Contacts of the helix formed by residues 15 - 34 (chain A) in PDB entry 2KG4
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 ARG 15 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLN* 4.1 21.6 + - - +
13A THR* 3.8 19.1 + - + +
14A GLU* 1.3 73.3 - - - +
16A MET* 1.3 75.6 + - + +
17A ASP* 3.3 25.8 + - - +
18A LYS* 3.0 25.9 + - + +
19A VAL* 3.3 11.2 + - - +
146A PHE* 6.2 0.4 - - - -
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Residues in contact with MET 16 (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 ARG* 1.3 77.7 - - + +
17A ASP* 1.3 72.1 + - + +
19A VAL* 3.2 27.3 - - - +
20A GLY 4.2 0.9 + - - -
146A PHE* 5.3 9.8 - - + -
160A ILE* 3.9 29.7 - - + +
161A ASN 5.8 0.2 - - - -
162A LEU* 5.9 0.2 - - - -
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Residues in contact with ASP 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 3.3 31.8 + - - +
16A MET* 1.3 82.8 - - + +
18A LYS* 1.3 64.4 + - - +
20A GLY 3.3 4.0 + - - +
21A ASP* 3.2 20.0 + - - +
161A ASN 5.2 6.5 - - - +
162A LEU* 5.2 0.9 - - - +
163A PRO* 3.7 34.9 - - + +
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Residues in contact with LYS 18 (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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11A GLN* 4.9 18.2 + - + +
13A THR* 3.9 23.6 - - + +
14A GLU* 5.3 0.7 - - - -
15A ARG* 3.0 27.3 + - + +
17A ASP* 1.3 81.6 - - - +
19A VAL* 1.3 57.0 + - - +
21A ASP* 4.0 21.9 + - + +
22A ALA* 2.9 46.5 + - + +
139A ALA* 5.2 6.7 - - - +
142A GLN* 4.7 19.6 + - + -
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Residues in contact with VAL 19 (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 ARG 3.3 10.9 + - - +
16A MET* 3.2 18.8 - - - +
17A ASP 3.2 0.2 - - - -
18A LYS* 1.3 75.8 - - - +
20A GLY* 1.3 56.9 + - - +
22A ALA* 4.4 0.9 - - - -
23A LEU 3.1 21.0 + - - -
90A LEU* 4.3 12.6 - - + -
142A GLN* 5.0 5.8 - - + +
143A LEU* 3.4 46.2 - - + +
146A PHE* 3.4 48.5 - - + -
147A CYS* 5.0 0.4 - - - -
160A ILE* 4.6 5.8 - - + -
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Residues in contact with GLY 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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16A MET 4.2 1.2 + - - -
17A ASP 3.3 5.8 + - - -
19A VAL* 1.3 76.9 - - - +
21A ASP* 1.3 62.9 + - - +
23A LEU* 3.5 11.4 + - - +
24A GLU* 3.2 22.2 + - - +
90A LEU* 6.1 0.7 - - - -
92A VAL* 6.3 0.2 - - - -
101A LEU* 5.8 0.2 - - - +
160A ILE* 5.0 6.3 - - - +
162A LEU* 3.7 38.9 - - - +
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Residues in contact with ASP 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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17A ASP 3.2 13.7 + - - +
18A LYS* 3.6 29.0 + - + +
20A GLY* 1.3 72.8 - - - +
22A ALA* 1.3 65.5 + - - +
24A GLU* 3.2 33.6 + - - +
25A GLU* 3.3 12.3 + - - +
162A LEU* 4.8 1.7 - - - +
163A PRO* 4.9 9.5 - - + +
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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 LYS* 2.9 34.8 + - + +
19A VAL* 3.6 6.1 - - - +
21A ASP* 1.3 74.3 + - - +
23A LEU* 1.3 60.9 + - - +
25A GLU* 3.2 15.2 + - - +
26A VAL* 3.2 18.7 + - - +
139A ALA* 3.5 38.0 - - + +
142A GLN* 4.8 2.9 - - + -
143A LEU* 3.7 4.9 - - + -
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Residues in contact with LEU 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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19A VAL 3.1 16.9 + - - +
20A GLY* 3.5 13.0 - - - +
22A ALA* 1.3 75.8 - - - +
24A GLU* 1.3 56.2 + - - +
26A VAL* 3.5 2.5 + - - -
27A LEU* 3.0 56.3 + - + +
56A LEU* 4.8 0.7 - - + -
58A LEU* 3.6 48.7 - - + -
90A LEU* 4.7 7.2 - - + -
92A VAL* 4.7 3.8 - - + -
98A LEU* 4.1 20.6 - - + -
101A LEU* 4.8 5.6 - - + -
140A LEU* 4.7 6.7 - - + -
143A LEU* 3.4 18.8 - - + +
162A LEU* 5.3 1.1 - - + -
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Residues in contact with GLU 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 GLY 3.2 9.4 + - - +
21A ASP* 3.2 27.2 + - - +
23A LEU* 1.3 78.5 - - - +
25A GLU* 1.3 65.5 + - - +
28A SER* 3.3 23.6 + - - -
101A LEU* 3.5 35.0 - - + +
104A LEU* 4.0 24.7 - - + +
162A LEU* 4.9 10.2 - - + +
165A ARG* 6.0 2.1 - - - +
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Residues in contact with GLU 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 ASP* 3.3 10.1 + - - +
22A ALA* 3.2 13.5 + - - +
24A GLU* 1.3 78.6 - - + +
26A VAL* 1.3 65.7 + - + +
28A SER* 3.4 7.6 + - - -
29A LYS* 3.2 41.3 + - + +
139A ALA* 4.7 9.6 - - + -
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Residues in contact with VAL 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA 3.2 15.3 + - - +
23A LEU 4.0 1.8 - - - +
25A GLU* 1.3 76.0 - - + +
27A LEU* 1.3 62.5 + - + +
29A LYS* 3.1 10.5 + - - +
30A ALA* 2.8 25.6 + - - +
127A VAL* 4.9 8.3 - - + -
135A TRP* 3.9 25.1 - - + -
137A ASP* 4.5 11.7 - - + +
139A ALA* 3.6 20.6 - - + -
140A LEU* 3.8 40.6 - - + +
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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
----------------------------------------------------------
23A LEU* 3.0 43.5 + - + +
24A GLU 4.4 0.2 - - - +
26A VAL* 1.3 78.5 - - + +
28A SER* 1.3 62.2 + - - +
30A ALA* 3.2 8.1 + - + +
31A LEU 3.0 15.6 + - - -
36A ILE* 5.0 9.9 - - + -
56A LEU* 6.1 0.7 - - + -
58A LEU* 5.6 1.3 - - + -
101A LEU* 4.3 11.7 - - + -
106A THR* 2.9 33.8 + - + +
125A VAL* 3.6 38.4 - - + -
127A VAL* 3.6 31.6 - - + +
140A LEU* 5.5 0.9 - - + -
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Residues in contact with SER 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 GLU 3.3 18.1 + - - -
25A GLU* 3.4 9.4 + - - -
27A LEU* 1.3 77.2 - - - +
29A LYS* 1.3 68.3 + - - +
31A LEU* 3.4 5.7 + - - +
32A SER* 3.3 17.8 + - - -
101A LEU* 5.2 1.1 - - - -
105A GLU* 3.2 40.0 + - - +
106A THR* 3.6 22.4 - - - +
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Residues in contact with LYS 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 GLU* 3.2 26.0 + - + +
26A VAL* 3.1 9.9 + - - +
28A SER* 1.3 88.4 - - - +
30A ALA* 1.3 56.0 + - - +
32A SER* 3.0 13.5 + - - -
33A GLN* 2.9 43.2 + - - +
105A GLU* 3.1 20.6 + - - -
135A TRP* 4.3 9.0 - - + -
137A ASP* 6.5 0.7 - - - -
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Residues in contact with ALA 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 VAL 2.8 19.6 + - - +
27A LEU* 3.2 11.6 + - + +
29A LYS* 1.3 69.8 - - - +
31A LEU* 1.3 63.8 + - - +
33A GLN* 3.3 5.5 + - - +
34A ARG* 3.1 16.3 + - - -
35A THR 3.7 8.1 + - - -
36A ILE* 3.5 28.8 - - + +
127A VAL* 4.6 8.3 - - + -
135A TRP* 3.6 24.8 - - + -
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Residues in contact with LEU 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 3.0 6.9 + - - -
28A SER 3.6 8.7 - - - +
29A LYS 3.4 0.2 - - - -
30A ALA* 1.3 75.0 - - - +
32A SER* 1.3 57.8 + - - +
34A ARG* 2.9 35.4 + - + +
36A ILE* 4.3 18.6 - - + +
105A GLU 3.3 21.8 - - - +
106A THR* 3.8 13.5 - - - +
107A ASP* 3.5 22.2 - - - +
108A ALA* 3.3 26.0 - - + +
109A GLY* 4.7 4.5 - - - +
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Residues in contact with SER 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 SER 3.3 9.5 + - - -
29A LYS* 3.0 24.7 + - - -
31A LEU* 1.3 77.8 - - - +
33A GLN* 1.3 69.2 + - - +
34A ARG* 3.7 5.1 + - - +
105A GLU* 6.0 0.7 - - - -
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Residues in contact with GLN 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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29A LYS* 2.9 32.6 + - - +
30A ALA 3.7 3.4 - - - +
31A LEU 3.2 0.4 - - - -
32A SER* 1.3 86.3 + - - +
34A ARG* 1.3 66.9 + - - +
35A THR* 3.5 27.2 + - + +
135A TRP* 4.0 21.8 - - + -
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Residues in contact with ARG 34 (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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30A ALA 3.1 3.4 + - - -
31A LEU* 2.9 29.0 + - + +
32A SER 4.3 5.2 - - - +
33A GLN* 1.3 78.8 - - - +
35A THR* 1.3 60.3 + - - +
36A ILE* 3.7 4.2 + - - -
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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