA* 1.3 75.7 - - - +
27A LEU* 1.3 58.9 + - - +
29A MET* 3.4 9.6 + - + +
30A GLY* 2.8 25.1 + - - -
98A PHE* 5.3 1.3 - - + -
111A THR* 3.4 29.5 - - + +
116A LYS* 3.6 21.1 - - - -
119A LEU* 4.3 10.2 - - + +
120A LEU* 4.9 0.2 - - + -
183A MET* 3.5 21.8 - - + -
186A ILE* 4.5 11.9 - - - -
187A CYS* 3.9 23.3 - - - -
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Residues in contact with LEU 27 (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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23A GLN* 3.1 18.4 + - + +
24A ALA* 4.1 5.4 - - - +
26A MET* 1.3 79.2 - - - +
28A PHE* 1.3 57.3 + - - +
31A SER* 2.7 54.7 + - - +
98A PHE* 3.8 40.4 - - + -
107A SER 4.1 7.4 - - - +
108A GLU* 4.2 12.1 - - + +
111A THR* 3.6 15.9 - - + +
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Residues in contact with PHE 28 (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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24A ALA 3.0 19.3 + - - +
25A ALA 3.8 2.7 - - - +
27A LEU* 1.3 72.9 - - - +
29A MET* 1.3 68.7 + - - +
31A SER* 4.8 0.4 - - - -
32A LYS* 3.0 53.5 + - + +
33A LEU* 3.6 28.2 + - + -
128A ALA* 3.9 19.7 - - + -
131A GLN* 3.9 36.3 - - + -
132A PHE* 4.1 16.2 - + + -
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Residues in contact with MET 29 (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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25A ALA* 3.0 43.4 + - + +
26A MET* 3.8 9.6 - - - +
28A PHE* 1.3 78.6 - - - +
30A GLY* 1.3 62.7 + - - +
33A LEU* 3.2 29.9 + - + +
34A THR* 3.4 9.9 + - - +
119A LEU* 3.8 21.0 - - + +
120A LEU* 4.4 11.0 - - + -
124A ARG* 3.9 39.7 - - + +
125A LEU* 4.0 28.7 - - + -
128A ALA* 4.1 9.0 - - + -
183A MET* 4.2 10.5 - - + -
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Residues in contact with GLY 30 (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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26A MET 2.8 13.2 + - - -
29A MET* 1.3 77.8 - - - +
31A SER* 1.3 56.3 + - - +
34A THR* 2.8 21.9 + - - -
107A SER* 4.7 1.5 + - - -
110A VAL* 3.6 17.6 - - - +
111A THR* 3.6 25.4 - - - -
119A LEU* 3.7 14.3 - - - +
122B ARG* 4.0 2.1 + - - -
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Residues in contact with SER 31 (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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27A LEU* 2.7 45.1 + - - +
28A PHE* 4.8 0.2 - - - -
30A GLY* 1.3 77.6 - - - +
32A LYS* 1.3 80.6 + - - +
107A SER* 3.5 25.0 + - - -
122B ARG* 3.2 29.4 + - - +
191B VAL 4.7 0.5 - - - +
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Residues in contact with LYS 32 (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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28A PHE* 3.0 44.8 + - + +
31A SER* 1.3 95.2 - - - +
33A LEU* 1.3 66.4 + - + +
34A THR 3.5 2.6 - - - +
122B ARG* 4.0 11.3 + - - +
191B VAL* 5.3 7.4 - - - +
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Residues in contact with LEU 33 (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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28A PHE* 3.9 39.0 - - + +
29A MET* 3.2 19.0 + - + +
32A LYS* 1.3 84.9 - - + +
34A THR* 1.3 61.2 + - - +
35A THR* 4.1 3.5 + - - +
124A ARG* 3.2 55.3 + - + +
127A ALA* 3.8 23.3 - - + -
128A ALA 4.0 0.2 - - - +
131A GLN* 6.3 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