Contacts of the helix formed by residues 48 - 63 (chain C) in PDB entry 3DAB
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 THR 48 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ILE* 3.3 9.6 - - - -
25C ASN* 3.7 35.0 - - + +
27C VAL* 4.0 2.0 - - - -
47C PHE* 1.3 80.9 - - - +
49C VAL* 1.3 60.0 + - - +
50C LYS* 3.6 11.5 + - - +
51C GLU* 3.0 36.3 + - - +
52C VAL* 3.2 23.2 + - - +
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Residues in contact with VAL 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ILE* 2.8 51.0 + - + +
27C VAL* 4.0 19.3 - - + -
48C THR* 1.3 69.4 - - - +
50C LYS* 1.3 68.2 + - - +
51C GLU 3.2 0.2 - - - -
52C VAL* 3.2 7.4 + - + +
53C MET* 3.0 39.5 + - + +
99C TYR* 6.0 4.7 - - + -
102C LEU* 6.0 2.2 - - + -
106C LEU* 4.6 11.9 - - + -
500C ILE* 5.0 2.7 - - + -
27D PRO* 4.6 9.9 - - + +
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Residues in contact with LYS 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ILE* 5.2 2.2 - - - +
48C THR* 3.7 10.3 - - - +
49C VAL* 1.3 78.9 - - - +
51C GLU* 1.3 59.1 + - + +
53C MET* 3.5 6.2 + - - +
54C HIS* 2.9 30.6 + - + +
27D PRO 5.5 3.8 - - - -
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Residues in contact with GLU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C MET 4.2 1.6 - - - +
47C PHE* 3.1 29.1 - - + +
48C THR* 3.0 43.3 + - - +
50C LYS* 1.3 75.9 - - + +
52C VAL* 1.3 65.7 + - - +
54C HIS* 3.1 7.1 + - - +
55C TYR* 3.0 44.1 + - + -
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Residues in contact with VAL 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C VAL* 3.8 20.4 - - + -
29C PRO* 4.4 1.8 - - + -
33C LEU* 4.5 4.9 - - + -
37C LEU* 3.4 33.2 - - + +
47C PHE* 3.9 11.0 - - + -
48C THR 3.2 13.9 + - - +
49C VAL* 3.2 9.6 + - + +
51C GLU* 1.3 77.7 - - - +
53C MET* 1.3 61.5 + - - +
55C TYR* 5.2 0.4 - - - -
56C LEU* 3.0 31.9 + - + +
102C LEU* 4.0 27.6 - - + -
106C LEU* 4.2 12.1 - - + -
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Residues in contact with MET 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C VAL* 3.0 34.6 + - + +
50C LYS* 3.7 4.7 - - - +
52C VAL* 1.3 74.3 - - - +
54C HIS* 1.3 67.1 + - - +
56C LEU* 3.2 9.3 + - - +
57C GLY 3.0 8.5 + - - -
98C LEU* 4.1 14.8 - - + -
99C TYR* 3.8 19.7 - - + +
102C LEU* 3.6 27.6 - - - -
23D TRP* 2.9 29.6 + - + +
26D LEU* 3.7 34.8 - - + -
27D PRO 4.5 11.0 - - - +
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Residues in contact with HIS 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C LYS* 2.9 17.7 + - + +
51C GLU* 3.1 10.5 + - - +
53C MET* 1.3 78.5 - - - +
55C TYR* 1.3 90.4 + + - +
57C GLY* 3.1 2.6 + - - -
58C GLN* 3.0 56.3 + - + +
23D TRP* 4.5 4.7 + - - +
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Residues in contact with TYR 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C LEU* 3.8 20.8 - - + +
40C ALA* 3.0 35.3 - - + +
41C GLY 3.6 11.7 + - - -
42C ALA* 3.6 39.5 - - + -
43C GLN* 5.0 3.4 + - - +
47C PHE* 5.1 6.3 - + - -
51C GLU* 3.0 45.7 + - + +
52C VAL* 5.2 0.4 - - - -
54C HIS* 1.3 95.8 - + - +
56C LEU* 1.3 60.6 + - - +
58C GLN* 4.1 3.8 - - + -
59C TYR* 2.9 25.3 + - - +
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Residues in contact with LEU 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C LEU* 4.5 7.0 - - + -
36C ILE* 4.0 23.1 - - + -
37C LEU* 3.9 8.9 - - + +
52C VAL* 3.0 25.5 + - + +
53C MET* 3.5 11.9 - - - +
55C TYR* 1.3 76.7 - - - +
57C GLY* 1.3 60.9 + - - +
59C TYR* 3.4 5.3 + - + +
60C ILE* 3.1 31.7 + - + +
81C LEU* 4.2 25.6 - - + -
98C LEU* 4.3 17.9 - - + -
101C MET* 4.5 0.4 - - + -
102C LEU* 3.8 32.5 - - + -
23D TRP* 3.7 11.2 - - + -
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Residues in contact with GLY 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C MET 3.0 10.5 + - - -
54C HIS 3.5 3.1 - - - -
56C LEU* 1.3 76.4 - - - +
58C GLN* 1.3 60.6 + - - +
60C ILE 3.6 0.5 + - - -
61C MET* 3.1 24.6 + - - +
19D PHE* 3.4 16.8 - - - -
23D TRP* 3.4 33.8 - - - +
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Residues in contact with GLN 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ALA* 3.9 19.7 - - + +
54C HIS* 3.0 49.5 + - + +
55C TYR* 3.7 8.3 - - + +
56C LEU 3.3 0.6 - - - -
57C GLY* 1.3 77.2 - - - +
59C TYR* 1.3 58.8 + - - +
61C MET* 3.5 31.2 + - - +
62C VAL* 2.9 32.1 + - - +
20D SER* 5.1 5.7 + - - -
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Residues in contact with TYR 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ILE* 3.4 58.6 - - + +
39C ALA* 4.1 17.0 - - + -
40C ALA* 3.4 10.9 - - + +
55C TYR 2.9 13.7 + - - +
56C LEU* 3.5 8.1 - - + +
58C GLN* 1.3 73.6 - - - +
60C ILE* 1.3 65.4 + - + +
62C VAL* 3.3 5.7 + - + +
63C LYS* 3.0 68.3 + - + +
65C LEU* 4.1 8.3 - - + -
79C ASP* 2.6 29.9 + - - -
80C LEU* 4.5 5.0 - - - +
81C LEU* 4.1 16.1 + - + -
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Residues in contact with ILE 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C LEU* 3.1 20.0 + - + +
59C TYR* 1.3 80.8 - - + +
61C MET* 1.3 56.2 + - - +
63C LYS 3.7 0.2 - - - -
64C GLN* 2.9 8.0 + - - -
65C LEU* 2.9 35.5 + - + -
66C TYR* 4.0 19.4 - - + +
74C VAL* 4.1 9.6 - - + -
81C LEU* 3.7 31.2 - - + -
90C PHE* 4.2 11.7 - - + -
98C LEU* 6.2 0.4 - - + -
19D PHE* 3.2 35.2 - - + -
23D TRP* 3.7 32.8 - - + -
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Residues in contact with MET 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C GLY 3.1 18.6 + - - +
58C GLN* 3.5 37.9 - - - +
59C TYR 3.2 0.2 - - - -
60C ILE* 1.3 77.4 - - - +
62C VAL* 1.3 71.3 + - + +
64C GLN* 2.8 35.1 + - - +
66C TYR* 3.9 21.3 - - + +
19D PHE* 4.3 7.2 - - + -
20D SER* 4.7 13.2 - - - +
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Residues in contact with VAL 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ALA 4.9 12.3 - - - +
40C ALA* 5.5 1.6 - - - -
58C GLN 2.9 18.5 + - - +
59C TYR* 3.6 15.0 - - + +
61C MET* 1.3 84.7 - - + +
63C LYS* 1.3 71.6 + - + +
64C GLN* 3.2 5.6 + - - +
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Residues in contact with LYS 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ALA* 6.2 0.2 - - + -
59C TYR* 3.0 53.6 + - + +
62C VAL* 1.3 85.7 - - + +
64C GLN* 1.3 71.2 + - - +
65C LEU* 3.4 21.3 + - + +
79C ASP* 2.8 26.7 + - - +
80C LEU 5.5 0.4 - - - +
78E GLY* 6.2 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
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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