Contacts of the helix formed by residues 58 - 76 (chain C) in PDB entry 3LDZ
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 ASP 58 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B PRO* 6.5 1.8 - - - -
101B HIS* 5.0 7.5 + - - +
103B LYS* 5.3 5.7 - - - +
19C GLU* 3.5 33.0 - - - +
56C HIS* 3.1 23.7 - - + +
57C LYS* 1.4 78.1 - - + +
59C PRO* 1.4 71.3 - - - +
60C HIS* 3.2 26.0 + - - +
61C VAL* 3.2 8.9 + - + +
62C ALA* 3.2 19.4 + - - +
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Residues in contact with PRO 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ASP* 5.7 2.2 - - - +
60B HIS* 5.0 18.2 - - + +
56C HIS 5.3 0.2 - - - +
57C LYS 3.4 10.3 - - - +
58C ASP* 1.4 89.8 - - - +
60C HIS* 1.3 51.5 + - - +
62C ALA* 3.5 9.5 - - + +
63C MET* 2.8 41.1 + - - +
101C HIS* 3.8 45.3 - - + +
103C LYS* 4.5 13.5 - - - +
104C VAL* 4.2 5.3 - - + +
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Residues in contact with HIS 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LYS* 3.9 22.0 + - - -
19C GLU* 3.1 33.0 + - + -
21C ASN 2.7 30.6 + - - -
22C THR* 5.1 6.5 - - - -
58C ASP* 3.2 14.0 + - - +
59C PRO* 1.3 75.1 - - - +
61C VAL* 1.4 62.4 + - - +
63C MET* 4.0 6.2 - - - +
64C GLN* 3.2 53.8 + - + +
103C LYS* 5.7 2.2 - - - +
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Residues in contact with VAL 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C THR* 3.3 28.3 - - - +
19C GLU* 3.7 32.5 - - + +
53C ARG* 3.7 28.7 - - - +
56C HIS* 3.7 31.2 - - + +
58C ASP* 3.2 19.6 + - + +
60C HIS* 1.4 74.4 - - - +
62C ALA* 1.4 57.9 + - - +
64C GLN* 3.4 6.9 + - - +
65C ALA* 3.0 26.5 + - - +
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Residues in contact with ALA 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ARG 3.5 12.7 + - - +
54C VAL* 3.4 24.4 - - - +
56C HIS 4.4 5.4 - - - +
58C ASP 3.2 12.5 + - - +
59C PRO* 3.4 9.8 + - + +
61C VAL* 1.4 76.0 - - - +
63C MET* 1.4 56.0 + - - +
65C ALA* 3.3 5.5 + - - +
66C LEU* 3.0 31.6 + - - +
104C VAL* 3.7 20.6 - - + -
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Residues in contact with MET 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C PRO 2.8 27.9 + - - +
60C HIS* 4.0 7.6 - - - +
61C VAL 3.4 0.2 - - - -
62C ALA* 1.4 68.2 - - - +
64C GLN* 1.4 64.7 + - - +
66C LEU* 3.2 7.8 + - - +
67C THR* 3.2 31.3 + - + +
103C LYS* 3.6 53.4 - - + +
104C VAL* 3.9 12.1 - - + -
107C LYS* 3.9 28.5 - - + -
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Residues in contact with GLN 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ALA 3.4 13.5 + - - +
17C THR* 3.5 17.4 - - - +
18C SER 2.8 20.4 + - - +
21C ASN* 3.0 39.6 - - - +
23C ALA 5.2 1.8 + - - -
24C GLU* 6.1 7.0 - - + +
29C ILE* 5.7 0.9 - - - +
60C HIS* 3.2 38.2 + - + +
61C VAL 3.4 9.1 + - - +
63C MET* 1.4 75.7 - - + +
65C ALA* 1.4 56.6 + - - +
67C THR* 3.2 12.3 + - - -
68C LEU* 3.1 26.0 + - - +
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Residues in contact with ALA 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C THR* 3.6 12.3 - - + +
50C ILE* 3.4 16.1 - - + +
53C ARG* 3.8 14.4 - - + -
54C VAL* 3.6 32.1 - - + +
61C VAL 3.0 13.6 + - - +
62C ALA 3.3 11.4 - - - +
64C GLN* 1.4 73.2 - - - +
66C LEU* 1.3 56.7 + - - +
68C LEU* 3.5 2.9 + - - +
69C LEU* 3.0 22.9 + - - +
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Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C VAL* 3.8 21.5 - - + -
62C ALA 3.0 17.4 + - - +
63C MET* 3.2 11.6 + - - +
65C ALA* 1.3 73.7 - - - +
67C THR* 1.4 60.9 + - - +
69C LEU* 4.1 14.1 - - + -
70C GLY* 3.1 20.6 + - - -
104C VAL* 3.5 43.1 - - + +
107C LYS* 3.7 28.4 - - + -
108C LEU* 3.9 31.2 - - + +
111C LEU* 3.4 14.7 - - + +
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Residues in contact with THR 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLU* 4.1 24.4 + - - +
26C TRP* 4.7 12.1 - - - -
29C ILE* 4.3 15.2 - - - +
63C MET* 3.2 21.0 + - + +
64C GLN* 3.2 10.6 + - - -
66C LEU* 1.4 75.2 - - - +
68C LEU* 1.4 61.3 + - - +
70C GLY* 3.5 1.7 + - - -
71C ALA* 3.0 28.2 + - - +
107C LYS* 4.4 18.2 - - + +
47F GLY* 5.8 0.5 - - - -
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Residues in contact with LEU 68 (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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13C VAL* 4.0 19.7 - - + -
16C ALA* 4.4 3.6 - - + +
17C THR* 4.2 13.7 - - + -
29C ILE* 3.9 32.1 - - + +
32C ILE* 3.9 44.2 - - + -
33C CYS* 5.3 0.2 - - - -
50C ILE* 3.8 26.2 - - + -
64C GLN 3.1 13.1 + - - +
65C ALA* 3.7 9.0 - - - +
67C THR* 1.4 74.8 + - - +
69C LEU* 1.3 63.5 + - - +
71C ALA* 3.3 5.6 + - - +
72C CYS* 3.0 28.8 + - - +
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Residues in contact with LEU 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU* 3.7 29.4 - - + -
50C ILE* 3.9 17.9 - - + +
51C MET* 4.1 17.9 - - - -
54C VAL* 5.1 0.2 - - + -
65C ALA 3.0 16.8 + - - +
66C LEU* 3.7 25.1 - - + +
67C THR 3.4 0.4 - - - -
68C LEU* 1.3 74.9 - - - +
70C GLY* 1.3 60.7 + - - +
72C CYS* 3.2 6.2 + - - +
73C VAL* 3.2 20.1 + - - +
80C PHE* 4.1 12.8 - - + -
84C VAL* 4.4 2.9 - - + -
89C PHE* 4.2 7.6 - - + -
108C LEU* 4.3 6.5 - - + -
111C LEU* 4.4 2.5 - - + -
115C TRP* 3.7 28.5 - - + -
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Residues in contact with GLY 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU 3.1 12.2 + - - -
67C THR* 3.5 3.8 + - - -
68C LEU 3.4 0.2 - - - -
69C LEU* 1.3 75.5 - - - +
71C ALA* 1.3 56.1 + - - +
73C VAL* 3.4 4.9 + - - +
74C SER* 2.9 32.6 + - - -
107C LYS* 6.0 0.2 - - - -
111C LEU* 3.8 26.2 - - - +
115C TRP* 4.4 6.8 + - - -
47F GLY* 5.7 1.8 - - - -
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Residues in contact with ALA 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TRP* 4.4 6.5 - - + -
29C ILE* 3.4 32.8 - - + -
33C CYS* 4.1 2.7 - - - -
67C THR 3.0 16.0 + - - +
68C LEU 3.3 3.3 + - - +
70C GLY* 1.3 75.5 - - - +
72C CYS* 1.3 53.5 + - - +
74C SER* 3.3 1.3 + - - -
75C ASN* 2.9 43.9 + - - +
47F GLY* 4.0 21.7 - - - +
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Residues in contact with CYS 72 (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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32C ILE* 4.5 7.4 - - - -
33C CYS* 4.2 10.3 - - - -
36C VAL* 4.7 0.9 - - - -
46C CYS* 4.1 14.6 - - - -
50C ILE* 3.8 19.7 - - - -
68C LEU* 3.0 17.7 + - - +
69C LEU* 3.2 10.7 + - - +
71C ALA* 1.3 72.6 - - - +
73C VAL* 1.3 58.3 + - - +
76C CYS* 2.8 51.4 + - - +
80C PHE* 3.5 29.5 - - + +
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Residues in contact with VAL 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LEU 3.2 7.8 + - - +
70C GLY 3.8 6.5 - - - +
72C CYS* 1.3 75.6 - - - +
74C SER* 1.3 64.4 + - - +
75C ASN 3.5 0.2 + - - -
76C CYS 4.3 1.2 + - - -
77C GLY 4.4 0.5 + - - -
80C PHE* 3.8 20.6 - - + -
81C HIS* 2.8 43.7 - - + +
84C VAL* 4.2 11.0 - - + -
115C TRP* 3.4 58.1 - - + +
118C GLU* 3.8 15.8 - - - +
119C PHE* 4.2 4.7 - - + -
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Residues in contact with SER 74 (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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70C GLY 2.9 18.9 + - - -
71C ALA* 3.5 5.8 - - - -
72C CYS 3.3 0.2 - - - -
73C VAL* 1.3 80.3 - - - +
75C ASN* 1.3 59.1 + - - +
77C GLY 5.2 1.0 + - - -
118C GLU* 5.3 5.6 + - - -
46F ALA 4.8 4.2 + - - -
47F GLY 4.0 5.1 - - - -
48F LYS* 3.2 60.8 + - - +
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Residues in contact with ASN 75 (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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30C LEU* 4.0 13.9 - - - +
33C CYS* 4.0 22.9 - - + +
71C ALA* 2.9 28.7 + - - +
74C SER* 1.3 77.3 - - - +
76C CYS* 1.3 62.0 + - - +
77C GLY 3.4 2.8 + - - -
47F GLY 3.0 18.5 + - - -
48F LYS* 3.6 4.3 + - - +
49F GLN* 2.8 42.5 + - + +
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Residues in contact with CYS 76 (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 CYS* 3.6 43.1 - - - -
36C VAL* 4.0 23.3 - - + -
72C CYS* 2.8 36.6 + - - +
75C ASN* 1.3 71.7 - - - +
77C GLY* 1.3 60.1 + - - +
79C ILE* 2.9 31.8 - - + +
80C PHE* 3.7 15.0 - - + -
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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