Contacts of the helix formed by residues 59 - 70 (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 TYR 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.2 20.2 - - + -
38A VAL* 4.9 1.3 - - + -
55A PHE* 3.2 30.3 + + + +
56A LEU 3.8 0.2 - - - -
57A SER 3.2 1.3 - - - -
58A ARG* 1.3 103.3 - - + +
60A LYS* 1.3 56.0 + - - +
61A ASP 2.4 21.4 + - - -
62A THR* 2.5 24.0 + - - -
63A ILE* 3.2 16.0 + - + -
24B GLU* 2.9 37.1 + - + +
25B VAL* 3.7 23.6 - - + -
29B CYS* 4.3 3.9 + - + +
30B LEU* 5.6 1.1 - - + -
395B VAL* 3.0 42.6 + - + +
396B GLY* 3.8 8.7 - - - -
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Residues in contact with LYS 60 (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* 4.5 18.7 - - + +
42A ASP* 2.9 36.4 + - - +
47A ARG* 5.5 7.0 - - - +
56A LEU* 2.8 34.8 + - + +
57A SER 5.0 0.4 - - - +
59A TYR* 1.3 72.9 - - - +
61A ASP* 1.3 71.4 + - - +
63A ILE* 3.6 4.3 + - - +
64A ASN* 3.0 48.1 + - - +
370C ASP* 5.0 14.1 + - - +
371C LEU* 5.0 12.1 - - - -
372C GLU* 4.5 15.0 - - + +
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Residues in contact with ASP 61 (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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57A SER 5.2 2.5 + - - +
59A TYR 2.4 8.3 + - - -
60A LYS* 1.3 77.6 - - - +
62A THR* 1.3 67.3 + - - +
64A ASN* 3.0 20.0 + - - +
65A LYS* 3.1 16.6 + - + +
371C LEU* 3.6 15.2 - - - +
372C GLU* 3.0 50.5 - - + +
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Residues in contact with THR 62 (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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58A ARG 3.9 11.6 + - - -
59A TYR* 2.5 19.9 + - - -
61A ASP* 1.3 71.5 - - - +
63A ILE* 1.3 64.5 + - - -
65A LYS* 2.9 20.4 + - + +
66A ILE* 3.0 15.4 + - + +
17B LEU* 5.9 4.5 - - + -
23B SER* 5.6 0.9 - - - +
24B GLU* 4.5 16.6 + - + +
25B VAL* 3.4 37.2 - - + +
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Residues in contact with ILE 63 (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* 5.2 3.8 - - + -
34A LEU* 3.4 34.3 - - + -
35A ASP* 4.1 17.9 - - + +
38A VAL* 3.6 21.8 - - + -
59A TYR* 3.2 12.2 + - + +
60A LYS 3.7 8.1 - - - +
62A THR* 1.3 78.5 - - - +
64A ASN* 1.3 54.4 + - - +
66A ILE* 3.0 25.2 + - + +
67A ARG* 2.7 69.8 + - + +
25B VAL* 5.4 1.3 - - + -
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Residues in contact with ASN 64 (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* 6.5 0.2 - - - -
60A LYS* 3.0 44.6 + - - +
61A ASP* 3.0 21.6 + - - +
63A ILE* 1.3 76.2 - - - +
65A LYS* 1.3 62.4 - - + +
67A ARG* 3.5 33.8 + - - +
68A ASP* 3.2 21.2 + - - +
371C LEU* 5.0 6.1 - - - +
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Residues in contact with LYS 65 (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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61A ASP* 3.1 12.5 + - + +
62A THR* 2.9 11.2 + - - +
64A ASN* 1.3 74.8 - - + +
66A ILE* 1.3 63.0 + - + +
67A ARG 3.1 1.3 - - - -
68A ASP* 2.8 36.7 + - - +
69A LEU* 3.2 26.3 + - + +
17B LEU* 5.6 7.6 - - + -
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Residues in contact with ILE 66 (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* 3.4 34.3 - - + -
62A THR* 3.0 19.0 + - + +
63A ILE* 3.0 18.6 + - + +
65A LYS* 1.3 75.8 - - - +
67A ARG* 1.3 58.0 + - + +
68A ASP 3.1 0.2 - - - -
69A LEU* 3.4 2.0 + - - +
70A ARG* 2.8 49.0 + - + +
14B MET* 4.1 24.7 - - + -
17B LEU* 4.5 8.1 - - + -
18B LEU* 5.9 0.4 - - + -
25B VAL* 3.2 43.7 - - + -
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Residues in contact with ARG 67 (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* 2.7 38.4 + - - +
38A VAL* 3.5 27.5 - - - +
39A TYR* 3.5 44.8 + - - +
63A ILE* 2.7 29.4 + - + +
64A ASN* 3.6 26.3 + - - +
65A LYS 3.1 0.4 - - - -
66A ILE* 1.3 72.9 - - + +
68A ASP* 1.3 62.2 - - - +
70A ARG* 3.9 14.2 - - + +
72A LYS* 3.4 23.2 - - - +
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Residues in contact with ASP 68 (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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64A ASN 3.2 16.3 + - - +
65A LYS* 2.8 26.4 + - - +
67A ARG* 1.3 82.9 - - - +
69A LEU* 1.3 58.4 + - + +
70A ARG 4.0 0.2 - - - -
72A LYS* 2.8 31.4 + - - +
10B ARG* 2.6 38.6 + - - -
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Residues in contact with LEU 69 (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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65A LYS* 3.2 23.3 + - + +
66A ILE 3.4 2.0 + - - +
68A ASP* 1.3 77.2 - - + +
70A ARG* 1.3 71.0 + - - +
71A MET* 3.5 0.7 + - - -
9B THR 5.2 0.2 - - - +
10B ARG* 3.3 53.7 + - + +
11B PHE* 4.6 13.1 - - + -
13B LYS* 3.9 11.2 - - + +
14B MET* 3.3 63.9 - - + +
17B LEU* 4.3 9.4 - - + -
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Residues in contact with ARG 70 (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* 3.0 48.1 + - - +
31A LEU* 3.7 26.9 - - - +
32A ASP* 2.9 32.7 + - - +
35A ASP* 5.5 9.5 + - - +
66A ILE* 2.8 39.4 + - + +
67A ARG* 3.9 12.4 - - - +
68A ASP 3.9 0.9 - - - +
69A LEU* 1.3 86.2 - - - +
71A MET* 1.3 54.3 + - - +
72A LYS* 2.8 25.9 + - - +
75A ASP* 3.8 1.0 - - - +
398A THR* 3.4 16.2 + - - +
400A TYR* 3.2 21.1 + - - +
11B PHE* 5.8 1.1 - - - -
14B MET* 4.6 8.1 - - - -
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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