Contacts of the helix formed by residues 24 - 41 (chain F) in PDB entry 2NPP
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 SER 24 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F GLN* 5.4 0.2 - - - +
22F GLN* 4.2 0.4 + - - +
23F LEU* 1.3 73.3 - - - +
25F GLU* 1.3 68.0 + - - +
26F SER* 3.5 10.2 + - - -
27F GLN* 2.7 44.7 + - - +
28F VAL* 2.8 22.8 + - - +
137F TYR* 4.4 1.6 - - - -
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Residues in contact with GLU 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F SER* 1.3 73.1 - - - +
26F SER* 1.3 66.2 + - - +
28F VAL* 3.4 3.3 + - - +
29F LYS* 3.2 17.8 + - - +
137F TYR* 3.6 24.9 - - + +
139F ASN* 2.8 27.9 + - - +
141F ASN* 3.0 34.2 + - + +
142F VAL* 4.0 20.2 - - + -
145F TYR* 3.8 14.4 + - + -
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Residues in contact with SER 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F SER* 2.9 10.8 + - - -
25F GLU* 1.3 78.3 - - - +
27F GLN* 1.3 69.0 + - - +
29F LYS* 2.8 22.0 + - - +
30F SER* 3.2 13.9 + - - -
145F TYR* 5.9 0.2 - - - -
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Residues in contact with GLN 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F GLN* 4.7 4.2 + - - -
13F TRP* 2.8 52.4 - - + +
16F GLN* 4.7 6.6 + - - -
23F LEU* 3.5 17.0 - - + +
24F SER* 2.7 45.8 + - - +
26F SER* 1.3 81.0 + - - +
28F VAL* 1.3 52.6 + - - +
30F SER* 3.2 5.1 + - - +
31F LEU* 2.7 37.8 + - - +
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Residues in contact with VAL 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F LEU* 3.8 13.0 - - + +
24F SER 2.8 24.8 + - - +
25F GLU* 3.6 9.4 - - - +
27F GLN* 1.3 72.0 - - - +
29F LYS* 1.3 63.0 + - - +
31F LEU* 3.7 7.0 - - - +
32F CYS* 3.0 35.0 + - - -
98F THR* 5.3 3.6 - - + +
137F TYR* 3.6 25.1 - - + +
142F VAL* 4.0 11.2 - - + -
145F TYR* 4.7 7.4 - - + -
146F PHE* 3.4 40.2 - - + -
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Residues in contact with LYS 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F GLU 3.2 2.7 + - - +
26F SER* 2.8 13.5 + - - +
28F VAL* 1.3 81.1 - - - +
30F SER* 1.3 62.6 + - - +
32F CYS* 3.2 3.0 + - - +
33F GLU* 2.9 44.4 + - + +
145F TYR* 3.2 57.1 + - + +
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Residues in contact with SER 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F PHE* 5.9 3.1 - - - -
9F GLU* 5.6 1.1 - - - -
13F TRP* 4.1 15.0 - - - -
26F SER* 3.2 11.5 + - - -
27F GLN* 3.6 7.7 - - - -
29F LYS* 1.3 76.8 - - - +
31F LEU* 1.3 67.0 + - - +
33F GLU* 3.0 10.6 + - - +
34F LYS* 3.0 26.9 + - - +
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Residues in contact with LEU 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F LEU* 4.3 1.1 - - + -
13F TRP* 3.6 28.6 - - + -
23F LEU* 4.4 6.7 - - + -
27F GLN 2.7 22.0 + - - +
28F VAL* 3.7 6.3 - - - +
30F SER* 1.3 72.2 - - - +
32F CYS* 1.3 58.5 + - - +
34F LYS* 3.7 4.7 + - - +
35F ALA* 2.9 26.9 + - - +
98F THR* 3.8 41.7 - - + +
101F VAL* 3.9 14.1 - - + -
102F ALA* 3.8 16.6 - - + +
105F VAL* 3.5 26.9 - - + +
146F PHE* 5.3 5.4 - - + -
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Residues in contact with CYS 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F VAL* 3.0 32.7 + - - +
29F LYS* 3.6 5.6 - - - +
31F LEU* 1.3 76.4 - - - +
33F GLU* 1.3 70.6 + - - +
35F ALA* 2.9 9.7 + - - +
36F LYS* 2.8 25.1 + - - +
101F VAL* 5.4 0.2 - - - -
145F TYR* 3.7 27.4 - - + +
146F PHE* 3.9 31.4 - - - -
149F LEU* 3.5 16.2 - - + +
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Residues in contact with GLU 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F LYS* 2.9 46.6 + - + +
30F SER* 3.0 10.5 + - - +
32F CYS* 1.3 76.0 - - - +
34F LYS* 1.3 65.8 + - - +
35F ALA 2.7 2.4 + - - -
36F LYS* 2.7 39.6 + - - +
37F GLU* 3.3 19.9 + - - +
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Residues in contact with LYS 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F PHE* 3.5 41.5 - - + -
10F LEU* 6.1 0.2 - - - +
30F SER 3.0 12.9 + - - +
31F LEU* 3.7 5.8 - - - +
33F GLU* 1.3 79.7 - - - +
35F ALA* 1.3 59.4 + - - +
37F GLU* 3.7 21.3 + - + +
38F ILE* 3.4 30.0 + - + +
105F VAL* 4.2 19.7 + - + +
108F ARG* 3.9 22.0 - - - +
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Residues in contact with ALA 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F LEU 2.9 16.3 + - - +
32F CYS* 2.9 15.7 + - - +
33F GLU 2.7 4.8 + - - -
34F LYS* 1.3 72.6 - - - +
36F LYS* 1.3 62.4 + - - +
38F ILE* 3.1 6.3 + - - +
39F LEU* 2.9 28.6 + - + +
101F VAL* 4.0 11.0 - - + -
104F LYS* 6.5 0.7 - - + -
105F VAL* 4.0 11.2 - - + -
149F LEU* 3.3 25.1 - - + -
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Residues in contact with LYS 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F CYS* 2.8 19.3 + - - +
33F GLU* 2.7 34.3 + - - +
35F ALA* 1.3 70.5 - - - +
37F GLU* 1.3 54.5 + - + +
39F LEU* 2.8 8.8 + - - +
40F THR* 2.7 36.8 + - - -
145F TYR 5.1 2.9 + - - -
148F ASP* 4.3 26.4 + - - +
149F LEU* 3.6 20.2 - - + +
152F TYR* 3.8 44.3 + - + +
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Residues in contact with GLU 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F GLU* 3.3 11.4 + - - +
34F LYS* 3.7 31.4 + - + +
36F LYS* 1.3 79.5 - - + +
38F ILE* 1.3 60.9 + - + +
40F THR* 4.2 8.6 + - - -
41F LYS* 4.1 23.6 + - - +
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Residues in contact with ILE 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F LYS* 3.4 20.4 - - + +
35F ALA* 3.1 6.4 + - - +
36F LYS 3.0 1.0 - - - -
37F GLU* 1.3 78.4 - - + +
39F LEU* 1.3 64.8 + - - +
40F THR 3.4 0.4 - - - -
41F LYS* 3.8 13.8 + - + +
42F GLU* 3.6 14.9 - - + +
104F LYS* 4.5 21.5 - - + +
105F VAL* 3.8 34.3 - - + +
108F ARG* 3.3 63.9 - - + +
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Residues in contact with LEU 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F ALA* 2.9 14.9 + - + +
36F LYS* 2.8 5.1 + - - +
38F ILE* 1.3 77.7 - - + +
40F THR* 1.3 67.8 + - - +
42F GLU* 3.1 31.3 + - - +
101F VAL* 6.4 0.2 - - + -
104F LYS* 4.5 18.6 - - + -
113F ILE* 4.6 11.4 - - + -
149F LEU* 3.8 33.0 - - + +
152F TYR* 3.4 22.4 - - + +
153F LEU* 4.0 23.8 - - + -
154F PRO* 3.9 17.7 - - + -
185F ARG* 3.2 15.2 + - - -
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Residues in contact with THR 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F LYS* 2.7 23.4 + - - +
37F GLU* 4.4 8.0 - - - -
38F ILE 3.4 0.2 - - - -
39F LEU* 1.3 73.1 - - - +
41F LYS* 1.3 57.9 + - + +
42F GLU 2.7 22.5 + - - +
152F TYR* 3.6 25.9 - - + -
185F ARG* 4.0 5.2 + - - +
186F LEU* 5.5 9.9 - - + -
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Residues in contact with LYS 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F GLU 4.1 16.6 - - - +
38F ILE* 3.8 10.5 + - + +
39F LEU 3.3 0.4 - - - -
40F THR* 1.3 80.8 - - + +
42F GLU* 1.3 60.9 + - + +
43F SER 3.7 1.2 + - - -
108F ARG* 4.3 18.5 - - - +
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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