Contacts of the helix formed by residues 30 - 51 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LYS 4.9 2.9 - - - +
29A LEU* 1.3 79.1 - - - +
31A LYS* 1.3 65.7 + - - +
32A LYS* 2.7 19.4 + - + +
33A TYR* 2.8 52.1 + - + +
34A ILE* 3.2 8.4 + - - +
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Residues in contact with LYS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A VAL* 4.1 7.1 - - + +
16A ASP* 3.4 35.0 - - - +
19A ALA* 4.2 26.3 - - + +
23A LYS* 5.6 6.1 - - - +
29A LEU 3.5 3.0 + - - +
30A GLU* 1.3 70.1 - - - +
32A LYS* 1.3 55.3 + - - +
34A ILE* 3.2 12.7 + - + +
35A ARG* 2.8 64.1 + - - +
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Residues in contact with LYS 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 2.7 11.6 + - + -
31A LYS* 1.3 80.6 - - - +
33A TYR* 1.3 89.8 + - + +
35A ARG* 3.4 15.8 + - - +
36A LEU* 3.0 26.7 + - + +
27B LEU* 6.1 5.8 - - - +
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Residues in contact with TYR 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 3.4 33.7 - - + -
30A GLU* 2.8 50.2 + - + +
32A LYS* 1.3 107.1 + - + +
34A ILE* 1.3 60.5 + - - +
36A LEU* 3.3 15.1 - - + +
37A VAL* 2.9 34.1 + - - +
28B LYS 6.2 0.4 - - - -
29B LEU* 4.2 25.1 - - + +
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Residues in contact with ILE 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 4.0 20.0 - - + +
18A ILE* 3.7 29.2 - - + -
19A ALA* 3.7 35.7 - - + +
22A ILE* 4.3 6.7 - - + -
29A LEU* 3.9 30.5 - - + +
30A GLU 3.2 9.4 + - - +
31A LYS* 3.2 12.3 + - - +
33A TYR* 1.3 74.0 - - - +
35A ARG* 1.3 66.7 + - - +
36A LEU 3.1 0.3 + - - -
37A VAL* 3.1 3.3 + - - +
38A ILE* 3.0 28.6 + - + +
37B VAL* 4.0 16.4 - - + -
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Residues in contact with ARG 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 5.8 0.8 - - - +
12A SER* 5.4 6.7 + - - +
15A VAL* 3.5 30.6 - - + +
16A ASP* 5.8 1.0 + - - -
31A LYS* 2.8 60.0 + - - +
32A LYS* 3.6 14.0 - - - +
34A ILE* 1.3 75.7 - - - +
36A LEU* 1.3 62.8 + - - +
38A ILE* 3.5 2.5 + - - +
39A ASP* 3.0 35.4 + - - +
234D A 6.1 1.3 - - - -
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Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LYS* 3.0 15.5 + - + +
33A TYR* 3.3 20.9 - - + +
35A ARG* 1.3 74.4 - - - +
37A VAL* 1.3 64.3 + - - +
39A ASP* 3.2 8.6 + - + +
40A ALA* 3.1 21.6 + - + +
21B ASN* 6.1 0.2 - - - +
22B ILE* 3.7 39.9 - - + -
27B LEU* 4.0 29.2 - - + -
29B LEU* 4.4 10.3 - - + -
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Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TYR 2.9 21.6 + - - +
34A ILE 3.1 3.6 + - - +
36A LEU* 1.3 73.0 - - - +
38A ILE* 1.3 55.2 + - - +
40A ALA* 3.0 3.6 + - - +
41A PHE* 2.6 35.7 + - - +
18B ILE* 4.2 3.8 - - + +
22B ILE* 4.3 11.7 - - + -
29B LEU* 3.4 26.2 - - + -
34B ILE* 3.9 22.9 - - + -
37B VAL* 3.7 27.1 - - + -
38B ILE* 3.7 27.4 - - + -
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Residues in contact with ILE 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 4.2 19.7 - - + -
14A ILE* 6.1 1.1 - - + -
15A VAL* 4.3 14.4 - - + -
18A ILE* 4.0 4.7 - - + -
34A ILE* 3.0 20.4 + - + +
35A ARG* 3.7 6.7 - - - +
37A VAL* 1.3 77.3 - - + +
39A ASP* 1.3 61.5 + - - +
41A PHE* 3.2 7.2 - - + +
42A PHE* 3.1 47.4 + - + -
37B VAL* 3.7 22.0 - - + -
38B ILE* 4.9 4.5 - - + -
41B PHE* 3.5 35.4 - - + -
57B PHE* 5.3 1.3 - - + -
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Residues in contact with ASP 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 3.4 33.9 + - - +
35A ARG* 3.0 29.4 + - - +
36A LEU* 3.7 6.6 + - + +
37A VAL 3.2 0.2 - - - -
38A ILE* 1.3 72.7 - - - +
40A ALA* 1.3 66.2 + - - +
42A PHE* 3.3 6.9 + - - +
43A GLU* 3.0 24.4 + - - +
234D A 4.5 10.0 + - - -
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Residues in contact with ALA 40 (chain A).
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* 3.1 12.5 + - + +
37A VAL 3.0 3.7 + - - +
39A ASP* 1.3 77.3 - - - +
41A PHE* 1.3 54.8 + - - +
43A GLU* 3.6 5.3 - - - +
44A GLU* 2.8 39.8 + - - +
18B ILE* 3.5 28.9 - - + -
21B ASN* 3.6 27.6 - - - +
22B ILE* 4.1 7.0 - - + -
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Residues in contact with PHE 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A VAL 2.6 13.5 + - - +
38A ILE* 3.2 15.7 - - + +
40A ALA* 1.3 77.0 - - - +
42A PHE* 1.3 80.1 + + - +
44A GLU* 3.7 2.1 - - - +
45A LEU* 2.9 46.5 + - + +
57A PHE* 3.9 28.0 - + - -
63A PHE* 5.9 1.8 - + - -
14B ILE* 4.1 10.2 - - + +
18B ILE* 3.4 18.5 - - + +
38B ILE* 3.5 28.5 - - + -
41B PHE* 3.5 29.8 - + - -
42B PHE* 4.0 23.1 - + - -
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Residues in contact with PHE 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LYS* 4.6 11.4 - - + -
38A ILE* 3.1 35.2 + - + +
39A ASP* 3.3 6.9 + - - +
41A PHE* 1.3 94.0 - + - +
43A GLU* 1.3 67.9 + - - +
45A LEU* 3.6 1.3 - - - +
46A LYS* 2.9 36.4 + - - +
41B PHE* 4.0 11.4 - + - -
57B PHE* 3.3 51.1 - + + -
60B PHE* 3.5 51.5 - + + -
63B PHE* 5.4 1.8 - + - -
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Residues in contact with GLU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ASP 3.0 18.1 + - - +
40A ALA* 3.6 4.5 - - - +
42A PHE* 1.3 80.2 - - - +
44A GLU* 1.3 65.2 + - - +
46A LYS* 3.0 22.0 + - - +
47A SER* 3.1 21.0 + - - -
21B ASN* 3.7 23.1 - - - +
98B ASP* 5.4 0.5 - - - +
102B ARG* 4.1 17.2 + - - -
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Residues in contact with GLU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ALA 2.8 24.7 + - - +
41A PHE 3.7 3.1 - - - +
43A GLU* 1.3 77.4 - - - +
45A LEU* 1.3 60.7 + - - +
47A SER* 3.1 10.7 + - - -
48A ASN* 2.9 31.6 + - - -
14B ILE* 4.5 7.4 - - + -
17B GLN* 3.0 47.2 + - + +
18B ILE* 4.0 17.0 - - + -
21B ASN* 3.1 30.1 + - + +
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Residues in contact with LEU 45 (chain A).
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* 2.9 41.7 + - + +
42A PHE* 3.6 4.5 - - - +
43A GLU 3.2 0.4 - - - -
44A GLU* 1.3 74.0 - - - +
46A LYS* 1.3 61.6 + - - +
48A ASN* 3.3 4.0 + - + +
49A LEU* 2.8 36.2 + - + +
55A ILE* 3.3 46.4 - - + -
57A PHE* 4.6 2.9 - - + -
63A PHE* 4.1 31.2 - - + -
14B ILE* 4.8 4.7 - - + +
60B PHE* 3.5 29.4 - - + -
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Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PHE* 2.9 29.9 + - - +
43A GLU* 3.4 16.8 + - - +
45A LEU* 1.3 76.2 - - - +
47A SER* 1.3 63.4 + - - +
49A LEU* 2.9 4.9 + - - +
50A CYS* 2.9 27.9 + - - -
59B SER 3.7 15.9 + - - +
60B PHE* 3.7 21.7 - - + +
98B ASP* 3.0 31.4 + - + +
99B LEU* 3.7 34.4 - - + +
102B ARG* 3.6 15.5 - - + +
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Residues in contact with SER 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A GLU* 3.1 19.4 + - - -
44A GLU* 3.1 23.4 + - - -
46A LYS* 1.3 77.7 - - - +
48A ASN* 1.3 67.2 + - - +
50A CYS* 3.2 2.3 + - - +
51A SER* 3.0 28.5 + - - -
17B GLN* 5.1 0.3 + - - -
102B ARG* 3.5 18.1 - - - +
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Residues in contact with ASN 48 (chain A).
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 2.9 20.3 + - - +
45A LEU* 3.4 6.1 - - - +
47A SER* 1.3 84.0 + - - +
49A LEU* 1.3 64.0 + - - +
51A SER* 3.4 3.9 + - - -
53A ASN* 2.8 54.5 + - - +
55A ILE* 4.0 14.4 - - + -
9B VAL* 3.4 15.6 - - - +
14B ILE* 3.2 21.9 - - - +
17B GLN* 2.9 30.4 + - - +
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU* 2.8 22.3 + - + +
46A LYS 2.9 8.3 + - - +
48A ASN* 1.3 76.8 - - - +
50A CYS* 1.3 54.2 + - - +
52A ASN* 2.7 26.9 + - - -
53A ASN 4.0 8.1 - - - +
55A ILE* 3.3 25.1 - - + -
63A PHE* 4.2 19.1 - - + -
64A GLU* 4.0 25.4 - - - +
65A VAL* 3.4 14.8 - - + +
91A ALA* 4.2 17.3 - - + -
92A TYR 5.7 0.2 - - - +
60B PHE* 5.7 0.7 - - + -
99B LEU* 3.7 31.0 - - + -
103B VAL* 4.3 7.2 - - + -
106B ILE* 4.2 0.3 - - - +
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Residues in contact with CYS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LYS* 2.9 13.8 + - - -
47A SER 3.6 6.5 - - - +
49A LEU* 1.3 71.3 - - - +
51A SER* 1.3 57.7 - - - +
52A ASN* 2.8 12.2 + - - +
99B LEU* 5.9 0.7 - - - -
102B ARG* 3.0 68.0 - - - +
103B VAL* 4.5 4.0 - - - -
106B ILE* 3.6 26.1 - - - +
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Residues in contact with SER 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER* 3.0 17.0 + - - -
48A ASN* 3.7 0.6 - - - -
49A LEU 3.2 0.4 - - - -
50A CYS* 1.3 74.7 - - - +
52A ASN* 1.3 71.3 + - - +
53A ASN* 3.5 29.3 + - - +
7B PRO* 5.7 0.7 - - - +
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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