Contacts of the helix formed by residues 26 - 42 (chain A) in PDB entry 3NDM
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 ASN 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A LEU 3.5 9.7 + - - +
18A LEU 3.9 6.3 - - - +
19A ARG 4.7 2.5 - - - +
20A ASP 3.8 21.3 - - - +
21A PRO* 3.5 23.5 + - + +
23A SER 3.5 9.7 + - - +
24A GLU 3.6 2.2 - - - -
25A VAL* 1.3 83.0 - - - +
27A SER* 1.3 67.9 + - - +
28A ASP* 2.7 41.2 + - - +
29A CYS* 2.8 38.3 + - - -
30A LEU* 3.1 6.5 + - - +
125A ARG* 4.7 6.5 - - - +
398A THR 4.9 1.8 + - - -
399A TYR* 5.5 2.0 - - - -
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Residues in contact with SER 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 2.9 24.6 + - - +
19A ARG* 5.7 0.2 - - - +
26A ASN* 1.3 76.0 - - - +
28A ASP* 1.3 70.6 + - - +
29A CYS 3.2 0.5 + - - -
30A LEU* 3.3 28.6 - - - +
31A LEU* 3.4 14.6 + - - +
18B LEU* 4.6 18.5 - - - +
30B LEU* 5.0 0.9 - - - +
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Residues in contact with ASP 28 (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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26A ASN* 2.7 19.4 + - - +
27A SER* 1.3 78.2 - - - +
29A CYS* 1.3 51.3 + - - -
31A LEU* 4.2 2.9 - - - +
32A ASP* 2.4 29.4 + - - +
70A ARG* 3.0 27.3 + - - +
398A THR* 3.7 18.3 - - + +
399A TYR* 5.2 0.2 - - - -
400A TYR* 2.8 46.3 + - - +
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Residues in contact with CYS 29 (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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23A SER 3.9 4.3 - - - -
24A GLU* 3.2 28.7 - - - +
25A VAL 4.2 0.4 - - - -
26A ASN* 2.8 41.1 + - - +
28A ASP* 1.3 76.5 - - - +
30A LEU* 1.3 68.4 + - - +
31A LEU 3.1 1.6 - - - -
32A ASP* 2.8 23.9 + - - +
33A GLY* 3.4 3.8 + - - -
125A ARG* 4.8 2.0 - - - -
395A VAL* 4.6 3.5 - - - +
396A GLY* 3.8 29.0 - - - -
398A THR 4.5 3.6 - - - -
34B LEU* 5.4 1.2 - - - +
59B TYR* 4.7 2.5 - - + +
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Residues in contact with LEU 30 (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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18A LEU* 4.1 21.8 - - + -
25A VAL* 3.7 21.3 - - + +
26A ASN 3.3 15.3 - - - +
27A SER* 3.3 16.2 - - - +
29A CYS* 1.3 75.7 - - - +
31A LEU* 1.3 64.3 + - - +
33A GLY* 3.1 13.0 + - - -
34A LEU* 3.2 12.5 + - - +
27B SER* 4.9 3.4 - - - +
30B LEU* 3.9 30.2 - - + +
31B LEU* 3.7 37.7 - - + -
34B LEU* 4.5 19.7 - - + +
66B ILE* 5.5 0.2 - - + -
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER* 3.4 17.4 + - - +
28A ASP* 4.5 2.5 - - - +
29A CYS 3.1 0.4 - - - -
30A LEU* 1.3 82.1 - - - +
32A ASP* 1.3 52.7 + - - +
34A LEU* 3.1 6.8 + - - +
35A ASP* 2.6 38.9 + - + +
63A ILE* 5.2 5.5 - - + +
66A ILE* 3.4 46.0 - - + -
70A ARG* 3.7 33.0 - - - +
14B MET* 5.4 3.4 - - + -
18B LEU* 4.3 19.5 - - + -
30B LEU* 3.4 29.6 - - + -
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Residues in contact with ASP 32 (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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28A ASP 2.4 25.9 - - - +
29A CYS* 2.8 16.8 + - - +
31A LEU* 1.3 72.7 - - - +
33A GLY* 1.3 53.6 + - - +
35A ASP* 3.5 9.3 - - - +
36A ALA* 2.7 35.9 + - - +
70A ARG* 2.9 11.4 + - - -
144A GLN* 3.3 23.9 + - - +
395A VAL* 4.3 2.4 - - - +
396A GLY* 3.6 18.4 - - - +
398A THR* 2.9 36.6 + - - -
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Residues in contact with GLY 33 (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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29A CYS 3.4 3.2 + - - -
30A LEU 3.1 7.1 + - - -
32A ASP* 1.3 76.0 - - - +
34A LEU* 1.3 66.3 + - - +
36A ALA* 3.7 0.9 - - - +
37A LEU* 3.0 31.7 + - - +
395A VAL* 3.8 24.1 - - - +
33B GLY 6.3 0.4 - - - -
34B LEU* 4.5 13.0 - - - -
37B LEU* 5.1 6.1 - - - +
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Residues in contact with LEU 34 (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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30A LEU 3.2 10.7 + - - +
31A LEU* 3.1 7.6 + - - +
33A GLY* 1.3 78.6 - - - +
35A ASP* 1.3 58.3 + - - +
37A LEU* 3.8 5.9 + - + +
38A VAL* 3.0 31.7 + - + +
55A PHE* 4.4 18.4 - - + -
59A TYR* 4.2 20.6 - - + -
63A ILE* 3.4 29.8 - - + -
25B VAL* 5.3 0.7 - - + -
30B LEU* 3.9 31.9 - - + +
33B GLY* 4.2 25.1 - - - -
34B LEU* 5.6 1.8 - - - +
395B VAL* 4.8 5.6 - - + -
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Residues in contact with ASP 35 (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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31A LEU* 2.6 21.5 + - + +
32A ASP* 3.5 13.1 - - - +
34A LEU* 1.3 71.8 - - - +
36A ALA* 1.3 66.1 + - - +
38A VAL* 3.2 13.5 + - - +
39A TYR* 3.2 26.3 + - - -
63A ILE* 4.1 13.9 - - + +
67A ARG* 2.7 47.8 + - - +
70A ARG* 5.5 8.4 + - - +
144A GLN* 5.2 11.6 - - - +
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Residues in contact with ALA 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 ASP 2.7 22.3 + - - +
33A GLY* 3.2 4.5 + - - +
35A ASP* 1.3 74.1 - - - +
37A LEU* 1.3 56.5 + - - +
39A TYR* 2.8 29.6 + - - +
40A ASP* 2.9 17.7 + - - +
144A GLN* 6.6 0.4 - - - -
391A GLN* 3.9 20.6 - - + +
392A LEU* 5.0 3.1 - - + +
395A VAL* 3.8 21.8 - - + -
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Residues in contact with LEU 37 (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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33A GLY 3.0 19.1 + - - +
34A LEU* 3.9 12.1 - - + +
36A ALA* 1.3 74.4 - - - +
38A VAL* 1.3 64.2 + - - +
39A TYR 2.9 1.9 + - - -
40A ASP* 3.1 4.8 + - - +
41A LEU* 3.0 56.2 + - + +
55A PHE* 4.4 20.4 - - + -
387A PHE* 5.1 10.3 - - + -
33B GLY* 4.7 10.1 - - - +
37B LEU* 3.6 43.7 - - + -
387B PHE* 5.2 4.3 - - + -
392B LEU* 4.5 14.1 - - + -
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Residues in contact with VAL 38 (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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34A LEU* 3.0 23.1 - - + +
35A ASP 3.2 10.3 + - - +
37A LEU* 1.3 75.1 - - - +
39A TYR* 1.3 58.6 + - - +
41A LEU 4.3 0.2 - - - -
42A ASP* 3.3 30.5 + - - +
55A PHE* 4.5 14.3 - - + -
56A LEU* 4.3 14.1 - - + +
59A TYR* 4.9 5.4 - - + -
60A LYS* 4.5 16.6 - - + +
63A ILE* 3.6 31.0 - - + -
67A ARG* 3.5 18.6 + - - +
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Residues in contact with TYR 39 (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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35A ASP* 3.2 44.1 + - - -
36A ALA* 2.8 15.9 + - - +
38A VAL* 1.3 73.9 - - - +
40A ASP* 1.3 58.2 + - - +
41A LEU 2.9 11.1 + - - -
42A ASP* 3.4 11.3 + - - +
43A PHE* 3.8 19.6 - - + -
67A ARG* 3.5 31.6 + - - +
145A ASP* 3.8 15.2 - - - +
146A ASP* 3.2 50.6 + - + -
391A GLN* 4.2 20.4 - - + -
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Residues in contact with ASP 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 ALA* 2.9 11.9 + - - +
37A LEU* 3.1 4.2 + - - +
39A TYR* 1.3 76.9 - - - +
41A LEU* 1.3 59.5 + - - +
43A PHE* 4.5 18.2 - - - -
46A LEU* 3.8 7.1 - - - +
387A PHE* 3.4 37.2 - - + -
388A VAL* 4.5 5.7 + - + +
389A GLY* 3.7 5.8 + - - +
390A ASN* 3.3 26.2 + - - +
391A GLN* 2.9 44.7 + - - +
392A LEU* 4.1 1.7 + - - +
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Residues in contact with LEU 41 (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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37A LEU* 3.2 45.3 - - + +
39A TYR 3.0 0.8 - - - -
40A ASP* 1.3 86.3 - - - +
42A ASP* 1.3 55.4 + - - +
43A PHE* 2.8 24.4 + - - +
46A LEU* 3.9 20.3 - - + +
47A ARG* 4.1 2.8 - - - +
52A ILE* 4.0 24.2 - - + +
55A PHE* 4.4 10.8 - - + -
56A LEU* 4.0 15.3 - - + +
387A PHE* 4.0 19.1 - - + -
387B PHE* 4.2 16.2 - - + -
392B LEU* 3.9 22.2 - - + -
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Residues in contact with ASP 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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38A VAL* 3.3 24.1 + - - +
39A TYR* 3.4 7.0 + - - +
41A LEU* 1.3 76.2 - - - +
43A PHE* 1.3 62.1 + - + +
44A PRO* 3.3 11.8 - - - +
47A ARG* 3.6 19.5 + - - -
56A LEU* 4.0 13.6 - - + +
60A LYS* 2.9 42.4 + - - +
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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