Contacts of the helix formed by residues 12 - 39 (chain B) in PDB entry 4N78
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 LYS 12 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B SER 5.2 1.4 + - - -
10B GLN* 3.2 16.2 - - - +
11B GLN* 1.3 78.9 - - - +
13B LEU* 1.3 58.9 + - - +
14B ALA 3.4 2.5 - - - -
15B GLU* 3.4 38.8 + - + +
16B LYS* 3.0 40.8 + - + +
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Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PRO 5.5 4.7 - - - +
11B GLN* 3.8 27.4 - - + +
12B LYS* 1.3 73.8 - - - +
14B ALA* 1.3 61.2 + - - +
16B LYS* 4.0 5.6 - - + +
17B LEU* 2.8 50.3 + - + +
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Residues in contact with ALA 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LYS 3.4 0.6 - - - -
13B LEU* 1.3 77.2 - - - +
15B GLU* 1.3 65.2 + - - +
17B LEU* 4.1 7.0 - - - +
18B THR* 2.8 33.9 + - - +
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Residues in contact with GLU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LYS* 3.4 49.5 - - + +
14B ALA* 1.3 82.2 + - - +
16B LYS* 1.3 60.9 + - + +
18B THR* 3.3 4.6 + - - -
19B ILE* 2.9 45.6 + - + +
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Residues in contact with LYS 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLN* 3.4 32.6 + - - +
12B LYS* 3.0 26.4 + - + +
13B LEU* 4.0 6.3 - - + +
15B GLU* 1.3 76.5 - - + +
17B LEU* 1.3 58.3 + - + +
19B ILE* 4.7 4.7 - - + -
20B LEU* 2.9 45.0 + - + +
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Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 2.8 39.7 + - + +
14B ALA* 4.1 5.6 - - - +
16B LYS* 1.3 73.4 - - + +
18B THR* 1.3 63.8 + - - +
20B LEU* 4.2 3.5 - - + +
21B ASN* 3.0 42.7 + - - +
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Residues in contact with THR 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ALA 2.8 21.2 + - - -
15B GLU* 3.6 5.6 - - - -
17B LEU* 1.3 80.1 - - - +
19B ILE* 1.3 66.2 + - + +
21B ASN* 3.8 5.0 - - - +
22B ASP* 3.2 23.9 + - + +
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Residues in contact with ILE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLU* 2.9 32.1 + - + +
16B LYS* 4.1 5.2 - - - +
18B THR* 1.3 81.0 - - + +
20B LEU* 1.3 63.6 + - + +
22B ASP* 3.5 5.7 + - - +
23B ARG* 3.0 27.0 + - + +
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Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LYS* 2.9 28.8 + - + +
17B LEU* 4.2 4.5 - - + +
19B ILE* 1.3 80.2 - - + +
21B ASN* 1.3 56.9 + - - +
23B ARG* 3.0 15.3 + - + +
24B GLY* 2.6 34.3 + - - -
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Residues in contact with ASN 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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17B LEU* 3.0 36.8 + - - +
18B THR* 3.8 5.5 - - - +
20B LEU* 1.3 75.5 - - - +
22B ASP* 1.3 61.9 + - - +
24B GLY* 3.3 3.0 + - - -
25B VAL* 3.3 26.4 + - - +
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Residues in contact with ASP 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B THR* 3.2 15.6 + - + +
19B ILE* 3.7 6.3 - - - +
20B LEU 3.2 0.6 - - - -
21B ASN* 1.3 76.2 - - - +
23B ARG* 1.3 66.7 + - - +
25B VAL* 3.3 10.2 + - - +
26B GLY* 3.2 16.8 + - - -
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Residues in contact with ARG 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 3.0 17.5 + - + +
20B LEU* 3.0 21.9 + - + +
22B ASP* 1.3 76.2 - - - +
24B GLY* 1.3 57.7 + - - +
26B GLY* 3.1 4.1 + - - -
27B MET* 2.9 52.9 + - + +
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Residues in contact with GLY 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU 2.6 18.4 + - - -
21B ASN* 3.3 4.5 + - - -
22B ASP 3.2 0.2 - - - -
23B ARG* 1.3 73.1 - - - +
25B VAL* 1.3 56.3 + - - +
27B MET* 3.1 9.8 + - - +
28B LEU* 2.9 36.1 + - - +
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Residues in contact with VAL 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ASN 3.3 15.9 + - - +
22B ASP* 3.3 11.4 + - - +
24B GLY* 1.3 75.0 - - - +
26B GLY* 1.3 53.7 + - - +
28B LEU* 3.4 15.3 + - + +
29B THR* 2.7 44.9 + - - +
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Residues in contact with GLY 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ASP 3.2 7.2 + - - -
23B ARG* 3.1 8.1 + - - -
25B VAL* 1.3 80.2 - - - +
27B MET* 1.3 63.3 + - - +
29B THR* 3.3 7.3 + - - -
30B ARG* 3.0 33.1 + - - +
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Residues in contact with MET 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ARG* 2.9 46.8 + - + +
24B GLY* 3.5 9.6 - - - +
26B GLY* 1.3 76.8 - - - +
28B LEU* 1.3 61.1 + - + +
30B ARG* 3.3 23.4 + - - +
31B LEU* 2.8 36.6 + - + +
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLY 2.9 18.4 + - - +
25B VAL* 3.6 18.8 - - + +
27B MET* 1.3 74.8 - - - +
29B THR* 1.3 54.1 + - - +
31B LEU* 3.3 10.8 + - + +
32B TYR* 2.8 36.5 + - - +
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Residues in contact with THR 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL* 2.7 30.5 + - - +
26B GLY* 3.5 8.1 - - - -
28B LEU* 1.3 78.5 - - - +
30B ARG* 1.3 63.1 + - + +
32B TYR* 3.5 6.9 + - + +
33B ASN* 3.1 39.0 + - - +
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Residues in contact with ARG 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLY 3.0 20.1 + - - +
27B MET* 3.7 25.6 - - + +
29B THR* 1.3 74.3 - - + +
31B LEU* 1.3 69.2 + - + +
33B ASN* 3.3 9.2 + - - +
34B ILE* 3.2 31.2 + - + +
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Residues in contact with LEU 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 MET* 2.8 19.8 + - + +
28B LEU* 3.7 11.0 - - + +
30B ARG* 1.3 74.6 - - + +
32B TYR* 1.3 66.7 + - - +
34B ILE* 3.1 22.2 + - + +
35B LYS* 2.9 24.0 + - - +
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Residues in contact with TYR 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 LEU 2.8 21.5 + - - +
29B THR* 3.5 9.4 - - + +
31B LEU* 1.3 74.5 - - - +
33B ASN* 1.3 78.8 + - - +
35B LYS* 3.3 9.9 + - + +
36B LYS* 3.1 62.5 + - + +
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Residues in contact with ASN 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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29B THR* 3.1 30.1 + - - +
30B ARG* 3.7 7.8 - - - +
31B LEU 3.2 0.4 - - - -
32B TYR* 1.3 92.5 - - - +
34B ILE* 1.3 62.1 + - + +
36B LYS* 3.5 5.6 + - - +
37B ALA* 2.9 30.9 + - - +
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Residues in contact with ILE 34 (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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30B ARG* 3.2 18.5 + - + +
31B LEU* 3.1 26.5 + - + +
33B ASN* 1.3 76.2 - - + +
35B LYS* 1.3 58.9 + - - +
37B ALA* 3.7 4.4 - - - -
38B CYS* 2.8 47.0 + - + -
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Residues in contact with LYS 35 (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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31B LEU 2.9 13.1 + - - +
32B TYR* 3.3 13.4 + - + +
34B ILE* 1.3 78.7 - - - +
36B LYS* 1.3 74.7 + - - +
38B CYS* 3.4 3.3 + - - +
39B GLY* 2.8 28.6 + - - -
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Residues in contact with LYS 36 (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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32B TYR* 3.1 61.0 + - + +
33B ASN* 3.8 6.3 - - - +
34B ILE 3.3 0.2 - - - -
35B LYS* 1.3 93.5 - - + +
37B ALA* 1.3 62.4 + - - +
39B GLY* 3.3 11.5 + - - -
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Residues in contact with ALA 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ASN 2.9 19.0 + - - +
34B ILE* 3.8 5.8 - - - +
36B LYS* 1.3 79.1 - - - +
38B CYS* 1.3 63.7 + - - +
39B GLY* 3.4 0.9 + - - -
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Residues in contact with CYS 38 (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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34B ILE* 2.8 37.8 + - + +
35B LYS* 3.7 3.8 - - - +
37B ALA* 1.3 78.9 - - - +
39B GLY* 1.3 56.9 + - - +
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Residues in contact with GLY 39 (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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35B LYS* 2.8 18.8 + - - -
36B LYS* 3.3 7.8 + - - -
37B ALA 3.2 4.2 - - - -
38B CYS* 1.3 81.3 - - - +
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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
------------------------------------------------------------
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