Contacts of the helix formed by residues 30 - 51 (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 GLU 30 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LYS 4.9 2.8 - - - +
29B LEU* 1.3 77.5 - - - +
31B LYS* 1.3 64.9 + - - +
32B LYS* 2.7 18.1 + - + +
33B TYR* 2.7 52.1 + - + +
34B ILE* 3.2 10.0 + - - +
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Residues in contact with LYS 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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15B VAL* 4.7 6.1 - - + -
16B ASP* 3.4 35.0 - - - +
19B ALA* 4.2 25.7 - - + +
23B LYS* 5.5 5.7 - - - +
29B LEU 3.5 3.0 + - - +
30B GLU* 1.3 71.3 - - - +
32B LYS* 1.3 55.9 + - - +
34B ILE* 3.2 12.3 + - + +
35B ARG* 2.8 64.5 + - - +
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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
----------------------------------------------------------
27A LEU* 6.0 6.0 - - - +
30B GLU* 2.7 11.8 + - + -
31B LYS* 1.3 79.7 - - - +
33B TYR* 1.3 89.1 + - + +
35B ARG* 3.4 16.9 + - - +
36B LEU* 3.1 26.7 + - + +
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Residues in contact with TYR 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LYS 6.2 0.2 - - - -
29A LEU* 4.1 26.4 - - + +
29B LEU* 3.4 34.1 - - + -
30B GLU* 2.7 52.2 + - + +
32B LYS* 1.3 107.2 + - + +
34B ILE* 1.3 58.8 + - - +
36B LEU* 3.2 15.2 - - + +
37B VAL* 2.9 33.8 + - - +
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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
----------------------------------------------------------
37A VAL* 3.9 15.9 - - + -
15B VAL* 4.0 18.2 - - + +
18B ILE* 3.7 31.0 - - + -
19B ALA* 3.7 35.2 - - + +
22B ILE* 4.4 6.3 - - + -
29B LEU* 3.9 30.5 - - + +
30B GLU 3.2 9.4 + - - +
31B LYS* 3.5 12.8 - - - +
33B TYR* 1.3 74.5 - - - +
35B ARG* 1.3 67.4 + - - +
36B LEU 3.2 0.2 + - - -
37B VAL* 3.2 2.4 + - - +
38B ILE* 3.0 29.2 + - + +
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Residues in contact with ARG 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LYS* 5.7 0.8 - - - +
12B SER* 5.3 7.9 + - - +
15B VAL* 3.5 29.9 - - + +
16B ASP* 5.8 1.4 + - - -
31B LYS* 2.8 59.8 + - - +
32B LYS* 3.6 13.8 - - - +
34B ILE* 1.3 75.6 - - - +
36B LEU* 1.3 57.5 + - - +
38B ILE* 3.5 2.3 + - - +
39B ASP* 3.0 40.4 + - - +
234C A 6.1 1.1 - - - -
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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
----------------------------------------------------------
21A ASN* 6.1 0.2 - - - +
22A ILE* 3.7 40.6 - - + -
27A LEU* 4.0 27.6 - - + -
29A LEU* 4.5 10.3 - - + -
32B LYS* 3.1 14.9 + - + +
33B TYR* 3.2 21.3 - - + +
35B ARG* 1.3 75.0 - - - +
37B VAL* 1.3 65.5 + - - +
39B ASP* 3.2 9.1 + - + +
40B ALA* 3.0 22.2 + - + +
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 4.2 9.8 - - + +
22A ILE* 4.3 6.5 - - + -
29A LEU* 3.5 26.0 - - + -
34A ILE* 4.0 22.2 - - + -
37A VAL* 3.7 28.3 - - + -
38A ILE* 3.7 27.1 - - + -
33B TYR 2.9 23.5 + - - +
34B ILE 3.8 3.4 - - - +
36B LEU* 1.3 71.4 - - - +
38B ILE* 1.3 53.8 + - - +
40B ALA* 3.0 3.6 + - - +
41B PHE* 2.6 35.2 + - - +
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Residues in contact with ILE 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A VAL* 3.7 21.8 - - + -
38A ILE* 4.9 4.5 - - + -
41A PHE* 3.5 35.4 - - + -
57A PHE* 5.2 1.3 - - + -
11B LYS* 4.2 19.7 - - + -
14B ILE* 6.1 0.7 - - + -
15B VAL* 4.3 13.2 - - + -
18B ILE* 4.0 7.2 - - + -
34B ILE 3.0 19.5 + - - +
35B ARG* 3.6 6.5 - - - +
37B VAL* 1.3 78.3 - - + +
39B ASP* 1.3 60.4 + - - +
41B PHE* 3.2 7.2 - - + +
42B PHE* 3.1 48.0 + - + -
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Residues in contact with ASP 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LYS* 3.3 34.7 + - - +
35B ARG* 3.0 28.3 + - - +
36B LEU* 3.7 7.1 + - + +
37B VAL 3.2 0.2 - - - -
38B ILE* 1.3 73.6 - - - +
40B ALA* 1.3 60.9 - - - +
42B PHE* 3.4 7.1 + - - +
43B GLU* 3.0 43.0 + - - +
234C A 5.0 6.9 + - - -
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Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 3.6 25.8 - - + -
21A ASN* 3.6 22.4 - - - +
22A ILE* 4.2 7.0 - - + -
36B LEU* 3.0 12.1 + - + +
37B VAL 3.0 7.7 + - - +
39B ASP* 1.3 75.0 - - - +
41B PHE* 1.3 57.6 + - - +
43B GLU* 3.5 13.3 + - - +
44B GLU* 2.8 36.9 + - - +
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Residues in contact with PHE 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 4.1 9.3 - - + +
18A ILE* 3.5 18.1 - - + +
38A ILE* 3.5 27.1 - - + -
41A PHE* 3.5 29.4 - + - -
42A PHE* 4.0 23.3 - + - -
37B VAL 2.6 13.7 + - - +
38B ILE* 3.2 15.3 - - + +
40B ALA* 1.3 78.4 - - - +
42B PHE* 1.3 80.0 + + - +
44B GLU* 3.7 2.3 - - - +
45B LEU* 2.9 45.4 + - + +
57B PHE* 3.9 28.7 - + - -
63B PHE* 5.9 1.3 - + - -
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Residues in contact with PHE 42 (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* 4.0 11.2 - + - -
57A PHE* 3.3 51.8 - + + -
60A PHE* 3.4 44.9 - + + -
63A PHE* 5.4 0.9 - + - -
11B LYS* 4.6 10.1 - - + -
38B ILE* 3.1 36.0 + - + +
39B ASP* 3.9 7.0 - - - +
41B PHE* 1.3 94.2 - + - +
43B GLU* 1.3 68.4 + - - +
45B LEU* 3.1 4.3 + - - +
46B LYS* 2.9 41.1 + - - +
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Residues in contact with GLU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASN* 2.6 37.7 + - - +
25A ASN* 5.7 0.9 - - - +
102A ARG* 5.0 1.8 + - - +
39B ASP* 3.0 33.2 + - - +
40B ALA* 3.5 7.5 + - - +
42B PHE* 1.3 80.7 - - - +
44B GLU* 1.3 61.2 + - - +
46B LYS* 3.1 22.2 + - - +
47B SER* 3.1 14.9 + - - -
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Residues in contact with GLU 44 (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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14A ILE* 4.6 7.6 - - + -
17A GLN* 3.0 44.2 + - + +
18A ILE* 4.0 18.8 - - + +
21A ASN* 3.1 30.6 + - + +
40B ALA 2.8 24.3 + - - +
41B PHE 3.7 3.8 - - - +
43B GLU* 1.3 70.8 - - - +
45B LEU* 1.3 60.4 + - - +
47B SER* 3.1 11.4 + - - -
48B ASN* 2.9 35.8 + - - -
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Residues in contact with LEU 45 (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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14A ILE* 4.9 5.1 - - + +
60A PHE* 3.7 28.9 - - + -
41B PHE* 2.9 42.8 + - + +
42B PHE* 3.1 5.4 + - - +
44B GLU* 1.3 74.9 - - - +
46B LYS* 1.3 62.1 + - - +
48B ASN* 3.3 3.8 + - + +
49B LEU* 2.8 37.9 + - + +
55B ILE* 3.3 47.8 - - + -
57B PHE* 4.6 2.5 - - + -
63B PHE* 4.1 28.5 - - + -
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Residues in contact with LYS 46 (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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58A ARG 5.5 0.2 + - - -
59A SER* 3.4 29.6 + - - +
60A PHE* 4.0 17.3 - - + +
98A ASP* 3.2 25.7 + - - +
99A LEU* 3.7 31.8 - - + +
102A ARG* 3.5 17.9 - - - +
42B PHE* 2.9 30.9 + - - +
43B GLU* 3.4 14.0 - - - +
45B LEU* 1.3 73.5 - - - +
47B SER* 1.3 61.2 + - - +
49B LEU* 2.9 5.4 + - - +
50B CYS* 2.8 33.3 + - - -
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Residues in contact with SER 47 (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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17A GLN* 5.1 0.3 + - - -
102A ARG* 3.6 18.3 - - - +
43B GLU 3.1 9.4 + - - -
44B GLU* 3.1 23.7 + - - -
46B LYS* 1.3 77.7 - - - +
48B ASN* 1.3 65.1 + - - +
50B CYS* 3.2 3.6 + - - +
51B SER* 3.0 28.7 + - - -
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Residues in contact with ASN 48 (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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9A VAL* 3.4 15.9 - - - +
14A ILE* 3.2 21.4 - - - +
17A GLN* 3.0 29.3 + - - +
44B GLU 2.9 21.2 + - - +
45B LEU* 3.4 5.6 - - - +
47B SER* 1.3 84.8 + - - +
49B LEU* 1.3 63.0 + - - +
51B SER* 3.4 3.9 + - - -
53B ASN* 2.8 54.1 + - - +
55B ILE* 4.0 13.7 - - + -
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Residues in contact with LEU 49 (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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60A PHE* 5.7 0.9 - - + -
99A LEU* 3.9 25.4 - - + -
103A VAL* 4.3 11.9 - - + -
106A ILE* 4.0 0.3 - - - +
45B LEU* 2.8 22.7 + - + +
46B LYS 2.9 7.8 + - - +
48B ASN* 1.3 74.4 - - - +
50B CYS* 1.3 56.3 + - - +
52B ASN* 2.7 27.4 + - - -
53B ASN 4.0 7.2 - - - +
55B ILE* 3.4 26.5 - - + -
63B PHE* 4.2 18.8 - - + -
64B GLU* 4.0 26.2 - - - +
65B VAL* 3.4 14.1 - - + +
91B ALA* 4.2 17.9 - - + -
92B TYR 5.6 0.4 - - - +
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Residues in contact with CYS 50 (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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99A LEU* 5.8 0.7 - - - -
102A ARG* 3.0 66.2 - - - +
103A VAL* 4.4 4.2 - - - +
106A ILE* 3.5 26.4 - - + +
46B LYS* 2.8 14.9 + - - -
47B SER* 3.5 7.6 - - - +
49B LEU* 1.3 70.2 - - - +
51B SER* 1.3 58.3 + - - +
52B ASN* 2.8 10.9 + - - +
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Residues in contact with SER 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG 4.9 3.6 + - - -
7A PRO* 5.0 0.2 - - - +
47B SER* 3.0 16.8 + - - -
48B ASN* 4.6 0.2 - - - -
49B LEU 3.2 0.4 - - - -
50B CYS* 1.3 74.9 - - - +
52B ASN* 1.3 70.9 + - - +
53B ASN* 3.3 28.6 + - - +
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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