Contacts of the helix formed by residues 22 - 37 (chain B) in PDB entry 1NPP
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 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B GLU* 2.9 43.2 + - + +
20B PRO 4.5 0.9 - - - +
21B GLY* 1.3 87.6 - - - +
23B GLU* 1.3 59.9 + - - +
25B GLU* 3.0 31.6 + - + +
26B ALA* 2.8 29.4 + - - +
158B HIS* 4.0 34.9 - - + +
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Residues in contact with GLU 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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18B VAL* 3.6 25.6 - - + -
19B GLU 3.8 1.8 + - - -
21B GLY* 3.0 30.5 + - - -
22B LYS* 1.3 80.3 + - - +
24B ASN* 1.3 63.7 + - - +
26B ALA* 3.2 2.8 + - - +
27B LYS* 3.0 22.0 + - - +
48B VAL* 3.8 16.1 - - + +
130B LEU* 5.4 0.7 - - + -
132B ASN* 3.0 36.3 + - - +
136B PRO* 3.4 5.4 - - - +
137B GLY 2.8 24.9 + - - +
138B TYR 3.9 8.7 - - - +
139B ILE* 3.8 8.1 - - + +
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Residues in contact with ASN 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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22B LYS 3.4 0.8 - - - -
23B GLU* 1.3 77.7 + - - +
25B GLU* 1.3 68.3 + - - +
27B LYS* 3.2 14.2 + - - +
28B GLU* 2.9 42.3 + - - +
48B VAL* 4.3 8.6 - - - +
113B PRO* 3.6 37.2 - - + +
130B LEU* 3.5 30.2 - - + +
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Residues in contact with GLU 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 GLY 3.8 3.8 - - - +
22B LYS* 3.0 43.5 - - + +
24B ASN* 1.3 83.4 + - - +
26B ALA* 1.3 65.9 + - - +
28B GLU* 4.4 6.7 - - - +
29B ASN* 2.9 34.7 + - - +
158B HIS* 4.0 18.4 - - + +
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Residues in contact with ALA 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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18B VAL* 3.7 31.6 - - + -
22B LYS 2.8 17.1 + - - +
23B GLU 3.2 9.2 + - - +
25B GLU* 1.3 74.1 - - - +
27B LYS* 1.3 58.3 + - - +
29B ASN* 3.7 1.9 - - - +
30B LEU* 2.9 30.9 + - - +
139B ILE* 4.5 3.6 - - + -
156B THR* 4.2 2.3 - - - +
157B PRO 4.2 3.8 - - - -
158B HIS* 3.8 22.2 - - + +
159B VAL* 4.0 6.3 - - + +
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Residues in contact with LYS 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 GLU 3.0 12.3 + - - +
24B ASN* 3.4 16.1 - - - +
26B ALA* 1.3 77.6 - - - +
28B GLU* 1.3 80.1 + - - +
30B LEU* 3.2 7.5 + - - +
31B LEU* 3.1 35.8 + - + +
46B VAL* 2.8 43.5 + - + +
47B ILE* 4.5 3.8 - - - +
48B VAL* 4.1 21.7 - - + +
139B ILE* 4.4 9.1 - - + +
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Residues in contact with GLU 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 ASN* 2.9 35.1 + - - +
25B GLU* 4.0 6.3 - - - +
26B ALA 3.3 0.2 - - - -
27B LYS* 1.3 99.7 - - - +
29B ASN* 1.3 66.0 + - - +
31B LEU* 3.5 17.5 + - - +
32B LYS* 3.2 24.8 + - - +
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Residues in contact with ASN 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 GLU* 2.9 24.7 + - - +
26B ALA 3.7 1.3 - - - +
28B GLU* 1.3 78.8 - - - +
30B LEU* 1.3 57.3 + - - +
32B LYS* 3.2 8.0 + - - +
33B VAL* 2.9 32.1 + - + +
156B THR* 3.5 18.8 - - + -
157B PRO* 3.1 33.1 + - + +
158B HIS* 3.3 19.2 - - - -
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Residues in contact with LEU 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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16B LEU* 3.7 28.5 - - + -
26B ALA 2.9 17.6 + - - +
27B LYS* 3.2 6.5 + - - +
29B ASN* 1.3 77.2 - - - +
31B LEU* 1.3 57.5 + - - +
33B VAL* 3.2 3.2 + - + -
34B LEU* 2.8 55.4 + - + +
43B VAL* 6.1 0.7 - - + -
46B VAL* 4.2 14.1 - - + -
139B ILE* 4.3 3.6 - - + -
141B ILE* 3.9 17.7 - - + -
153B ILE* 4.2 23.3 - - + +
156B THR* 3.5 25.9 - - + +
159B VAL* 5.1 3.8 - - + -
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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 LYS* 3.1 24.4 + - + +
28B GLU* 3.9 30.3 - - - +
29B ASN 3.4 0.2 - - - -
30B LEU* 1.3 75.7 - - - +
32B LYS* 1.3 63.2 + - - +
34B LEU* 3.4 14.4 + - + +
35B GLU* 3.2 20.8 + - - +
40B LYS* 5.1 2.6 - - - +
43B VAL* 5.9 0.2 - - + -
46B VAL* 3.8 32.5 - - + -
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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 GLU 3.2 12.4 + - - +
29B ASN* 3.2 11.7 + - - +
30B LEU 3.2 0.8 - - - -
31B LEU* 1.3 77.8 - - - +
33B VAL* 1.3 59.9 + - + +
35B GLU* 3.1 25.5 + - - +
36B LEU* 2.9 49.2 + - + +
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Residues in contact with VAL 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 ASN* 2.9 19.4 + - + +
30B LEU* 3.7 5.4 - - + +
32B LYS* 1.3 76.0 - - + +
34B LEU* 1.3 59.7 + - + +
36B LEU* 3.2 13.9 + - + +
37B GLU* 2.8 47.6 + - + +
152B ALA* 3.7 30.1 - - + +
155B LYS* 5.1 3.1 - - + +
156B THR* 3.5 26.5 - - + +
157B PRO* 4.7 6.5 - - + -
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Residues in contact with LEU 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 LEU* 2.8 44.9 + - + +
31B LEU* 3.6 22.2 - - + +
32B LYS 3.2 0.2 - - - -
33B VAL* 1.3 78.7 - - - +
35B GLU* 1.3 59.7 + - - +
37B GLU* 4.7 0.4 - - - -
38B GLY 3.1 2.3 + - - -
39B LEU* 2.8 46.0 + - + +
40B LYS* 3.5 19.8 + - + +
43B VAL* 4.0 31.9 - - + -
46B VAL* 4.7 0.4 - - + -
149B LEU* 3.7 29.8 - - + -
152B ALA* 5.3 2.5 - - + -
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Residues in contact with GLU 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 3.2 9.8 + - - +
32B LYS* 3.1 28.9 + - - +
34B LEU* 1.3 75.8 - - - +
36B LEU* 1.3 78.7 + - - +
38B GLY* 3.2 11.5 + - - -
40B LYS* 4.0 32.7 + - + +
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Residues in contact with LEU 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 LYS* 2.9 36.4 + - + +
33B VAL* 3.5 16.2 - - + +
35B GLU* 1.3 92.7 - - - +
37B GLU* 1.3 64.8 + - + +
38B GLY 3.4 0.3 + - - -
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Residues in contact with GLU 37 (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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33B VAL* 2.8 38.9 + - + +
34B LEU 4.3 0.4 - - - +
36B LEU* 1.3 76.2 - - + +
38B GLY* 1.3 61.7 + - - +
39B LEU* 3.7 20.2 - - + +
148B LYS* 3.5 42.1 + - - +
152B ALA* 4.2 11.9 - - + +
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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