Contacts of the helix formed by residues 14 - 35 (chain I) in PDB entry 6NR8
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 GLY 14 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I THR* 1.3 78.2 - - - +
15I GLU* 1.3 56.1 + - - -
16I THR* 3.2 3.6 - - - -
17I ILE* 2.8 29.7 + - - +
18I ARG* 2.8 30.4 + - - +
530I LEU* 5.4 0.4 - - - +
468L ASN* 4.7 11.4 - - - -
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Residues in contact with GLU 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I GLY* 1.3 70.7 - - - -
16I THR* 1.3 52.2 + - + +
18I ARG* 3.5 9.5 - - - +
19I SER* 2.6 44.7 + - - +
469L ALA 3.0 25.7 - - - +
470L GLY* 3.2 21.3 - - - +
471L LEU* 3.7 24.8 - - - +
473L PRO* 5.7 2.6 - - - +
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Residues in contact with THR 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I GLU* 2.9 44.3 - - + +
3I GLY* 4.2 9.0 - - - +
12I SER* 3.3 29.1 + - - -
14I GLY 4.3 0.5 + - - -
15I GLU* 1.3 79.9 - - + +
17I ILE* 1.3 52.9 + - - +
19I SER* 3.0 0.6 + - - -
20I GLN* 2.6 33.3 + - - +
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Residues in contact with ILE 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I ASP 3.7 22.0 - - - +
12I SER* 3.7 23.3 - - - +
13I THR 4.0 3.6 - - - +
14I GLY 2.8 28.1 + - - +
16I THR* 1.3 76.3 + - - +
18I ARG* 1.3 84.4 + - - +
20I GLN* 3.5 17.3 - - + +
21I ASN* 3.0 43.7 + - - +
530I LEU* 4.5 9.0 - - + -
57L MET* 4.1 0.9 - - + -
58L ASP 5.3 3.8 - - - +
59L LYS* 4.1 17.5 - - + +
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Residues in contact with ARG 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I GLY 2.8 34.2 + - - +
15I GLU* 3.8 15.3 - - - +
17I ILE* 1.3 99.2 - - - +
19I SER* 1.3 58.3 + - - +
21I ASN 4.3 0.2 - - - -
22I VAL* 3.3 26.5 + - - +
105I ASP* 3.5 28.7 - - + +
530I LEU* 3.4 27.1 - - - +
50L THR* 4.6 0.4 - - - +
56L GLY* 3.3 11.7 - - - -
57L MET* 3.3 52.2 - - + +
468L ASN* 2.7 34.9 + - - +
469L ALA* 4.1 6.3 - - - +
470L GLY* 4.9 4.9 - - - +
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Residues in contact with SER 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I GLU* 3.3 18.8 - - - -
15I GLU* 2.6 30.2 + - - +
16I THR* 3.2 1.1 - - - -
18I ARG* 1.3 73.3 - - - +
20I GLN* 1.3 63.9 + - - +
22I VAL* 3.3 20.5 - - - +
23I MET* 3.4 23.8 - - - +
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Residues in contact with GLN 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I MET* 4.1 22.5 - - + +
2I GLU* 4.5 10.1 - - + +
10I ASP 5.9 0.4 + - - -
12I SER* 6.0 0.9 - - - +
16I THR 2.6 19.3 + - - +
17I ILE* 3.6 20.9 - - + +
18I ARG 3.3 0.6 - - - -
19I SER* 1.3 75.4 - - - +
21I ASN* 1.3 87.3 + - - +
23I MET* 3.1 11.3 + - - +
24I ALA* 2.9 27.5 + - - +
69I HIS* 3.1 35.5 + - - -
70I PRO* 5.2 2.2 - - - +
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Residues in contact with ASN 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I ILE* 3.0 19.0 + - - +
18I ARG 4.1 0.4 + - - -
20I GLN* 1.3 102.8 + - - +
22I VAL* 1.3 61.2 + - - +
24I ALA* 3.9 5.6 - - - +
25I ALA* 2.8 32.4 + - - +
69I HIS* 4.6 0.2 - - - +
70I PRO* 4.1 22.6 - - - +
71I ALA* 3.3 16.0 - - + +
101I LEU* 3.9 1.7 - - - +
524I ILE* 4.2 6.1 - - + +
57L MET* 2.8 45.8 - - + +
58L ASP 5.3 1.4 + - - -
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Residues in contact with VAL 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I ARG 3.3 19.3 + - - +
19I SER* 3.3 23.8 - - - +
21I ASN* 1.3 79.1 - - - +
23I MET* 1.3 61.9 + - + +
25I ALA* 4.6 0.2 - - - +
26I ALA* 3.3 24.6 + - - +
98I ALA 5.2 3.9 - - - +
101I LEU* 3.7 36.3 - - + +
102I LYS* 4.0 22.7 - - + -
57L MET* 4.4 2.0 - - + -
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Residues in contact with MET 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I GLU* 5.3 8.3 - - - +
19I SER* 3.4 22.2 - - - +
20I GLN* 3.1 10.8 + - - +
22I VAL* 1.3 83.2 - - + +
24I ALA* 1.3 63.7 + - - +
25I ALA 3.3 0.2 - - - -
26I ALA* 4.3 2.4 - - - +
27I SER* 3.3 25.3 + - - -
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Residues in contact with ALA 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I GLN* 2.9 29.3 + - - +
21I ASN* 3.2 1.7 + - - +
23I MET* 1.3 76.8 - - - +
25I ALA* 1.3 59.4 + - - +
27I SER* 3.2 16.4 + - - -
28I ILE* 3.3 17.2 - - - +
69I HIS* 3.8 25.6 - - + +
71I ALA* 3.7 19.5 - - + -
72I ALA* 4.4 3.7 + - - +
14K THR* 5.2 2.6 - - - +
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Residues in contact with ALA 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I ASN 2.8 17.8 + - - +
22I VAL 4.6 0.4 - - - +
24I ALA* 1.3 78.8 - - - +
26I ALA* 1.3 59.1 + - - +
28I ILE* 3.3 5.4 + - - +
29I ALA* 3.0 26.0 + - - +
71I ALA* 3.8 18.4 - - + +
75I LEU* 3.7 12.3 - - + +
98I ALA* 4.1 6.7 - - + -
101I LEU* 3.7 31.9 - - + -
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Residues in contact with ALA 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I VAL 3.3 19.8 + - - +
23I MET* 4.3 3.6 - - - +
24I ALA 3.5 0.2 - - - -
25I ALA* 1.3 78.4 - - - +
27I SER* 1.3 52.2 + - - +
29I ALA* 3.0 2.5 + - - +
30I ASN* 2.6 48.9 + - - +
33I LYS* 5.3 2.0 - - - +
98I ALA* 3.8 18.8 - - + +
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Residues in contact with SER 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I MET 3.3 13.7 + - - -
24I ALA* 3.2 15.8 + - - -
26I ALA* 1.3 77.6 - - - +
28I ILE* 1.3 69.3 + - - +
30I ASN* 3.6 16.6 + - - +
31I ILE* 3.3 22.4 + - - +
14K THR* 4.5 11.3 - - - +
15K LYS 5.9 0.7 - - - -
16K ARG* 3.8 22.7 - - - +
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Residues in contact with ILE 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I ALA 3.3 18.8 - - - +
25I ALA* 3.3 6.9 + - - +
26I ALA 3.2 0.4 - - - -
27I SER* 1.3 81.9 + - - +
29I ALA* 1.3 61.1 + - - +
31I ILE* 3.3 31.2 + - + +
32I VAL* 3.7 8.3 - - - +
62I LEU* 4.6 19.6 - - + +
65I LEU* 4.7 11.2 - - + -
67I VAL* 6.3 0.4 - - + -
72I ALA* 4.1 29.4 - - + +
75I LEU* 3.9 23.6 - - + -
76I CYS* 5.4 3.4 - - - -
94I VAL* 4.2 8.7 - - + -
13K ASN 5.3 0.9 - - - +
14K THR* 4.7 16.6 - - + +
15K LYS 5.7 1.1 - - - +
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Residues in contact with ALA 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I ALA 3.0 13.2 + - - +
26I ALA 3.0 7.9 + - - +
28I ILE* 1.3 77.5 - - - +
30I ASN* 1.3 61.2 + - - +
32I VAL 3.2 10.2 + - - -
33I LYS* 3.2 28.8 + - - +
94I VAL* 3.5 32.5 - - - +
95I ILE* 3.6 13.5 - - - +
98I ALA* 3.9 12.1 - - + -
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Residues in contact with ASN 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I ALA* 2.6 41.0 + - - +
27I SER* 3.6 10.1 - - - +
28I ILE 3.2 0.6 - - - -
29I ALA* 1.3 71.2 - - - +
31I ILE* 1.3 62.8 + - - +
32I VAL 3.3 0.2 - - - -
33I LYS* 3.1 41.8 + - + +
34I SER* 3.7 3.5 + - - -
16K ARG* 3.4 39.0 + - + +
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Residues in contact with ILE 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I SER 3.3 18.6 - - - +
28I ILE* 3.5 18.8 - - + +
29I ALA 3.2 0.4 - - - -
30I ASN* 1.3 78.1 - - - +
32I VAL* 1.3 63.1 + - + +
34I SER* 2.8 26.5 + - - +
35I SER* 3.6 6.2 + - - -
43I LYS* 5.1 6.7 - - + -
45I LEU* 5.8 0.7 - - + -
61I ILE* 3.9 32.5 - - + -
62I LEU* 6.0 0.9 - - + -
65I LEU* 4.1 24.0 - - + -
15K LYS 4.2 17.0 - - - +
16K ARG* 3.7 17.7 - - - +
521K ASP* 4.4 17.3 - - + +
523K VAL* 5.3 2.0 - - + -
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Residues in contact with VAL 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I ILE 3.7 15.5 - - - +
29I ALA 3.2 6.6 + - - +
31I ILE* 1.3 77.8 - - + +
33I LYS* 1.3 58.5 + - - +
35I SER* 3.1 7.1 + - - +
36I LEU* 2.9 30.2 + - + +
58I GLY* 5.1 12.6 - - - -
61I ILE* 5.9 1.1 - - + -
62I LEU* 4.9 11.9 - - + -
91I THR* 3.4 48.0 - - + +
94I VAL* 3.8 22.4 - - + -
95I ILE* 3.7 10.8 - - + -
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Residues in contact with LYS 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I ALA* 4.1 2.8 + - - +
29I ALA* 3.2 36.7 + - - +
30I ASN* 3.1 35.9 + - - +
31I ILE 3.2 0.4 - - - -
32I VAL* 1.3 77.9 - - - +
34I SER* 1.3 50.4 + - - +
36I LEU* 3.6 3.5 + - - +
95I ILE* 3.8 32.7 + - + +
98I ALA* 5.5 1.2 - - - +
447I VAL* 5.9 2.7 - - - -
451I THR* 3.9 29.9 - - + +
455I ASN* 2.5 33.3 + - - +
16K ARG* 5.9 0.2 - - - +
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Residues in contact with SER 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I ASN 3.7 5.7 + - - -
31I ILE* 2.8 22.5 + - - -
33I LYS* 1.3 79.1 - - - +
35I SER* 1.3 51.9 + - - +
36I LEU 3.4 0.4 - - - -
41I LEU* 2.4 33.9 + - - +
43I LYS* 3.4 37.0 - - - +
455I ASN* 2.9 18.7 - - - +
16K ARG* 5.1 5.5 + - - -
520K ASP* 4.1 11.4 - - - -
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Residues in contact with SER 35 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I ILE 3.6 6.4 + - - -
32I VAL* 3.1 12.2 + - - +
34I SER* 1.3 81.3 + - - +
36I LEU* 1.3 62.1 + - - +
37I GLY 3.4 6.9 + - - +
40I GLY* 3.6 5.5 - - - -
41I LEU 2.6 26.0 + - - +
43I LYS* 3.7 11.4 - - - +
55I THR 4.0 0.2 + - - -
56I ASN* 3.2 37.6 - - - +
58I GLY* 5.7 0.9 - - - -
61I ILE* 4.2 8.7 - - - +
91I THR* 5.1 4.9 - - - +
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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
------------------------------------------------------------
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