Contacts of the helix formed by residues 11 - 25 (chain B) in PDB entry 2NP2
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 11 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A GLU 3.6 5.1 + - - -
57A PHE* 3.8 23.9 - - + +
58A ARG 5.2 5.9 + - - -
10B THR* 1.3 71.4 - - - +
12B SER* 1.3 57.5 + - - +
14B ILE* 3.8 1.3 - - - +
15B VAL* 3.0 36.8 + - + +
35B ARG* 5.7 0.9 - - - +
38B ILE* 4.2 17.7 - - + -
39B ASP* 3.3 26.4 + - - +
42B PHE* 4.6 11.1 - - + -
233C A 3.0 38.3 + - - +
234C A 2.9 32.5 + - - -
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Residues in contact with SER 12 (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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10B THR* 2.8 12.5 + - - -
11B LYS* 1.3 79.8 - - - +
13B ASP* 1.3 62.9 + - - -
15B VAL* 3.1 9.4 + - - +
16B ASP* 2.6 37.1 + - - +
35B ARG* 5.3 7.5 + - - +
233C A 4.0 7.1 + - - -
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Residues in contact with ASP 13 (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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8B LYS 4.0 5.0 - - - +
9B VAL* 3.6 19.6 - - + +
10B THR* 2.8 38.2 + - - +
12B SER* 1.3 73.9 - - - +
14B ILE* 1.3 64.6 + - - +
16B ASP* 2.9 10.9 + - - +
17B GLN* 2.9 34.2 + - + +
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Residues in contact with ILE 14 (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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41A PHE* 4.1 20.9 - - + +
44A GLU* 4.5 11.9 - - + +
45A LEU* 4.8 5.2 - - + +
48A ASN* 3.2 32.5 - - + +
55A ILE* 3.8 21.3 - - + -
57A PHE* 4.3 5.6 - - + -
9B VAL* 3.4 17.3 - - + -
10B THR 3.0 15.1 + - - +
11B LYS* 3.8 5.8 - - - +
13B ASP* 1.3 75.1 - - - +
15B VAL* 1.3 58.0 + - + +
17B GLN* 3.0 6.6 + - - +
18B ILE* 2.8 47.6 + - + +
38B ILE* 6.1 0.9 - - + -
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Residues in contact with VAL 15 (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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11B LYS* 3.0 32.0 + - + +
12B SER* 3.1 11.4 + - - +
14B ILE* 1.3 76.2 - - + +
16B ASP* 1.3 65.2 + - - +
18B ILE* 3.6 4.6 + - + +
19B ALA* 3.1 19.2 + - - +
31B LYS* 4.1 13.2 - - + +
34B ILE* 4.0 19.2 - - + +
35B ARG* 3.5 48.9 - - + +
38B ILE* 4.3 17.7 - - + -
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Residues in contact with ASP 16 (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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12B SER* 2.6 35.8 + - - +
13B ASP* 2.9 12.7 + - - +
15B VAL* 1.3 77.7 - - - +
17B GLN* 1.3 60.9 + - + +
19B ALA* 2.9 27.6 + - - +
20B LEU* 3.0 14.1 + - + +
31B LYS* 3.4 27.1 - - - +
35B ARG* 5.8 1.4 + - - -
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Residues in contact with GLN 17 (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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44A GLU* 3.0 30.5 + - + +
47A SER* 5.1 0.6 + - - -
48A ASN* 2.9 37.1 + - - +
9B VAL* 4.4 4.7 - - - +
13B ASP* 2.9 29.7 + - + +
14B ILE* 3.5 6.1 - - - +
16B ASP* 1.3 74.0 - - + +
18B ILE* 1.3 60.8 + - - +
20B LEU* 3.1 14.5 + - + +
21B ASN* 2.8 31.5 + - - +
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Residues in contact with ILE 18 (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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37A VAL* 4.2 5.8 - - + +
40A ALA* 3.5 19.3 - - + -
41A PHE* 3.4 50.5 - - + +
44A GLU* 4.0 10.5 - - + -
14B ILE* 2.8 25.5 + - + +
15B VAL* 3.8 5.2 - - - +
17B GLN* 1.3 74.1 - - - +
19B ALA* 1.3 67.1 + - - +
21B ASN* 4.2 2.9 - - - -
22B ILE* 2.9 38.1 + - + +
34B ILE* 3.7 17.9 - - + -
38B ILE* 4.0 13.9 - - + -
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Residues in contact with ALA 19 (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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15B VAL 3.1 13.3 + - - +
16B ASP* 2.9 16.7 + - - +
18B ILE* 1.3 79.6 - - - +
20B LEU* 1.3 63.3 + - + +
22B ILE* 3.3 4.1 + - - +
23B LYS* 3.0 32.5 + - - +
29B LEU 5.3 3.8 - - - +
31B LYS* 4.2 22.4 - - + +
34B ILE* 3.7 18.6 - - + -
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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
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16B ASP* 3.0 16.0 + - + +
17B GLN* 3.1 15.2 + - + +
19B ALA* 1.3 71.9 - - + +
21B ASN* 1.3 70.4 - - - +
23B LYS* 2.6 22.0 + - + +
24B ASN* 2.8 27.7 + - - +
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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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36A LEU* 6.1 0.3 - - - +
40A ALA* 3.6 18.8 - - - +
43A GLU* 3.7 27.5 - - - +
44A GLU* 3.1 29.9 + - + +
17B GLN 2.8 13.8 + - - +
18B ILE* 3.9 6.5 - - - +
20B LEU* 1.3 73.2 - - - +
22B ILE* 1.3 65.3 + - - +
24B ASN* 3.3 18.9 + - - +
25B ASN* 3.4 22.3 + - - +
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Residues in contact with ILE 22 (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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36A LEU* 3.7 38.1 - - + -
37A VAL* 4.3 6.1 - - + -
40A ALA* 4.1 8.3 - - + -
18B ILE* 2.9 43.6 + - + +
19B ALA* 3.6 4.9 - - - +
20B LEU 2.9 1.0 + - - -
21B ASN* 1.3 80.5 - - - +
23B LYS* 1.3 61.4 + - + +
25B ASN* 3.3 10.5 + - - +
27B LEU* 3.3 42.0 - - + +
29B LEU* 4.2 31.9 - - + +
34B ILE* 4.4 4.5 - - + -
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Residues in contact with LYS 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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19B ALA* 3.0 21.6 + - - +
20B LEU* 2.6 17.8 + - + +
22B ILE* 1.3 70.5 - - + +
24B ASN* 1.3 53.4 + - - +
25B ASN 2.7 15.5 + - - -
26B ASN* 2.7 16.5 + - - +
27B LEU 3.2 19.1 - - - +
28B LYS* 4.6 20.0 - - + +
29B LEU 4.7 14.4 - - - +
31B LYS* 5.5 6.1 - - - +
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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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20B LEU* 2.8 36.6 + - - +
21B ASN* 3.6 10.6 - - - +
22B ILE 3.3 0.4 - - - -
23B LYS* 1.3 75.2 - - - +
25B ASN* 1.3 71.0 + - - +
26B ASN* 3.4 8.0 + - - +
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Residues in contact with ASN 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 ASN* 3.4 20.2 + - - +
22B ILE* 3.3 7.7 + - - +
23B LYS 2.8 1.0 - - - -
24B ASN* 1.3 93.2 + - - +
26B ASN* 1.3 69.8 + - - +
27B LEU* 2.8 26.0 - - + +
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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