Contacts of the helix formed by residues 15 - 31 (chain A) in PDB entry 4K71
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 GLY 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A PHE* 2.7 26.0 + - - -
12A LYS 3.7 4.8 + - - -
13A ASP 3.6 1.4 - - - -
14A LEU* 1.3 73.9 - - - +
16A GLU* 1.3 65.3 + - - -
17A GLU 3.4 2.3 + - - -
18A ASN 3.4 0.7 + - - -
19A PHE* 3.0 22.6 + - - +
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Residues in contact with GLU 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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11A PHE* 3.6 33.9 - - + -
15A GLY* 1.3 69.4 - - - -
17A GLU* 1.3 67.3 + - - +
19A PHE* 4.3 0.2 - - - -
20A LYS* 3.0 53.2 + - + +
47A THR* 4.3 1.9 - - + +
51A LYS* 2.8 38.4 + - - +
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Residues in contact with GLU 17 (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 GLY 3.4 0.8 - - - -
16A GLU* 1.3 80.4 - - - +
18A ASN* 1.3 69.7 + - - +
20A LYS* 3.7 5.2 - - - +
21A ALA* 3.1 28.2 + - + +
162A LYS* 5.3 6.6 + - - -
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Residues in contact with ASN 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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14A LEU* 3.9 25.5 + - + +
15A GLY 3.4 2.0 + - - -
16A GLU 3.3 0.2 - - - -
17A GLU* 1.3 90.3 - - - +
19A PHE* 1.3 57.3 + - - +
21A ALA* 3.7 5.3 - - - +
22A LEU* 2.7 48.1 + - + +
155A LEU* 4.1 20.6 - - + +
283A LEU* 4.2 22.2 - - - +
284A LEU* 4.1 23.7 - - - +
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Residues in contact with PHE 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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7A VAL* 4.2 15.5 - - + -
10A ARG 4.3 1.6 - - - -
11A PHE* 3.6 46.4 - + + -
14A LEU* 4.3 7.7 - - + +
15A GLY 3.0 19.2 + - - +
16A GLU 3.8 2.5 - - - +
18A ASN* 1.3 77.7 - - - +
20A LYS* 1.3 60.2 + - + +
22A LEU* 3.2 2.0 + - - +
23A VAL* 3.0 50.2 + - + +
46A VAL* 4.1 11.9 - - + -
47A THR* 3.8 24.0 - - - -
50A ALA* 3.7 23.8 - - + -
70A PHE* 5.9 0.4 - + - -
251A LEU* 3.7 35.1 - - + +
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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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16A GLU* 3.0 44.4 + - + +
17A GLU* 3.7 4.7 - - - +
19A PHE* 1.3 76.7 - - + +
21A ALA* 1.3 67.3 + - - +
23A VAL* 3.5 0.8 + - - +
24A LEU* 3.1 23.9 + - - +
43A VAL* 3.6 18.7 - - + +
44A ASN* 3.6 25.6 + - - +
47A THR* 3.4 33.6 - - + +
132A GLU* 5.0 5.3 + - - -
136A LYS* 4.4 21.1 - - - +
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Residues in contact with ALA 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 GLU* 3.1 19.4 + - + +
18A ASN* 3.7 4.0 - - - +
20A LYS* 1.3 78.9 - - - +
22A LEU* 1.3 56.9 + - - +
24A LEU* 3.3 6.7 + - - +
25A ILE* 3.1 32.7 + - - +
139A LEU* 3.8 20.0 - - + +
155A LEU* 3.3 26.7 - - + -
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Residues in contact with LEU 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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14A LEU* 4.2 20.0 - - + -
18A ASN* 2.7 29.7 + - + +
21A ALA* 1.3 71.7 - - - +
23A VAL* 1.3 60.1 + - - +
25A ILE* 3.4 8.1 + - + +
26A ALA* 2.8 27.9 + - - +
151A ALA* 3.6 32.8 - - + -
155A LEU* 4.0 22.4 - - + -
250A LEU* 3.7 16.2 - - + +
251A LEU* 3.7 17.7 - - + -
254A ALA* 3.5 33.4 - - + -
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Residues in contact with VAL 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 PHE* 3.0 47.5 + - + +
20A LYS 4.0 3.8 - - - +
22A LEU* 1.3 74.1 - - - +
24A LEU* 1.3 60.7 + - - +
26A ALA* 3.5 6.9 - - - +
27A PHE* 2.8 63.6 + - + -
43A VAL* 3.8 15.3 - - + -
46A VAL* 4.3 10.3 - - + -
70A PHE* 4.0 22.0 - - + -
251A LEU* 4.3 6.7 - - + -
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Residues in contact with LEU 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 3.1 14.3 + - - +
21A ALA* 3.4 11.0 - - - +
22A LEU 3.3 0.2 - - - -
23A VAL* 1.3 77.9 - - - +
25A ILE* 1.3 57.8 + - - +
27A PHE* 3.6 0.7 - - - -
28A ALA* 2.9 32.8 + - + +
36A PHE* 5.4 0.2 - - + -
39A HIS* 4.0 28.0 - - + -
40A VAL* 4.7 9.4 - - + +
43A VAL* 3.6 18.5 - - + +
136A LYS* 3.6 50.5 - - + +
139A LEU* 4.2 15.7 - - + -
140A TYR* 4.7 15.0 - - + +
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Residues in contact with ILE 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 ALA 3.1 16.9 + - - +
22A LEU* 3.5 14.1 - - + +
24A LEU* 1.3 79.5 - - - +
26A ALA* 1.3 63.3 + - - +
28A ALA* 3.3 1.4 + - - +
29A GLN* 2.9 48.3 + - - +
139A LEU* 4.2 12.8 - - + -
143A ALA* 4.1 13.5 - - + -
151A ALA* 4.1 22.2 - - + +
154A LEU* 4.0 26.9 - - + -
155A LEU* 4.0 22.4 - - + -
250A LEU* 3.7 16.2 - - + -
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Residues in contact with ALA 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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22A LEU 2.8 20.8 + - - +
23A VAL 3.2 5.6 + - - +
25A ILE* 1.3 73.2 - - - +
27A PHE* 1.3 65.5 + - + +
29A GLN* 3.3 4.1 + - - +
30A TYR* 3.1 35.1 + - + -
70A PHE* 3.9 31.0 - - + -
248A GLY 5.1 2.5 - - - +
250A LEU* 3.5 21.0 - - + +
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Residues in contact with PHE 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 VAL* 2.8 49.5 + - + +
24A LEU 3.6 2.9 - - - +
26A ALA* 1.3 73.3 - - + +
28A ALA* 1.3 58.9 + - - +
30A TYR* 3.3 3.0 + + - +
31A LEU* 2.9 27.4 + - - +
39A HIS* 3.3 29.0 + - + +
42A LEU* 4.0 9.9 - - + -
43A VAL* 3.6 27.1 - - + -
46A VAL* 3.8 19.7 - - + -
70A PHE* 3.7 38.1 - + + -
73A LYS* 3.9 14.8 - - + -
74A LEU* 3.4 26.6 - - + +
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Residues in contact with ALA 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 LEU* 2.9 17.9 + - + +
27A PHE* 1.3 77.8 - - - +
29A GLN* 1.3 59.7 + - - +
31A LEU 3.5 0.6 - - - +
32A GLN* 3.5 27.0 - - - +
39A HIS* 3.6 19.6 + - + -
140A TYR* 4.1 23.8 - - + +
143A ALA* 3.6 23.1 - - + -
144A ARG* 3.7 7.0 - - + +
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Residues in contact with GLN 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 ILE* 2.9 30.1 + - - +
26A ALA* 3.8 3.5 - - - +
27A PHE 3.2 0.2 - - - -
28A ALA* 1.3 76.1 - - - +
30A TYR* 1.3 63.8 + - - +
32A GLN* 3.5 19.9 - - - +
106A LYS* 3.7 24.5 + - - +
143A ALA* 3.5 21.0 + - + +
146A HIS 3.2 17.2 + - - -
147A PRO* 3.0 32.2 + - + +
148A TYR* 5.1 0.2 - - - -
149A PHE* 3.4 23.8 + - - +
250A LEU* 3.8 25.6 - - - +
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Residues in contact with TYR 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 ALA* 3.1 29.2 + - + +
27A PHE* 3.9 1.8 - + - +
29A GLN* 1.3 76.7 - - - +
31A LEU* 1.3 60.4 + - - +
32A GLN* 3.8 2.5 + - - +
67A HIS* 4.4 6.4 - - - -
70A PHE* 4.3 27.3 - + + -
74A LEU* 3.4 35.7 - - + -
87A MET* 3.1 31.7 - - - +
99A ASN* 2.9 28.5 + - - -
102A PHE* 3.7 29.3 - + + +
103A LEU* 3.8 23.7 - - + +
106A LYS* 4.5 14.3 - - - +
247A HIS 4.7 0.2 + - - -
248A GLY* 3.6 22.7 + - - -
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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 PHE 2.9 5.6 + - - +
28A ALA* 3.5 4.4 - - - +
30A TYR* 1.3 79.5 - - - +
32A GLN* 1.3 64.2 + - - +
33A GLN 3.3 2.9 + - - -
34A CYS* 3.3 15.9 + - + +
39A HIS* 3.1 31.1 + - + -
42A LEU* 5.7 0.2 - - + -
74A LEU* 3.4 34.3 - - + +
77A VAL* 3.6 30.3 - - + -
78A ALA* 3.9 16.2 - - + -
84A TYR* 3.4 26.9 - - + -
87A MET* 4.3 15.7 - - + -
102A PHE* 6.0 2.0 - - + -
140A TYR* 5.6 0.2 - - - -
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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