Contacts of the helix formed by residues 19 - 38 (chain T) 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 T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18S GLY* 3.5 24.2 - - - +
61S THR* 3.4 25.4 - - - +
62S GLY* 4.6 0.4 - - - -
64S PHE* 3.8 23.6 - - + -
65S CYS* 4.0 15.0 - - + -
16T THR 3.4 21.0 + - - +
18T GLY* 1.3 75.6 - - - +
20T LEU* 1.3 52.1 + - - +
21T GLY 3.5 0.4 - - - -
22T ALA* 2.9 10.4 + - + +
23T GLY* 2.6 36.1 + - - +
62T GLY 3.4 21.6 + - - +
65T CYS* 4.9 1.4 - - - +
66T LEU* 3.8 27.7 - - + +
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Residues in contact with LEU 20 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K LEU* 3.8 23.1 - - + -
17S ILE* 3.8 18.2 - - + +
18S GLY* 4.0 11.9 - - - +
20S LEU* 3.7 29.4 - - + -
21S GLY* 3.3 38.7 - - - +
17T ILE* 2.7 27.9 + - + +
18T GLY 3.1 0.4 - - - -
19T LEU* 1.3 75.2 - - - +
21T GLY* 1.3 59.0 + - - +
23T GLY 3.0 15.2 + - - -
24T ILE* 3.1 11.9 + - + +
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Residues in contact with GLY 21 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K LEU* 3.3 23.1 - - - +
23K GLY* 2.9 15.1 - - - +
24K ILE* 3.8 17.5 - - - -
18T GLY 4.5 1.4 + - - -
20T LEU* 1.3 80.0 - - - +
22T ALA* 1.3 49.9 + - - +
24T ILE* 2.9 12.5 + - - +
25T GLY 2.4 31.4 + - - -
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Residues in contact with ALA 22 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K GLY* 3.7 11.3 + - - -
61S THR* 5.1 4.9 - - + -
18T GLY 4.6 1.2 + - - +
19T LEU* 2.9 14.4 + - + +
21T GLY* 1.3 74.2 - - - +
23T GLY* 1.3 58.7 + - - +
25T GLY* 3.0 14.5 + - - +
26T ILE* 3.3 24.0 + - + +
58T SER 3.9 8.5 - - - +
59T GLU* 5.5 4.7 - - - +
61T THR* 3.8 11.9 - - - +
62T GLY* 3.8 29.2 - - - -
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Residues in contact with GLY 23 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21S GLY* 2.9 26.0 - - - +
22S ALA 4.5 0.9 - - - -
25S GLY* 3.6 8.5 - - - -
58S SER* 4.0 9.7 + - - -
61S THR* 4.0 19.9 + - - -
62S GLY* 5.6 0.7 - - - -
19T LEU* 2.6 19.3 + - - -
20T LEU 3.0 6.4 + - - -
22T ALA* 1.3 73.9 - - - +
24T ILE* 1.3 58.7 + - - +
26T ILE* 5.1 0.2 - - - -
27T ALA* 3.8 5.9 - - - +
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Residues in contact with ILE 24 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K ILE* 4.7 22.4 - - + -
21S GLY* 4.1 5.6 - - - +
24S ILE* 3.8 46.4 - - + -
25S GLY* 4.3 4.3 - - - -
20T LEU* 3.1 11.1 + - + +
21T GLY* 2.9 20.5 + - - +
23T GLY* 1.3 76.4 - - - +
25T GLY* 1.3 56.8 + - - +
26T ILE 3.6 0.2 - - - -
27T ALA* 2.9 22.7 + - - +
28T ILE* 3.0 40.8 + - + +
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Residues in contact with GLY 25 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23K GLY 3.3 15.9 - - - -
27K ALA* 3.3 14.3 - - - +
21T GLY 2.4 23.4 + - - -
22T ALA* 3.0 6.8 + - - -
24T ILE* 1.3 68.4 - - - +
26T ILE* 1.3 61.0 + - - -
28T ILE* 3.1 22.3 + - - +
29T VAL* 3.2 10.2 + - - +
58T SER* 4.7 3.4 - - - -
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Residues in contact with ILE 26 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57S LEU* 3.3 37.2 - - + +
58S SER* 3.6 12.3 - - - +
61S THR* 4.1 5.2 - - + +
22T ALA 3.3 16.5 + - - +
23T GLY 4.7 0.2 - - - +
25T GLY* 1.3 70.3 - - - +
27T ALA* 1.3 64.6 + - - +
29T VAL* 3.1 21.5 + - - +
30T PHE* 3.2 20.4 + - + -
55T PHE* 3.6 37.2 - - + +
58T SER* 3.6 25.3 - - - +
59T GLU* 3.4 22.7 - - - +
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Residues in contact with ALA 27 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25S GLY* 3.3 34.5 - - - +
28S ILE* 3.4 8.5 - - + +
29S VAL* 3.6 9.8 - - + +
54S GLY 5.6 0.4 - - - -
58S SER* 3.3 20.0 - - - +
23T GLY 3.8 1.6 - - - +
24T ILE 2.9 14.2 + - - +
26T ILE* 1.3 81.1 - - - +
28T ILE* 1.3 56.8 + - - +
30T PHE* 3.0 10.1 + - - +
31T ALA 2.9 21.7 + - - -
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Residues in contact with ILE 28 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K ILE* 4.1 10.5 - - + +
27K ALA* 3.8 18.6 - - + -
28K ILE* 3.6 31.0 - - + -
31K ALA* 3.9 9.2 - - + +
24S ILE* 6.2 0.7 - - + -
28S ILE* 3.6 27.1 - - + -
24T ILE* 3.0 35.7 + - + +
25T GLY* 3.1 13.2 - - - +
27T ALA* 1.3 72.6 - - - +
29T VAL* 1.3 65.1 + - - +
31T ALA* 3.1 17.9 + - + +
32T ALA 3.2 5.7 + - - -
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Residues in contact with VAL 29 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27K ALA* 3.6 29.6 - - + +
30K PHE* 4.4 13.0 - - + -
31K ALA* 4.4 6.7 - - - -
34K ILE* 3.7 20.9 - - + +
25T GLY 3.2 15.1 + - - +
26T ILE* 3.1 11.2 + - - +
28T ILE* 1.3 76.0 - - - +
30T PHE* 1.3 67.3 + - + +
32T ALA* 3.0 16.6 + - - +
33T LEU* 3.1 8.0 + - - +
51T ALA* 4.4 22.2 - - + +
54T GLY 4.5 5.8 - - - +
55T PHE* 4.9 2.0 - - - +
58T SER* 4.2 10.8 - - - +
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Residues in contact with PHE 30 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29S VAL* 4.5 13.7 - - + -
50S MET 4.1 15.0 - - - +
53S LEU* 4.3 15.3 - - + -
54S GLY* 4.0 15.0 - - - -
57S LEU* 3.6 35.0 - - + -
26T ILE* 3.2 25.2 + - + -
27T ALA* 3.0 10.3 + - - +
29T VAL* 1.3 77.3 - - + +
31T ALA* 1.3 61.1 + - - +
33T LEU* 3.0 30.1 + - + +
34T ILE* 2.9 36.3 + - + +
48T PHE* 4.8 9.4 - + - -
51T ALA* 5.6 7.6 - - + -
52T ILE* 4.8 7.0 - - + -
55T PHE* 4.2 21.8 - + + -
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Residues in contact with ALA 31 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28S ILE* 3.8 19.7 - - + +
29S VAL* 4.8 1.3 - - - +
32S ALA* 3.6 24.8 - - + +
27T ALA 2.9 6.5 + - - -
28T ILE* 3.1 25.1 + - + +
30T PHE* 1.3 74.8 - - - +
32T ALA* 1.3 56.0 + - - +
34T ILE* 3.0 5.4 + - - -
35T ASN* 2.9 28.4 + - - +
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Residues in contact with ALA 32 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31K ALA* 3.3 40.6 - - + +
34K ILE* 3.4 11.5 - - + +
35K ASN* 3.4 23.8 - - - +
28T ILE 3.2 1.8 + - - -
29T VAL 3.0 9.9 + - - +
31T ALA* 1.3 78.3 - - - +
33T LEU* 1.3 52.0 + - - +
35T ASN* 3.0 4.7 + - - +
36T GLY* 2.5 34.1 + - - -
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Residues in contact with LEU 33 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34K ILE* 3.9 11.4 - - + +
50S MET* 3.9 31.4 - - + +
29T VAL 3.1 6.8 + - - +
30T PHE* 3.0 39.2 + - + +
32T ALA* 1.3 77.9 - - - +
34T ILE* 1.3 59.6 + - + +
36T GLY 2.9 12.7 + - - +
37T VAL* 3.0 28.7 + - + +
44T LYS* 6.0 0.9 - - - +
47T VAL* 3.7 29.8 - - + -
48T PHE* 4.0 16.8 - - + +
51T ALA* 4.8 13.7 - - + -
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Residues in contact with ILE 34 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29S VAL* 3.4 34.8 - - + +
32S ALA* 3.3 29.6 - - + +
33S LEU* 3.7 12.6 - - + +
36S GLY* 3.9 9.3 - - - -
47S VAL* 4.6 12.8 - - + -
50S MET* 5.5 2.0 - - + +
51S ALA* 3.7 30.3 - - + +
30T PHE* 2.9 17.3 + - + +
31T ALA 3.0 4.9 + - - +
33T LEU* 1.3 79.8 - - + +
35T ASN* 1.3 54.0 + - - +
36T GLY 3.5 0.3 + - - -
37T VAL* 4.8 4.3 - - - -
38T SER* 2.3 34.8 + - - -
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Residues in contact with ASN 35 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K ASN* 3.4 23.0 + - - +
32S ALA* 4.5 11.1 - - - +
35S ASN* 4.1 25.6 + - - +
39S ARG* 4.7 7.5 + - - +
31T ALA* 2.9 21.1 + - - +
32T ALA* 3.0 3.5 + - - +
34T ILE* 1.3 79.3 - - - +
36T GLY* 1.3 57.7 + - - +
38T SER* 4.0 4.1 + - - -
39T ARG* 2.9 44.1 + - - +
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Residues in contact with GLY 36 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34K ILE* 4.5 5.6 - - - -
38K SER* 3.6 26.8 - - - -
32T ALA 2.5 18.0 + - - -
33T LEU* 2.9 7.1 + - - -
35T ASN* 1.3 74.0 - - - +
37T VAL* 1.3 59.1 + - - +
39T ARG* 3.3 4.7 + - - +
40T ASN* 2.9 26.2 + - - +
43T ILE* 4.2 5.3 - - - +
47T VAL* 5.9 0.9 - - - -
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Residues in contact with VAL 37 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43S ILE* 3.3 11.1 - - + +
46S THR* 4.0 16.4 - - + -
47S VAL* 3.7 24.9 - - + -
50S MET* 5.5 7.2 - - + -
33T LEU* 3.0 27.9 + - + +
34T ILE* 4.8 0.4 - - - -
36T GLY* 1.3 72.7 - - - +
38T SER* 1.3 67.1 + - - +
40T ASN 2.9 22.6 - - - +
41T PRO* 3.7 12.8 - - + +
43T ILE* 4.2 6.7 - - + +
44T LYS* 3.7 35.2 - - + +
47T VAL* 5.9 0.2 - - + -
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Residues in contact with SER 38 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195G GLY 5.4 0.3 - - - +
35S ASN 4.1 4.0 + - - -
36S GLY* 3.3 35.6 - - - -
39S ARG* 3.4 17.3 + - - -
40S ASN* 3.3 17.0 + - - +
43S ILE* 4.2 15.0 - - - -
47S VAL* 4.9 6.5 - - - -
34T ILE 2.3 27.9 + - - -
35T ASN* 4.0 2.8 - - - -
37T VAL* 1.3 79.3 - - - +
39T ARG* 1.3 67.5 + - - +
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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