Contacts of the helix formed by residues 60 - 74 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A ALA* 4.5 0.7 - - - -
59A ARG* 1.3 76.5 - - - +
61A GLY* 1.3 65.1 + - - +
62A PRO* 3.2 17.9 - - - +
63A THR* 2.8 27.5 + - - -
64A VAL* 3.3 12.6 + - - +
15H C 2.9 31.4 + - - +
16H T 3.5 30.7 - - + +
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Residues in contact with GLY 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLN* 5.0 1.9 + - - -
51A ASN* 4.8 13.9 - - - -
54A ALA* 4.8 5.7 - - - +
59A ARG 4.0 0.4 + - - -
60A THR* 1.3 75.2 - - - +
62A PRO* 1.4 67.1 - - - +
64A VAL* 3.5 3.5 + - - +
65A SER* 3.1 22.2 + - - -
6G G 5.8 4.3 - - - -
7G T 3.9 11.7 - - - +
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Residues in contact with PRO 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A THR* 3.2 16.8 - - - +
61A GLY* 1.4 84.6 - - - +
63A THR* 1.3 61.9 + - - +
65A SER* 3.1 3.9 + - - -
66A ASN* 2.9 24.8 + - - +
7G T 4.1 15.5 - - + +
8G T 3.3 26.6 - - + +
9G A 4.1 3.6 - - - +
15H C 4.3 5.8 - - - +
16H T 3.0 34.8 - - + +
17H A 3.4 8.5 - - - +
18H A 5.3 0.4 - - - +
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Residues in contact with THR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ARG* 4.3 8.5 - - + -
60A THR* 2.8 15.6 + - - -
62A PRO* 1.3 76.7 - - - +
64A VAL* 1.3 63.7 + - + +
66A ASN* 3.2 5.2 + - - +
67A LEU* 3.1 20.3 + - - +
13H A 4.5 1.6 - - + -
14H T 3.1 66.8 - - + +
15H C 2.6 34.5 + - - +
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Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLN* 3.8 22.2 - - + +
53A ILE* 4.0 17.3 - - + +
54A ALA* 3.6 28.7 - - + +
57A LEU* 5.4 3.1 - - + -
59A ARG* 4.1 12.1 - - + -
60A THR 3.3 14.0 + - - +
61A GLY* 3.9 6.1 - - - +
62A PRO 3.2 0.6 - - - -
63A THR* 1.3 77.0 - - + +
65A SER* 1.3 62.9 + - - +
67A LEU* 3.1 6.1 + - + +
68A LEU* 2.8 51.8 + - + +
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Residues in contact with SER 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLN* 3.8 13.2 - - - +
61A GLY 3.1 14.9 + - - -
62A PRO* 3.3 12.6 - - - -
64A VAL* 1.3 76.0 - - - +
66A ASN* 1.3 63.3 + - - +
68A LEU* 4.1 2.9 - - - +
69A ARG* 3.3 22.2 + - - +
79A ARG* 4.6 2.4 + - - -
7G T 2.7 42.3 + - - +
8G T 4.1 10.7 - - - +
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Residues in contact with ASN 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A PRO 2.9 12.7 + - - +
63A THR 3.4 9.0 - - - +
64A VAL 3.1 0.2 - - - -
65A SER* 1.3 75.6 - - - +
67A LEU* 1.3 63.5 + - - +
69A ARG* 2.9 37.8 + - - +
70A ASN* 3.2 29.8 + - - +
8G T 5.7 1.3 - - + +
12H T 5.1 1.6 - - - +
13H A 4.7 11.1 + - - -
14H T 3.6 28.8 - - + +
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLU* 3.9 28.3 - - + -
33A GLN* 4.0 7.9 - - + +
36A THR* 3.4 34.1 - - + +
63A THR 3.1 13.1 + - - +
64A VAL* 3.1 8.7 + - + +
66A ASN* 1.3 74.2 - - - +
68A LEU* 1.3 70.1 + - + +
70A ASN* 2.9 5.2 + - - +
71A LEU* 2.8 48.0 + - + -
13H A 4.0 23.1 - - - +
14H T 4.2 13.2 - - - +
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Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A THR* 4.4 8.3 - - + -
40A LEU* 5.0 1.3 - - + -
50A GLN* 3.6 37.2 - - + +
53A ILE* 4.1 18.4 - - + -
64A VAL* 2.8 31.4 + - + +
65A SER* 4.1 4.5 - - - +
67A LEU* 1.3 91.3 - - + +
69A ARG* 1.3 52.3 + - - +
71A LEU* 3.1 4.7 + - + -
72A GLU* 2.6 32.4 + - - +
77A ILE* 3.2 26.0 - - + +
79A ARG* 4.2 10.1 - - - +
91A ILE* 3.7 22.2 - - + -
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Residues in contact with ARG 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A SER 3.3 16.9 + - - +
66A ASN* 2.9 39.0 + - - +
67A LEU 3.1 0.2 - - - -
68A LEU* 1.3 80.0 - - - +
70A ASN* 1.3 75.3 + - - +
72A GLU* 3.2 3.8 + - - +
73A ARG* 2.9 65.8 + - + +
79A ARG* 3.7 17.6 - - - +
8G T 5.7 4.9 - - - -
12H T 5.4 3.6 + - - -
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Residues in contact with ASN 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A GLN* 3.6 15.3 - - - +
66A ASN* 3.2 14.5 + - - +
67A LEU 2.9 9.7 + - - +
69A ARG* 1.3 100.8 + - - +
71A LEU* 1.3 62.0 + - - +
73A ARG* 3.3 20.7 + - - +
74A LYS* 3.3 28.4 + - - +
12H T 3.5 33.4 + - - +
13H A 2.8 23.8 + - - -
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A GLN* 3.7 32.5 - - + +
36A THR* 4.3 11.2 - - + -
37A LEU* 3.8 34.5 - - + +
40A LEU* 4.8 0.9 - - + -
67A LEU* 2.8 36.9 + - + +
68A LEU* 3.4 12.6 - - + +
70A ASN* 1.3 74.2 - - - +
72A GLU* 1.3 64.7 + - - +
74A LYS* 3.2 8.3 + - + +
75A LYS 3.2 3.5 + - - -
76A LEU* 3.1 34.6 + - + +
77A ILE* 3.7 22.4 - - + +
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Residues in contact with GLU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU 2.6 20.2 + - - +
69A ARG* 3.2 6.2 + - - +
71A LEU* 1.3 71.4 - - - +
73A ARG* 1.3 60.7 + - - +
75A LYS* 2.8 23.4 + - - +
77A ILE* 3.5 20.8 - - + +
78A TYR* 4.2 2.8 - - - +
79A ARG* 2.8 59.6 + - - +
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Residues in contact with ARG 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ARG* 2.9 60.5 + - + +
70A ASN* 3.4 25.8 + - - +
71A LEU 3.2 0.2 - - - -
72A GLU* 1.3 77.0 - - - +
74A LYS* 1.3 63.7 + - + +
75A LYS* 3.2 8.5 + - - +
12H T 5.1 9.7 + - - -
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Residues in contact with LYS 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ASP* 2.0 60.8 + - + +
29A ILE* 4.1 4.1 - - + +
30A THR* 6.2 0.2 - - - +
33A GLN* 4.0 20.8 + - - +
70A ASN* 3.3 15.9 + - - +
71A LEU* 3.2 10.3 + - + +
72A GLU 3.1 0.4 - - - -
73A ARG* 1.3 80.3 - - + +
75A LYS* 1.3 70.4 + - - +
76A LEU* 3.6 31.3 - - + +
96A SER* 5.0 1.4 + - - -
12H T 5.8 3.6 - - - -
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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