Contacts of the helix formed by residues 19 - 38 (chain N) in PDB entry 6CP3
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 LEU 19 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18M GLY 4.2 9.6 - - - +
21M GLY* 5.9 1.1 - - - -
61M THR* 3.4 37.2 - - - +
62M GLY* 3.8 10.8 - - - +
64M PHE* 4.7 6.3 - - + -
65M CYS* 3.8 31.0 - - + +
68M VAL* 6.2 0.2 - - + -
16N THR* 3.8 19.7 + - + +
17N ILE* 3.1 2.6 - - - -
18N GLY* 1.3 75.6 - - - +
20N LEU* 1.3 57.5 + - - +
21N GLY 3.8 0.2 - - - -
22N ALA* 4.2 5.8 - - - -
23N GLY* 2.8 32.0 + - - -
59N GLU* 6.1 0.9 - - - +
62N GLY* 4.7 17.5 - - - +
65N CYS* 4.1 3.1 - - - -
66N LEU* 4.7 19.1 - - + -
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Residues in contact with LEU 20 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M ILE* 3.8 5.2 - - + +
18M GLY* 3.5 26.7 - - - +
20M LEU* 3.7 29.8 - - + -
21M GLY* 3.2 38.9 - - - +
17N ILE* 2.8 31.5 + - + +
18N GLY 3.1 1.6 - - - -
19N LEU* 1.3 75.5 - - - +
21N GLY* 1.3 62.0 + - - +
23N GLY* 2.9 4.2 + - - -
24N ILE* 2.9 24.4 + - + -
20O LEU* 3.7 15.0 - - + -
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Residues in contact with GLY 21 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20N LEU* 1.3 78.8 - - - +
22N ALA* 1.3 55.5 + - - +
24N ILE* 2.9 18.5 + - - +
25N GLY 2.4 32.6 + - - -
20O LEU* 3.3 13.7 - - - +
24O ILE* 3.2 28.9 - - - +
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Residues in contact with ALA 22 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18N GLY 4.2 11.7 - - - +
19N LEU* 4.2 7.8 - - - +
21N GLY* 1.3 75.9 - - - +
23N GLY* 1.3 57.0 + - - +
25N GLY 3.0 12.5 + - - -
26N ILE* 3.0 25.1 + - + +
58N SER 4.9 4.0 - - - +
59N GLU* 5.3 4.3 - - - +
61N THR* 4.3 10.3 - - - +
62N GLY* 4.9 7.6 - - - +
19O LEU* 5.6 0.9 - - + +
20O LEU* 3.5 10.2 + - - +
23O GLY* 3.6 31.4 - - - +
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Residues in contact with GLY 23 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M GLY 3.6 12.7 - - - +
25M GLY* 4.7 1.0 - - - -
26M ILE* 5.5 0.7 + - - +
58M SER* 4.6 6.4 - - - +
61M THR* 3.8 21.7 + - - -
19N LEU* 2.8 25.8 + - - -
20N LEU 2.9 2.2 + - - -
22N ALA* 1.3 73.4 - - - +
24N ILE* 1.3 59.5 + - - +
26N ILE* 3.4 19.1 - - - +
27N ALA* 4.2 5.2 + - - +
59N GLU* 5.3 0.4 - - - -
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Residues in contact with ILE 24 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20M LEU* 4.4 1.1 - - + +
21M GLY* 3.3 26.5 - - - +
24M ILE* 3.7 39.0 - - + -
25M GLY* 3.8 21.3 - - - +
28M ILE* 5.2 7.6 - - + -
20N LEU* 2.9 16.7 + - + +
21N GLY* 2.9 23.1 + - - +
23N GLY* 1.3 77.5 - - - +
25N GLY* 1.3 56.6 + - - +
27N ALA* 2.9 27.7 + - - +
28N ILE* 3.3 7.7 + - + +
24O ILE* 5.1 8.5 - - + -
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Residues in contact with GLY 25 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21N GLY 2.4 24.1 + - - -
22N ALA 3.0 2.8 + - - -
24N ILE* 1.3 66.5 - - - +
26N ILE* 1.3 66.3 + - - +
28N ILE* 3.0 29.8 + - - +
29N VAL 3.4 1.2 + - - -
23O GLY 3.9 9.9 - - - -
24O ILE* 4.1 10.5 - - - -
27O ALA* 3.3 17.0 - - - +
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Residues in contact with ILE 26 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57M LEU 3.9 2.5 - - - +
58M SER* 3.8 25.4 - - - +
61M THR* 3.9 7.9 - - + -
22N ALA* 3.0 19.7 + - - +
23N GLY* 3.4 13.5 - - - +
25N GLY* 1.3 74.2 - - - +
27N ALA* 1.3 63.9 + - - +
29N VAL* 3.0 21.4 + - - +
30N PHE* 3.2 19.1 - - + -
55N PHE* 3.6 46.4 - - + +
58N SER* 4.2 16.4 - - - +
59N GLU* 3.3 28.7 - - - +
23O GLY 5.4 0.9 - - - +
27O ALA* 4.2 1.0 - - - +
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Residues in contact with ALA 27 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M GLY* 3.3 33.9 - - - +
26M ILE 4.3 1.1 - - - +
28M ILE* 4.3 2.0 - - + -
29M VAL* 3.6 15.4 - - + +
58M SER* 4.0 15.5 - - - +
23N GLY 4.3 2.9 - - - +
24N ILE 2.9 15.6 + - - +
26N ILE* 1.3 80.7 - - - +
28N ILE* 1.3 49.7 + - - +
30N PHE* 3.0 8.2 + - - +
31N ALA* 2.7 33.1 + - - +
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Residues in contact with ILE 28 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28M ILE* 3.7 24.8 - - + +
24N ILE* 3.3 6.5 + - + +
25N GLY* 3.0 22.3 + - - +
27N ALA* 1.3 77.4 - - - +
29N VAL* 1.3 63.0 + - - +
31N ALA* 3.1 7.3 + - + +
32N ALA* 3.0 18.5 + - - +
24O ILE* 5.8 2.5 - - + -
28O ILE* 3.6 48.7 - - + +
31O ALA* 3.7 10.5 - - + +
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Residues in contact with VAL 29 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25N GLY 3.6 13.0 - - - +
26N ILE* 3.0 12.3 + - - +
28N ILE* 1.3 75.6 - - - +
30N PHE* 1.3 66.5 + - + +
32N ALA 3.0 11.6 + - - -
33N LEU* 3.1 8.5 + - - +
51N ALA* 4.1 26.2 - - + +
54N GLY 5.4 0.4 - - - -
55N PHE* 5.0 7.9 - - - +
58N SER* 5.4 2.9 - - - +
27O ALA* 3.2 33.2 - - + +
30O PHE* 4.4 15.3 - - + -
31O ALA* 3.9 6.7 - - - +
34O ILE* 3.3 27.6 - - + +
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Residues in contact with PHE 30 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29M VAL* 4.4 12.6 - - + -
50M MET 5.2 2.0 - - - -
51M ALA* 6.4 0.2 - - - -
53M LEU* 4.1 20.9 - - + -
54M GLY* 4.0 17.5 - - - -
57M LEU* 3.6 35.4 - - + -
58M SER* 4.5 3.4 - - - -
26N ILE 3.2 24.6 + - - -
27N ALA* 3.0 8.8 + - - +
29N VAL* 1.3 80.0 - - + +
31N ALA* 1.3 62.5 + - - +
33N LEU* 3.0 33.6 + - + +
34N ILE* 3.1 20.5 + - + +
48N PHE* 5.7 3.8 - + - -
51N ALA* 5.1 11.0 - - + -
52N ILE* 5.2 8.1 - - + -
55N PHE* 3.8 33.7 - + + -
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Residues in contact with ALA 31 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28M ILE* 4.1 19.3 - - + +
29M VAL* 4.6 2.4 - - - +
32M ALA* 3.4 25.2 - - + +
27N ALA 2.7 16.7 + - - +
28N ILE* 3.1 21.5 + - + +
30N PHE* 1.3 72.3 - - - +
32N ALA* 1.3 55.5 + - - +
34N ILE* 3.0 4.8 + - - -
35N ASN* 2.9 34.5 + - - +
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Residues in contact with ALA 32 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N ILE 3.0 6.4 + - - +
29N VAL 3.0 8.3 + - - +
31N ALA* 1.3 75.5 - - - +
33N LEU* 1.3 52.1 + - - +
35N ASN* 3.0 12.3 + - - +
36N GLY 2.5 31.9 + - - -
31O ALA* 3.4 41.3 - - + +
34O ILE* 3.3 15.9 - - + +
35O ASN* 4.9 4.3 - - + +
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Residues in contact with LEU 33 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50M MET* 4.3 24.0 - - + +
29N VAL 3.1 8.3 + - - +
30N PHE* 3.0 34.9 + - + +
32N ALA* 1.3 75.6 - - - +
34N ILE* 1.3 58.6 + - + +
36N GLY* 3.0 1.0 + - - +
37N VAL* 3.0 45.1 + - + +
47N VAL* 3.8 30.3 - - + -
48N PHE* 4.1 27.8 - - + -
51N ALA* 4.7 15.0 - - + -
34O ILE* 4.0 10.0 - - + +
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Residues in contact with ILE 34 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29M VAL* 3.4 44.4 - - + +
32M ALA* 3.3 26.5 - - + +
33M LEU* 3.7 9.2 - - + +
36M GLY* 4.1 10.5 - - - -
47M VAL* 4.4 21.1 - - + -
50M MET* 6.1 1.8 - - + -
51M ALA* 3.8 20.6 - - + +
30N PHE* 3.3 13.5 - - + +
31N ALA 3.0 5.6 + - - +
33N LEU* 1.3 79.8 - - + +
35N ASN* 1.3 60.4 + - - +
37N VAL* 4.6 5.3 - - - +
38N SER* 2.9 25.8 + - - -
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Residues in contact with ASN 35 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32M ALA* 4.2 11.1 - - - +
35M ASN* 3.6 28.7 + - - +
39M ARG* 4.3 13.7 + - - +
31N ALA* 2.9 26.0 + - - +
32N ALA* 3.0 10.9 + - - +
34N ILE* 1.3 80.6 - - - +
36N GLY* 1.3 61.4 + - - +
38N SER* 3.5 9.3 + - - -
39N ARG* 3.7 19.9 + - - +
35O ASN* 6.1 4.7 - - - +
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Residues in contact with GLY 36 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32N ALA 2.5 19.7 + - - -
33N LEU* 3.0 1.9 + - - -
35N ASN* 1.3 74.8 - - - +
37N VAL* 1.3 59.6 + - - +
39N ARG* 3.0 24.4 + - - +
40N ASN* 3.0 11.5 + - - +
34O ILE* 4.5 3.4 - - - -
38O SER* 3.4 31.9 - - - -
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Residues in contact with VAL 37 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43M ILE* 3.3 14.1 - - - +
46M THR* 4.5 4.9 - - + -
47M VAL* 3.7 27.8 - - + -
50M MET* 4.1 11.4 - - + -
33N LEU* 3.0 29.6 + - + +
34N ILE* 4.6 0.7 - - - -
36N GLY* 1.3 71.3 - - - +
38N SER* 1.3 64.9 + - - +
40N ASN 3.3 16.2 - - - +
41N PRO* 3.3 14.2 - - + -
43N ILE* 4.5 7.2 - - + +
44N LYS* 3.7 42.8 - - + -
47N VAL* 5.6 0.6 - - + +
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Residues in contact with SER 38 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35M ASN 3.8 8.6 + - - -
36M GLY* 3.7 27.8 - - - -
39M ARG* 4.2 9.7 - - - +
40M ASN* 2.7 32.8 + - - +
43M ILE* 3.8 14.6 - - - -
47M VAL* 5.7 0.7 - - - -
34N ILE* 2.9 23.5 + - - -
35N ASN* 3.5 9.9 + - - -
37N VAL* 1.3 83.2 - - - +
39N ARG* 1.3 59.5 + - - +
40N ASN 3.9 0.2 + - - -
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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