Contacts of the helix formed by residues 39 - 52 (chain K) in PDB entry 2NVX
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 ASP 39 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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995B ARG* 5.5 1.0 + - - -
998B ASP* 5.6 3.9 - - - +
35C ARG* 5.1 2.7 - - - -
165C LYS* 3.1 26.3 + - - -
9K LEU* 5.4 4.2 - - - +
38K GLU* 1.3 83.1 + - - +
40K HIS* 1.3 65.8 + - + +
41K THR* 2.7 24.9 + - - -
42K LEU* 2.7 30.3 + - - +
43K GLY* 3.1 10.0 + - - -
63K VAL* 4.6 9.9 - - + -
69K ALA* 4.5 12.0 - - + +
71K PHE* 3.7 13.2 - - - -
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Residues in contact with HIS 40 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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998B ASP* 4.9 4.7 - - - -
1076B HIS* 3.2 57.5 + + + +
31C ASN* 5.2 0.2 + - - -
32C SER* 4.0 2.8 + - - -
35C ARG* 4.1 16.1 - - - +
39K ASP* 1.3 81.6 - - + +
41K THR* 1.3 62.1 + - - +
42K LEU 3.0 1.6 + - - -
43K GLY 3.9 3.8 - - - +
44K ASN* 3.3 27.5 + - - +
61K TYR* 3.4 27.6 + + - +
63K VAL* 3.2 47.1 - - + +
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Residues in contact with THR 41 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C SER* 2.5 30.8 + - - +
35C ARG* 2.5 45.4 + - + +
36C VAL* 3.5 31.0 - - + -
40C GLU* 3.6 25.0 + - - +
165C LYS* 4.4 1.9 + - - -
251C LEU* 4.1 8.1 - - + +
254C LYS* 5.7 2.0 - - + -
38K GLU* 5.4 2.5 - - - -
39K ASP* 2.7 17.0 + - - -
40K HIS* 1.3 74.2 - - - +
42K LEU* 1.3 57.7 + - - +
45K LEU* 4.3 1.7 - - - +
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Residues in contact with LEU 42 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C LEU* 5.4 1.8 - - + -
254C LYS* 3.5 36.3 - - + +
255C VAL* 3.8 20.9 - - + -
258C ILE* 3.3 29.8 - - + -
35K PHE* 4.2 9.9 - - + -
38K GLU* 3.3 25.6 - - - +
39K ASP 2.7 5.6 + - - +
41K THR* 1.3 78.3 - - - +
43K GLY* 1.3 61.4 + - - +
44K ASN 3.5 1.6 - - - -
45K LEU* 3.3 7.8 + - - +
46K ILE* 3.1 40.8 + - + +
71K PHE* 4.3 6.7 - - + -
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Residues in contact with GLY 43 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K ASP 3.1 11.4 + - - -
42K LEU* 1.3 73.6 - - - +
44K ASN* 1.3 63.4 + - - +
45K LEU 3.2 0.3 + - - -
46K ILE* 3.4 5.4 + - - +
47K ARG* 3.1 25.1 + - - +
61K TYR* 3.7 14.4 - - - +
71K PHE* 3.4 33.6 - - - -
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Residues in contact with ASN 44 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1076B HIS 4.4 7.6 - - - +
1077B THR* 3.6 33.2 + - - +
27C LEU* 5.8 0.4 - - - +
28C ALA* 3.4 33.0 + - - +
31C ASN* 4.2 5.1 - - - +
32C SER* 5.2 1.3 - - - +
40K HIS 3.3 17.1 + - - +
43K GLY* 1.3 74.5 - - - +
45K LEU* 1.3 57.0 + - - +
47K ARG* 3.4 18.9 + - - +
48K ALA* 3.2 27.6 + - - +
61K TYR* 3.3 29.6 + - - +
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Residues in contact with LEU 45 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ASP* 6.4 0.2 - - + -
28C ALA* 4.0 7.6 - - + +
29C MET* 3.7 49.4 - - + +
32C SER* 4.1 16.3 + - - +
251C LEU* 3.8 34.3 - - + -
255C VAL* 4.4 5.8 - - + -
40K HIS 4.6 1.0 + - - -
41K THR 4.3 1.1 - - - +
42K LEU* 3.3 11.8 + - - +
43K GLY 3.2 1.0 - - - -
44K ASN* 1.3 76.1 - - - +
46K ILE* 1.3 65.9 + - + +
48K ALA* 4.3 0.7 - - - +
49K GLU* 3.3 34.0 + - + +
94K ILE* 3.7 31.2 - - + +
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Residues in contact with ILE 46 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C VAL* 4.8 8.3 - - + -
258C ILE* 5.5 2.9 - - + -
35K PHE* 5.4 6.7 - - + -
42K LEU* 3.1 38.4 + - + +
43K GLY* 4.0 4.0 - - - +
45K LEU* 1.3 78.0 - - - +
47K ARG* 1.3 60.5 + - - +
49K GLU* 3.3 3.2 + - - +
50K LEU* 2.9 36.2 + - + +
71K PHE* 5.7 1.1 - - + -
73K LEU* 3.7 35.9 - - + -
87K LEU* 4.1 9.9 - - + -
90K ALA* 4.9 4.5 - - + +
91K CYS* 4.3 23.6 - - - +
94K ILE* 3.7 23.6 - - + -
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Residues in contact with ARG 47 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544A ASP* 4.0 27.5 + - - +
547A LEU* 5.3 1.0 - - - +
548A ASN* 3.3 37.6 - - - +
43K GLY 3.1 16.1 + - - +
44K ASN* 3.4 23.8 + - - -
46K ILE* 1.3 79.8 - - - +
48K ALA* 1.3 81.8 + - - +
50K LEU* 3.2 17.4 + - - +
51K LEU* 3.3 37.4 + - - +
59K ALA* 3.4 35.9 + - + +
60K ALA* 3.6 7.0 - - - +
61K TYR* 3.9 12.3 - - + +
73K LEU* 4.3 5.2 - - + -
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Residues in contact with ALA 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ASP* 4.3 12.1 - - + +
28C ALA* 3.7 19.7 - - + -
44K ASN* 3.2 18.2 + - - +
47K ARG* 1.3 97.2 - - - +
49K GLU* 1.3 60.8 + - + +
50K LEU 3.3 0.2 - - - -
51K LEU* 3.6 10.7 + - - +
52K ASN* 3.3 22.3 + - - +
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Residues in contact with GLU 49 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ASP* 4.8 8.7 - - + +
28C ALA* 6.2 0.4 - - + -
29C MET* 3.7 15.5 - - - +
45K LEU* 3.3 26.0 + - + +
46K ILE 3.3 4.4 + - - +
47K ARG 3.2 0.6 - - - -
48K ALA* 1.3 75.0 - - + +
50K LEU* 1.3 62.2 + - - +
51K LEU 3.2 1.6 - - - -
52K ASN* 3.6 29.2 + - - +
53K ASP* 4.2 5.7 + - - +
90K ALA* 3.9 19.0 - - + +
93K SER* 3.3 23.8 + - - -
94K ILE* 3.7 25.6 - - + -
97K LYS* 3.1 23.5 + - - +
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Residues in contact with LEU 50 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46K ILE* 2.9 35.6 + - + +
47K ARG* 3.2 11.8 + - - +
49K GLU* 1.3 77.2 - - - +
51K LEU* 1.3 62.6 + - - +
53K ASP* 3.9 5.0 + - + +
56K VAL* 3.7 34.3 - - + +
59K ALA* 3.9 12.4 - - + +
73K LEU* 4.1 4.7 - - + -
75K ILE* 3.6 51.1 - - + -
86K ALA* 4.0 26.5 - - + +
87K LEU* 4.7 2.5 - - + -
90K ALA* 4.2 11.2 - - + -
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Residues in contact with LEU 51 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A LEU* 4.0 31.6 - - + -
544A ASP* 4.4 9.6 - - + +
547A LEU* 4.2 8.5 - - + -
47K ARG* 3.3 50.7 + - - +
48K ALA* 3.7 10.8 - - - +
49K GLU 3.2 0.8 - - - -
50K LEU* 1.3 75.3 - - - +
52K ASN* 1.3 67.8 + - - +
53K ASP 3.1 10.0 + - - +
54K ARG* 5.3 0.7 - - - +
56K VAL 5.7 0.4 - - - +
59K ALA* 3.7 24.7 - - + +
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Residues in contact with ASN 52 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ASP* 3.9 24.7 + - - +
48K ALA 3.3 16.2 + - - +
49K GLU* 3.6 34.4 + - - +
50K LEU 3.5 0.4 - - - -
51K LEU* 1.3 80.6 - - - +
53K ASP* 1.3 58.3 + - - +
54K ARG* 3.5 11.7 + - - +
97K LYS* 4.2 5.9 - - - +
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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