Contacts of the helix formed by residues 60 - 74 (chain C) in PDB entry 4LLL
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 60 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ALA* 4.5 1.1 - - - -
59C ARG* 1.3 77.0 - - - +
61C GLY* 1.3 64.5 + - - +
62C PRO* 3.3 4.6 - - - +
63C THR* 2.9 16.6 + - - -
64C VAL* 3.1 21.1 + - - +
15F C 2.9 32.3 + - - +
16F T 3.3 44.2 - - + +
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Residues in contact with GLY 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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50C GLN* 5.1 1.9 - - - +
51C ASN* 5.8 2.7 - - - -
54C ALA* 4.7 10.8 - - - +
60C THR* 1.3 71.6 - - - +
62C PRO* 1.3 72.7 - - - +
64C VAL* 3.3 4.0 + - - +
65C SER* 2.9 22.3 + - - -
6E G 5.7 2.4 - - - +
7E T 3.9 10.9 - - - +
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Residues in contact with PRO 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C THR* 3.3 9.2 - - - +
61C GLY* 1.3 88.5 - - - +
63C THR* 1.3 63.6 + - - +
65C SER* 2.9 6.2 + - - -
66C ASN* 2.8 24.6 + - - +
7E T 3.9 17.7 - - + +
8E T 3.1 32.7 - - + +
9E A 4.0 4.3 - - - +
15F C 4.2 6.1 - - - +
16F T 3.2 30.7 - - + +
17F A 3.4 10.5 - - - +
18F A 5.9 0.2 - - - +
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Residues in contact with THR 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ARG* 3.8 12.1 - - + -
60C THR* 2.9 13.4 + - - -
62C PRO* 1.3 79.2 - - - +
64C VAL* 1.3 63.5 + - + +
66C ASN* 3.4 2.8 + - - +
67C LEU* 3.2 21.1 + - - +
13F A 4.8 0.8 - - + +
14F T 3.2 56.0 + - + +
15F C 2.5 42.2 + - - +
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Residues in contact with VAL 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C THR* 5.9 0.4 - - + -
50C GLN* 3.7 22.7 - - + +
53C ILE* 4.0 17.5 - - + +
54C ALA* 3.6 28.0 - - + +
57C LEU* 5.6 3.6 - - + -
59C ARG* 4.1 13.0 - - + -
60C THR 3.1 13.6 + - - +
61C GLY 3.9 5.6 - - - +
62C PRO 3.2 0.2 - - - -
63C THR* 1.3 75.6 - - - +
65C SER* 1.3 67.0 + - - +
66C ASN 3.2 0.2 + - - -
67C LEU* 3.3 5.2 + - + +
68C LEU* 3.0 51.4 + - + +
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Residues in contact with SER 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C GLN* 3.8 8.0 + - - -
61C GLY 2.9 12.5 + - - -
62C PRO* 2.9 13.8 + - - -
64C VAL* 1.3 77.4 - - - +
66C ASN* 1.3 57.4 - - - +
68C LEU* 3.5 2.6 + - - +
69C ARG* 2.9 29.5 + - - +
79C ARG* 4.4 2.8 + - - -
7E T 2.4 51.8 + - - +
8E T 4.5 5.6 - - - +
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Residues in contact with ASN 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C PRO 2.8 14.1 + - - +
63C THR 3.8 4.5 - - - +
65C SER* 1.3 75.6 - - - +
67C LEU* 1.3 65.6 + - - +
69C ARG* 3.1 8.0 + - - +
70C ASN* 2.9 43.8 + - - +
8E T 5.9 0.6 - - + +
12F T 5.1 2.0 - - - +
13F A 4.8 9.5 + - - -
14F T 3.7 29.2 - - + +
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Residues in contact with LEU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C GLU* 3.9 17.9 - - + +
33C GLN* 4.2 8.3 - - + -
36C THR* 3.2 38.1 - - + +
63C THR 3.2 13.1 + - - +
64C VAL* 3.9 5.2 - - + +
66C ASN* 1.3 76.5 - - - +
68C LEU* 1.3 69.3 + - + +
70C ASN* 2.9 5.2 + - - +
71C LEU* 2.9 34.6 + - + +
13F A 3.7 36.1 - - - +
14F T 3.6 22.9 - - - +
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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
----------------------------------------------------------
36C THR* 4.3 24.7 - - + -
40C LEU* 4.9 1.8 - - + -
50C GLN* 3.8 28.7 - - + -
53C ILE* 4.7 8.1 - - + -
64C VAL* 3.0 39.4 + - + +
65C SER 3.8 3.8 - - - +
67C LEU* 1.3 78.3 - - + +
69C ARG* 1.3 67.9 + - - +
71C LEU* 3.3 5.1 + - + -
72C GLU* 2.9 23.1 + - - +
77C ILE* 3.4 22.1 - - + +
79C ARG* 4.1 11.4 - - - +
91C ILE* 3.8 24.7 - - + -
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Residues in contact with ARG 69 (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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65C SER* 2.9 19.8 + - - +
66C ASN* 3.1 10.3 + - - +
68C LEU* 1.3 75.9 - - - +
70C ASN* 1.3 59.9 + - - +
72C GLU* 3.3 8.3 + - - +
73C ARG* 2.9 50.5 + - - +
79C ARG* 4.4 11.6 - - - +
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Residues in contact with ASN 70 (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 GLN* 3.5 17.0 - - - +
66C ASN* 2.9 29.8 + - - +
67C LEU 2.9 8.4 + - - +
69C ARG* 1.3 81.6 - - - +
71C LEU* 1.3 59.9 + - - +
73C ARG* 3.4 26.4 + - - +
74C LYS* 3.3 28.3 + - - +
12F T 3.7 31.5 + - - +
13F A 2.7 23.2 + - - -
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Residues in contact with LEU 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ILE* 5.0 0.4 - - + -
33C GLN* 3.8 29.6 - - + +
36C THR* 4.5 8.3 - - + -
37C LEU* 3.4 37.7 - - + -
40C LEU* 4.9 1.1 - - + -
67C LEU* 2.9 34.7 + - + +
68C LEU* 3.8 9.6 - - + +
70C ASN* 1.3 73.4 - - - +
72C GLU* 1.3 67.3 + - - +
74C LYS* 3.0 15.5 + - + +
75C LYS 3.0 8.5 + - - -
76C LEU* 3.1 27.4 + - + -
77C ILE* 3.6 24.5 - - + -
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Residues in contact with GLU 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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68C LEU 2.9 16.8 + - - +
69C ARG* 3.7 6.0 - - - +
71C LEU* 1.3 76.6 - - - +
73C ARG* 1.3 57.4 + - - +
75C LYS* 2.7 27.1 + - - +
77C ILE* 3.6 25.7 - - + +
78C TYR* 4.9 0.8 - - - -
79C ARG* 2.5 63.0 + - - +
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Residues in contact with ARG 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ARG* 2.9 33.6 + - - +
70C ASN* 3.4 26.6 + - - +
72C GLU* 1.3 77.3 - - - +
74C LYS* 1.3 58.2 + - + +
75C LYS* 3.3 14.2 + - - +
12F T 5.4 7.5 + - - -
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Residues in contact with LYS 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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28C ASP* 2.7 55.1 + - - +
29C ILE* 4.7 0.9 - - + -
33C GLN* 3.8 22.2 - - - +
70C ASN* 3.3 18.6 + - - +
71C LEU* 3.0 10.1 + - + +
73C ARG* 1.3 75.0 - - + +
75C LYS* 1.3 73.3 + - - +
76C LEU* 3.1 32.5 + - + +
96C SER* 5.2 0.2 + - - -
12F T 5.8 4.5 - - - -
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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
------------------------------------------------------------
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