Contacts of the helix formed by residues 22 - 38 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C GLU* 3.0 34.1 + - + +
20C PRO 4.2 2.7 - - - +
21C GLY* 1.3 80.8 - - - +
23C GLU* 1.3 64.7 + - - +
24C ASN 3.2 2.9 - - - -
25C GLU* 3.0 35.3 + - + +
26C ALA* 2.9 22.0 + - - +
158C HIS* 4.0 32.2 + - + +
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Residues in contact with GLU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C VAL* 4.2 10.8 - - + -
19C GLU 3.9 2.0 + - - -
20C PRO 3.7 0.2 - - - -
21C GLY* 2.8 38.7 + - - +
22C LYS* 1.3 71.1 - - - +
24C ASN* 1.3 61.8 + - - +
26C ALA* 3.1 4.9 + - - +
27C LYS* 3.0 24.8 + - - +
48C VAL* 3.7 24.9 - - + -
132C ASN* 2.9 29.5 - - + +
135C PHE 5.0 1.3 - - - +
137C GLY 3.0 25.1 + - - +
138C TYR 3.9 17.3 - - - +
139C ILE* 3.7 15.4 - - + +
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Residues in contact with ASN 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C GLY 5.5 2.4 + - - -
22C LYS 3.2 0.8 - - - -
23C GLU* 1.3 83.0 + - - +
25C GLU* 1.3 67.4 + - + +
27C LYS* 3.3 5.3 + - - +
28C GLU* 3.0 33.2 + - + +
48C VAL* 4.3 10.9 - - - +
113C PRO* 5.3 2.8 - - - +
129C VAL* 5.8 0.8 - - - +
130C LEU* 3.0 58.4 + - - +
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Residues in contact with GLU 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C GLY 4.2 4.5 - - - +
22C LYS* 3.0 46.1 + - + +
24C ASN* 1.3 85.6 + - + +
26C ALA* 1.3 60.6 + - - +
28C GLU* 4.5 6.3 - - - -
29C ASN* 3.0 40.8 + - - +
158C HIS* 4.0 17.9 - - + +
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Residues in contact with ALA 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C VAL* 3.9 24.9 - - + -
22C LYS 2.9 13.0 + - - +
23C GLU* 3.3 9.6 - - - +
25C GLU* 1.3 78.8 - - - +
27C LYS* 1.3 57.4 + - - +
29C ASN* 3.7 1.6 - - - +
30C LEU* 2.9 30.8 + - - +
139C ILE* 4.4 3.4 - - + -
157C PRO 4.3 1.6 - - - -
158C HIS* 4.1 15.0 - - + +
159C VAL* 3.8 23.6 - - + +
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Residues in contact with LYS 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C GLU 3.0 12.3 + - - +
24C ASN* 3.7 8.1 - - - +
26C ALA* 1.3 75.6 - - - +
28C GLU* 1.3 74.6 + - - +
30C LEU* 3.4 2.2 + - - +
31C LEU* 3.0 43.8 + - + +
46C VAL* 3.1 44.5 + - + +
47C ILE* 4.7 3.4 - - - +
48C VAL* 4.1 23.4 - - + +
130C LEU* 6.0 4.5 - - + +
139C ILE* 4.1 11.2 - - + +
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Residues in contact with GLU 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ASN* 3.0 21.8 + - + +
25C GLU* 3.9 6.7 - - - +
27C LYS* 1.3 86.0 - - - +
29C ASN* 1.3 68.1 + - - +
31C LEU* 3.2 22.7 + - - +
32C LYS* 3.1 40.4 + - + +
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Residues in contact with ASN 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C GLU* 3.0 26.3 + - - +
26C ALA 3.7 1.1 - - - +
28C GLU* 1.3 79.8 - - - +
30C LEU* 1.3 62.5 + - - +
32C LYS* 3.1 11.0 + - - +
33C VAL* 3.0 25.8 + - - +
156C THR* 3.4 17.7 - - + -
157C PRO* 2.9 41.6 + - + +
158C HIS* 4.2 10.5 - - - -
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Residues in contact with LEU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 3.8 26.5 - - + -
26C ALA 2.9 18.2 + - - +
27C LYS 3.7 4.3 - - - +
28C GLU 3.3 0.2 - - - -
29C ASN* 1.3 75.6 - - - +
31C LEU* 1.3 58.9 + - - +
33C VAL* 3.0 3.1 + - + -
34C LEU* 2.8 57.4 + - + +
43C VAL* 6.3 0.2 - - + -
46C VAL* 4.1 17.7 - - + -
139C ILE* 4.4 3.8 - - + -
141C ILE* 4.1 15.5 - - + -
149C LEU* 5.3 0.9 - - + -
152C ALA 4.6 1.3 - - - +
153C ILE* 4.2 25.1 - - + +
156C THR* 3.4 24.1 - - + +
159C VAL* 4.7 3.1 - - + -
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Residues in contact with LEU 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C LYS* 3.0 41.9 + - + +
28C GLU* 3.2 22.2 + - - +
30C LEU* 1.3 78.1 - - - +
32C LYS* 1.3 63.0 + - + +
34C LEU* 3.3 14.5 + - + +
35C GLU* 3.3 21.0 + - - +
40C LYS* 5.5 1.6 - - + +
46C VAL* 3.9 26.7 - - + -
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Residues in contact with LYS 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C GLU* 3.1 29.9 + - - +
29C ASN* 3.1 11.2 + - - +
31C LEU* 1.3 75.3 - - + +
33C VAL* 1.3 66.2 + - + +
35C GLU* 3.5 6.7 + - + +
36C LEU* 3.1 35.9 + - + +
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Residues in contact with VAL 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ASN 3.0 16.6 + - - +
30C LEU* 3.5 7.2 - - + +
32C LYS* 1.3 75.4 - - + +
34C LEU* 1.3 69.0 + - - +
36C LEU* 3.4 12.9 + - + +
37C GLU* 3.0 34.9 + - + +
152C ALA* 3.7 38.1 - - + +
155C LYS* 4.6 11.7 - - + -
156C THR* 3.5 23.6 - - + +
157C PRO* 5.1 4.9 - - + -
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Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LEU* 2.8 38.7 + - + +
31C LEU* 3.6 24.5 - - + +
32C LYS 3.3 0.4 - - - -
33C VAL* 1.3 78.0 - - - +
35C GLU* 1.3 61.8 + - - +
37C GLU* 3.4 0.8 + - - -
38C GLY 3.0 4.3 + - - -
39C LEU* 2.9 49.6 + - + -
40C LYS* 3.9 19.1 + - + +
43C VAL* 4.0 34.5 - - + -
46C VAL* 4.4 1.6 - - + -
149C LEU* 4.1 22.7 - - + -
152C ALA* 4.7 2.7 - - + -
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Residues in contact with GLU 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C LEU 3.3 10.0 + - - +
32C LYS* 3.7 11.0 - - + +
34C LEU* 1.3 78.8 - - - +
36C LEU* 1.3 69.5 + - + +
38C GLY* 3.0 14.0 + - - -
40C LYS* 3.3 41.4 + - + +
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Residues in contact with LEU 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LYS* 3.1 26.6 + - + +
33C VAL* 3.4 13.9 + - + +
35C GLU* 1.3 84.8 - - + +
37C GLU* 1.3 64.8 + - + +
38C GLY 3.4 0.2 + - - -
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Residues in contact with GLU 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C VAL* 3.0 30.0 + - + +
36C LEU* 1.3 79.7 - - + +
38C GLY* 1.3 64.1 + - - +
39C LEU* 3.5 21.2 + - + +
148C LYS* 3.4 39.6 + - - +
151C MET* 5.5 1.2 - - - +
152C ALA* 4.4 6.7 + - + +
155C LYS* 3.2 39.1 + - - +
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Residues in contact with GLY 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LEU 3.0 5.2 + - - -
35C GLU* 3.0 11.7 + - - -
36C LEU 3.3 1.4 + - - -
37C GLU* 1.3 78.6 - - - +
39C LEU* 1.3 62.7 + - - +
40C LYS* 3.6 4.0 + - - -
41C ASP* 5.2 2.3 + - - +
42C LEU* 5.8 1.2 - - - +
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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