Contacts of the helix formed by residues 19 - 38 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18L GLY* 3.7 24.7 - - - +
61L THR* 3.3 30.3 + - - +
62L GLY* 3.8 0.4 - - - +
64L PHE* 4.4 7.4 - - + -
65L CYS* 3.7 35.4 - - + +
68L VAL* 5.9 1.3 - - + -
16M THR* 3.3 23.8 + - + +
17M ILE* 4.5 1.8 - - - -
18M GLY* 1.3 71.7 - - - +
20M LEU* 1.3 54.7 + - - +
21M GLY 3.1 0.9 - - - -
22M ALA* 2.9 16.4 + - + +
23M GLY* 2.7 30.7 + - - -
62M GLY* 4.7 12.3 - - - +
65M CYS* 4.7 2.6 - - - +
66M LEU* 5.0 19.5 - - + -
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Residues in contact with LEU 20 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L ILE* 5.3 4.9 - - + +
18L GLY* 4.9 4.2 + - - +
20L LEU* 3.7 30.7 - - + -
21L GLY* 3.6 33.9 - - - +
24L ILE* 5.2 0.4 - - + -
17M ILE* 2.9 21.4 + - + +
19M LEU* 1.3 80.5 - - - +
21M GLY* 1.3 56.6 + - - +
23M GLY 2.9 14.5 + - - +
24M ILE* 3.0 39.9 + - + +
20N LEU* 3.7 27.6 - - + -
24N ILE* 5.3 0.2 - - + -
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Residues in contact with GLY 21 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M GLY 3.0 13.4 + - - -
20M LEU* 1.3 77.4 - - - +
22M ALA* 1.3 59.6 + - - +
25M GLY* 3.7 1.7 + - - -
26M ILE* 5.6 0.3 - - - +
61M THR* 5.9 0.9 - - - -
62M GLY* 5.5 1.6 - - - -
19N LEU* 5.1 1.3 - - - -
20N LEU* 3.2 31.0 - - - +
23N GLY* 3.6 9.8 - - - +
24N ILE* 3.3 31.0 + - - +
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Residues in contact with ALA 22 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61L THR* 4.5 19.1 - - + -
18M GLY 3.9 2.0 + - - -
19M LEU* 2.9 19.3 + - + +
21M GLY* 1.3 76.2 - - - +
23M GLY* 1.3 59.4 + - - +
25M GLY 2.9 19.8 + - - -
26M ILE* 3.2 25.2 + - - +
58M SER 6.0 0.4 - - - -
59M GLU* 4.6 17.9 - - + +
61M THR* 6.0 0.2 - - - -
62M GLY* 4.5 17.1 - - - +
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Residues in contact with GLY 23 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21L GLY* 2.9 30.2 - - - +
25L GLY* 3.4 9.7 - - - -
26L ILE* 5.9 0.2 - - - +
58L SER* 4.9 5.6 - - - -
61L THR* 3.8 17.7 - - - -
19M LEU* 2.7 16.7 + - - -
20M LEU 2.9 3.0 + - - -
22M ALA* 1.3 70.4 - - - +
24M ILE* 1.3 60.8 + - - +
26M ILE* 4.8 3.3 - - - +
27M ALA* 3.7 6.8 + - - +
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Residues in contact with ILE 24 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21L GLY* 4.7 1.1 - - - -
24L ILE* 4.0 38.6 - - + -
25L GLY* 4.4 5.1 - - - -
28L ILE* 5.7 2.2 - - + -
20M LEU* 3.0 35.8 + - + -
23M GLY* 1.3 75.8 - - - +
25M GLY* 1.3 67.9 + - - +
26M ILE 3.5 0.2 - - - -
27M ALA* 3.0 23.2 + - - +
28M ILE* 3.4 16.9 - - + +
24N ILE* 3.7 37.5 - - + -
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Residues in contact with GLY 25 (chain M).
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 3.7 5.5 + - - -
22M ALA 2.9 9.4 + - - -
24M ILE* 1.3 73.2 - - - +
26M ILE* 1.3 63.1 + - - +
28M ILE* 3.0 27.7 + - - +
29M VAL 3.5 0.5 + - - -
23N GLY 4.7 0.7 - - - -
24N ILE* 3.8 32.3 - - - -
27N ALA* 3.3 14.9 - - - +
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Residues in contact with ILE 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57L LEU 3.5 24.9 - - - +
58L SER* 3.6 17.9 - - - +
61L THR* 4.3 11.9 - - + -
21M GLY 5.6 0.2 - - - +
22M ALA* 3.2 20.4 + - - +
23M GLY* 4.8 1.3 - - - +
25M GLY* 1.3 73.7 - - - +
27M ALA* 1.3 65.7 + - - +
29M VAL* 3.0 26.5 + - - +
30M PHE* 3.2 14.2 - - - -
54M GLY 5.6 0.7 - - - -
55M PHE* 3.6 25.1 - - + +
58M SER* 3.7 22.9 - - - -
59M GLU* 3.7 31.0 - - + +
23N GLY 5.7 0.7 - - - +
27N ALA* 4.7 0.2 - - - -
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Residues in contact with ALA 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25L GLY* 3.4 34.8 - - - +
26L ILE 4.3 0.9 - - - +
28L ILE* 4.7 2.2 - - + -
29L VAL* 3.3 18.8 - - + +
58L SER* 3.9 14.1 - - - +
23M GLY 3.7 7.2 - - - +
24M ILE 3.0 15.4 + - - +
26M ILE* 1.3 81.0 - - - +
28M ILE* 1.3 54.2 + - - +
30M PHE* 3.0 5.7 + - - +
31M ALA* 2.9 22.9 + - - +
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Residues in contact with ILE 28 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L ILE* 3.6 22.2 - - + -
24M ILE* 3.4 28.3 - - + +
25M GLY* 3.0 16.5 + - - +
27M ALA* 1.3 74.2 - - - +
29M VAL* 1.3 52.4 + - - +
31M ALA* 3.0 11.3 + - + +
32M ALA* 2.6 35.6 + - - +
24N ILE* 4.9 6.5 - - + +
27N ALA* 4.5 4.0 - - + +
28N ILE* 3.7 47.3 - - + +
31N ALA* 4.1 12.2 - - + +
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Residues in contact with VAL 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25M GLY 3.9 0.2 - - - +
26M ILE* 3.0 14.3 + - - +
28M ILE* 1.3 76.5 - - - +
30M PHE* 1.3 55.6 + - + +
32M ALA* 3.0 6.7 + - - +
33M LEU* 2.6 31.9 + - - +
51M ALA* 3.7 28.0 - - + +
54M GLY* 4.2 17.0 - - - +
55M PHE* 4.7 2.0 - - - +
27N ALA* 3.6 41.3 - - + +
30N PHE* 4.4 7.2 - - + -
31N ALA* 4.6 1.6 - - - +
34N ILE* 3.4 22.5 - - + +
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Residues in contact with PHE 30 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29L VAL* 4.5 10.8 - - + -
50L MET* 5.0 3.8 - - + -
51L ALA* 5.7 2.0 - - - +
53L LEU* 4.8 7.2 - - + -
54L GLY* 3.5 35.7 - - - -
57L LEU* 3.6 25.1 - - + -
58L SER* 4.0 13.9 - - - -
26M ILE 3.2 24.2 + - - -
27M ALA* 3.0 7.2 + - - +
29M VAL* 1.3 79.5 - - + +
31M ALA* 1.3 57.5 + - - +
33M LEU* 3.0 26.7 + - + +
34M ILE* 2.9 34.6 + - + +
48M PHE* 6.2 2.7 - + - -
51M ALA* 5.6 5.4 - - + -
52M ILE* 5.3 10.5 - - + -
55M PHE* 3.9 32.5 - + + -
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Residues in contact with ALA 31 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28L ILE* 4.3 17.3 - - + +
29L VAL* 4.5 4.8 - - - +
32L ALA* 3.5 27.5 - - + +
27M ALA 2.9 12.3 + - - +
28M ILE* 3.1 19.5 - - + +
30M PHE* 1.3 75.2 - - - +
32M ALA* 1.3 59.5 + - - +
34M ILE* 3.0 18.7 + - - +
35M ASN* 3.1 12.4 + - - -
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Residues in contact with ALA 32 (chain M).
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 2.6 16.0 + - - +
29M VAL 3.4 7.0 - - - +
31M ALA* 1.3 72.3 - - - +
33M LEU* 1.3 51.6 + - - +
35M ASN* 3.0 12.1 + - - +
36M GLY 2.6 31.2 + - - -
31N ALA* 3.4 40.4 - - + +
34N ILE* 3.3 12.0 - - + +
35N ASN* 4.2 10.9 - - - +
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Residues in contact with LEU 33 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50L MET* 3.6 39.0 - - + -
29M VAL 2.6 17.8 + - - +
30M PHE* 3.1 35.2 - - + +
32M ALA* 1.3 73.8 - - - +
34M ILE* 1.3 60.4 + - + +
36M GLY* 3.0 2.4 + - - -
37M VAL* 3.0 23.1 + - + +
47M VAL* 3.8 28.3 - - + -
48M PHE* 4.4 15.7 - - + +
51M ALA* 3.9 22.4 - - + -
34N ILE* 3.7 9.1 - - + +
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Residues in contact with ILE 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L VAL* 3.3 39.0 - - + +
32L ALA* 3.2 24.7 - - + +
33L LEU* 3.5 17.5 - - + +
36L GLY* 4.1 5.8 - - - -
47L VAL* 3.7 27.1 - - + -
50L MET* 6.2 0.9 - - + -
51L ALA* 4.3 11.4 - - + -
30M PHE 2.9 20.6 + - - +
31M ALA* 3.3 5.4 - - - +
33M LEU* 1.3 76.1 - - + +
35M ASN* 1.3 53.6 + - - +
37M VAL* 3.0 7.4 + - - -
38M SER* 2.6 45.5 + - - +
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Residues in contact with ASN 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32L ALA* 4.3 18.8 - - - +
35L ASN* 5.3 5.4 - - - +
36L GLY* 5.2 3.3 + - - -
39L ARG* 5.2 9.0 + - - -
31M ALA 3.1 15.0 + - - +
32M ALA* 3.0 10.2 + - - +
34M ILE* 1.3 72.2 - - - +
36M GLY* 1.3 65.2 + - - +
38M SER* 3.7 10.1 + - - -
39M ARG* 3.3 33.4 + - - +
34N ILE 4.8 0.2 - - - -
35N ASN* 3.6 20.9 + - - +
38N SER* 3.8 7.5 + - - -
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Residues in contact with GLY 36 (chain M).
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 2.6 16.5 + - - -
33M LEU 3.0 5.2 + - - -
35M ASN* 1.3 75.6 - - - +
37M VAL* 1.3 58.7 + - - +
39M ARG* 3.0 5.9 + - - +
40M ASN* 2.8 27.9 + - - +
43M ILE* 4.1 9.9 - - - -
47M VAL* 5.3 1.3 - - - -
34N ILE* 4.1 11.2 - - - +
38N SER* 3.7 16.5 - - - -
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Residues in contact with VAL 37 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43L ILE* 4.3 9.3 - - + +
46L THR* 4.3 20.6 - - + -
47L VAL* 3.7 22.4 - - + -
50L MET* 4.3 19.3 - - - -
33M LEU* 3.0 19.3 + - + +
34M ILE* 3.0 5.6 + - - +
36M GLY* 1.3 69.7 - - - -
38M SER* 1.3 66.4 + - - +
40M ASN 3.3 23.9 - - - +
41M PRO* 3.7 13.2 - - + +
43M ILE* 4.4 4.2 - - + +
44M LYS* 4.3 27.6 - - + -
47M VAL* 5.7 0.7 - - + -
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Residues in contact with SER 38 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H ARG 4.0 3.5 - - - +
36L GLY* 3.3 40.6 - - - -
39L ARG* 4.0 9.0 + - - -
40L ASN* 2.7 32.6 + - - +
43L ILE* 4.8 5.4 - - - -
47L VAL* 4.8 3.8 - - - -
34M ILE* 2.6 34.8 + - - -
35M ASN* 3.7 8.1 + - - -
37M VAL* 1.3 75.8 - - - +
39M ARG* 1.3 59.8 + - - +
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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