Contacts of the helix formed by residues 60 - 74 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I ARG* 1.3 78.0 - - - +
61I GLY* 1.3 64.2 + - - +
62I PRO* 3.5 17.8 - - - +
63I THR* 3.0 26.5 + - - +
64I VAL* 3.2 10.1 + - - +
14J HIS* 6.3 1.3 - - - +
18J GLN* 5.8 5.8 - - - +
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Residues in contact with GLY 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I GLN* 5.8 0.5 + - - -
51I ASN* 5.3 5.4 + - - -
54I ALA* 4.4 13.6 - - - +
59I ARG 3.7 1.8 + - - -
60I THR* 1.3 70.7 - - - +
62I PRO* 1.3 67.9 - - - +
64I VAL* 3.5 4.8 + - - +
65I SER* 3.2 21.5 + - - -
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Residues in contact with PRO 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60I THR* 3.5 15.9 - - - +
61I GLY* 1.3 85.2 - - - +
63I THR* 1.3 67.9 + - - +
65I SER* 3.2 9.4 + - - -
66I ASN* 3.1 17.8 + - - +
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Residues in contact with THR 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59I ARG* 4.0 28.6 - - + +
60I THR* 3.0 25.2 + - - +
62I PRO* 1.3 76.5 - - - +
64I VAL* 1.3 56.9 + - + +
66I ASN* 2.7 30.3 + - + +
67I LEU* 3.0 20.5 + - + -
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Residues in contact with VAL 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I GLN* 3.7 25.6 - - + +
53I ILE* 4.3 14.4 - - + -
54I ALA* 3.6 34.3 - - + +
57I LEU* 6.2 1.3 - - + -
59I ARG* 4.2 11.9 - - + +
60I THR 3.2 7.0 + - - +
61I GLY* 3.8 7.6 - - - +
63I THR* 1.3 80.9 - - + +
65I SER* 1.3 57.1 + - - +
67I LEU* 3.9 5.1 - - - +
68I LEU* 2.9 56.9 + - + +
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Residues in contact with SER 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I GLN* 4.4 19.9 + - - +
61I GLY 3.2 12.5 + - - -
62I PRO* 3.6 10.5 - - - -
63I THR 3.1 0.8 + - - -
64I VAL* 1.3 76.3 - - - +
66I ASN* 1.3 57.5 + - - +
68I LEU* 4.0 2.7 - - - +
69I ARG* 2.8 29.8 + - - +
79I ARG* 4.6 8.5 + - - +
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Residues in contact with ASN 66 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62I PRO 3.1 9.7 + - - +
63I THR* 2.7 18.0 + - - +
65I SER* 1.3 72.2 - - - +
67I LEU* 1.3 64.5 + - - +
69I ARG* 3.3 7.5 + - - +
70I ASN* 3.1 43.5 + - - +
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Residues in contact with LEU 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I THR* 5.5 0.2 - - - +
32I GLU* 3.8 38.8 - - + +
33I GLN* 4.1 12.7 + - + +
36I THR* 4.1 22.7 - - + +
63I THR* 3.0 18.4 + - + +
64I VAL* 3.9 9.4 - - - +
66I ASN* 1.3 75.7 - - - +
68I LEU* 1.3 62.1 + - + +
70I ASN* 3.2 12.3 + - - +
71I LEU* 2.9 54.7 + - + +
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Residues in contact with LEU 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36I THR* 4.3 14.1 - - + -
40I LEU* 5.0 1.6 - - + -
50I GLN* 3.6 35.7 - - + +
53I ILE* 4.5 6.3 - - + -
64I VAL* 2.9 33.3 + - + +
65I SER* 4.0 4.3 - - - +
67I LEU* 1.3 81.4 - - + +
69I ARG* 1.3 55.4 + - - +
71I LEU* 4.2 14.4 - - + -
72I GLU* 2.7 37.5 + - - +
77I ILE* 3.5 22.8 - - + +
79I ARG* 4.4 10.1 - - - +
91I ILE* 4.2 20.4 - - + -
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Residues in contact with ARG 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65I SER 2.8 20.4 + - - +
66I ASN* 3.4 13.2 - - - +
67I LEU 3.3 0.2 - - - -
68I LEU* 1.3 75.8 - - - +
70I ASN* 1.3 67.4 + - - +
72I GLU* 3.5 7.0 + - - +
73I ARG* 3.0 22.3 + - - +
79I ARG* 4.8 10.7 - - - +
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Residues in contact with ASN 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I GLN* 4.0 20.9 - - - +
66I ASN* 3.1 31.0 + - - +
67I LEU* 3.4 9.3 - - - +
69I ARG* 1.3 81.7 - - - +
71I LEU* 1.3 62.9 + - - +
73I ARG* 3.1 17.0 + - - +
74I LYS* 3.1 22.2 + - - +
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Residues in contact with LEU 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I ILE* 5.3 0.7 - - + -
33I GLN* 3.7 26.0 - - + +
36I THR* 4.5 5.6 - - + -
37I LEU* 3.7 42.2 - - + -
67I LEU* 2.9 42.7 + - + +
68I LEU* 3.1 12.8 + - + +
70I ASN* 1.3 73.7 - - - +
72I GLU* 1.3 65.4 + - - +
74I LYS* 3.1 15.9 + - + +
75I LYS 3.2 7.8 + - - -
76I LEU* 3.3 24.5 + - + -
77I ILE* 3.6 23.3 + - + +
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Residues in contact with GLU 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68I LEU 2.7 19.4 + - - +
69I ARG* 3.8 6.5 - - - +
71I LEU* 1.3 71.8 - - - +
73I ARG* 1.3 57.8 + - - +
75I LYS* 2.9 20.8 + - - +
77I ILE* 3.6 18.6 - - + +
78I TYR* 4.0 2.8 - - - +
79I ARG* 2.4 70.8 + - - +
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Residues in contact with ARG 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69I ARG 3.0 14.3 + - - +
70I ASN* 3.1 13.0 + - - +
72I GLU* 1.3 78.5 - - - +
74I LYS* 1.3 61.4 + - + +
75I LYS* 3.4 2.8 + - - +
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Residues in contact with LYS 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I ASP* 2.3 49.8 + - - +
29I ILE* 3.7 3.6 - - + +
30I THR* 4.7 3.4 - - - +
33I GLN* 3.5 31.0 + - - +
70I ASN* 3.2 17.0 - - - +
71I LEU* 3.1 10.4 + - + +
73I ARG* 1.3 76.5 - - + +
75I LYS* 1.3 67.2 + - - +
76I LEU* 3.3 32.4 + - + +
96I SER* 5.0 0.3 + - - -
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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