Contacts of the helix formed by residues 63 - 76 (chain A) in PDB entry 4LGD
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 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A GLU 3.4 6.9 + - - +
62A SER* 1.3 79.8 - - - +
64A LEU* 1.3 64.1 + - - +
65A GLN* 3.3 3.5 + - + +
66A GLU* 3.1 45.6 + - + +
67A ILE* 3.8 13.5 + - - +
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Residues in contact with LEU 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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60A VAL* 4.0 23.7 + - + +
62A SER 3.7 0.8 - - - -
63A ASP* 1.3 71.9 - - - +
65A GLN* 1.3 87.1 + - + +
66A GLU 3.4 0.2 + - - -
67A ILE* 3.4 6.7 + - - +
68A ILE* 3.1 45.0 + - + +
95A LEU* 6.5 1.1 - - + -
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Residues in contact with GLN 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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63A ASP* 3.3 2.8 - - + -
64A LEU* 1.3 93.3 - - + +
66A GLU* 1.3 67.2 + - + +
68A ILE* 4.1 4.1 - - - +
69A LYS* 3.2 43.3 + - - +
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Residues in contact with GLU 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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38A TYR* 5.1 10.4 - - - -
63A ASP* 3.1 38.5 + - + +
64A LEU 3.3 0.6 - - - -
65A GLN* 1.3 80.6 - - + +
67A ILE* 1.3 69.5 + - + +
69A LYS* 3.5 19.1 + - - +
70A GLU* 3.6 10.6 + - - +
167A VAL* 6.0 1.7 - - - +
176A ALA* 5.0 11.8 - - - +
177A LYS* 5.2 17.4 - - + +
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Residues in contact with ILE 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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38A TYR* 4.6 23.8 - - + -
56A LYS* 5.7 2.9 - - - +
58A VAL* 4.4 28.7 - - + -
62A SER 4.8 4.3 - - - +
63A ASP 3.8 13.9 + - - +
64A LEU* 3.4 9.3 + - - +
65A GLN 3.4 0.4 - - - -
66A GLU* 1.3 78.8 - - + +
68A ILE* 1.3 64.0 + - + +
70A GLU* 3.2 17.0 + - - +
71A ILE* 3.1 35.1 + - + +
95A LEU* 4.3 13.9 - - + -
97A ILE* 4.1 15.9 - - + -
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Residues in contact with ILE 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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64A LEU* 3.1 39.9 + - + +
65A GLN* 4.1 4.7 - - - +
67A ILE* 1.3 76.0 - - - +
69A LYS* 1.3 58.8 + - - +
71A ILE* 3.1 19.0 + - + +
72A SER* 2.9 31.0 + - - -
95A LEU* 4.9 12.6 - - + -
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Residues in contact with LYS 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 GLN* 3.2 39.7 + - - +
66A GLU* 3.7 12.7 - - - +
67A ILE 3.2 0.6 - - - -
68A ILE* 1.3 76.8 - - - +
70A GLU* 1.3 59.7 + - - +
72A SER* 2.8 22.4 + - - +
73A ILE* 3.3 22.9 - - + +
167A VAL* 4.1 29.3 - - + +
168A ALA 5.6 2.1 + - - +
173A ASP* 4.3 16.0 + - - -
177A LYS* 6.1 0.2 - - - +
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Residues in contact with GLU 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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56A LYS* 5.8 2.3 + - - -
66A GLU 3.6 6.5 + - - +
67A ILE* 3.2 18.3 + - - +
69A LYS* 1.3 76.2 - - - +
71A ILE* 1.3 66.5 + - + +
73A ILE* 3.2 9.4 + - + +
74A MET* 3.1 40.7 + - + +
164A ASP* 3.5 33.4 + - - +
165A PHE* 3.7 20.4 + - + +
167A VAL* 5.4 9.8 - - + +
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Residues in contact with ILE 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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67A ILE* 3.1 25.0 + - + +
68A ILE* 3.3 20.6 - - + +
70A GLU* 1.3 78.1 - - + +
72A SER* 1.3 63.1 + - - +
74A MET* 3.4 8.8 + - + -
75A GLN* 3.1 29.4 + - - +
85A TYR* 3.5 39.3 - - + +
88A SER* 4.2 5.8 - - - +
95A LEU* 4.3 9.9 - - + -
97A ILE* 3.9 34.1 - - + -
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Residues in contact with SER 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 ILE* 2.9 16.4 + - - -
69A LYS* 2.8 26.3 + - - +
71A ILE* 1.3 80.2 - - - +
73A ILE* 1.3 62.7 + - - +
75A GLN* 4.1 7.7 - - - +
76A GLN* 3.4 24.5 + - - +
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Residues in contact with ILE 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 LYS* 3.3 22.2 - - + +
70A GLU* 3.2 10.7 + - - +
71A ILE 3.2 0.2 - - - -
72A SER* 1.3 80.2 - - - +
74A MET* 1.3 61.8 + - - +
76A GLN* 3.1 28.4 - - - +
77A CYS* 3.4 10.0 - - - -
142A LYS* 3.8 20.2 - - - +
165A PHE* 4.1 26.2 - - + -
166A GLY 4.6 4.7 - - - +
167A VAL* 4.3 28.5 - - + -
168A ALA 5.2 2.2 - - - +
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Residues in contact with MET 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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70A GLU* 3.1 36.7 + - + +
71A ILE* 4.1 8.7 - - + +
73A ILE* 1.3 75.0 - - + +
75A GLN* 1.3 64.9 + - - +
76A GLN 3.2 0.7 - - - -
77A CYS* 3.1 27.0 + - - +
82A VAL* 5.9 2.0 - - + -
83A VAL* 4.8 18.3 - - - +
85A TYR* 4.3 32.9 + - + +
97A ILE* 5.4 4.7 - - + -
99A MET* 4.1 28.9 - - + +
163A ALA* 5.3 3.4 - - - -
164A ASP 4.9 12.1 - - - -
165A PHE* 4.8 21.5 - - + -
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Residues in contact with GLN 75 (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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71A ILE* 3.1 22.5 + - - +
72A SER* 4.4 6.5 - - - +
74A MET* 1.3 77.1 - - - +
76A GLN* 1.3 58.4 + - - +
77A CYS 3.2 6.7 + - - +
85A TYR* 3.5 44.4 - - + +
86A TYR 4.5 12.3 + - - -
87A GLY* 4.5 4.2 - - - -
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Residues in contact with GLN 76 (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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72A SER 3.4 14.8 + - - +
73A ILE* 3.1 28.6 - - - +
75A GLN* 1.3 77.1 - - - +
77A CYS* 1.3 58.4 + - - +
78A ASP* 4.0 2.6 + - - +
136A TYR* 4.8 0.5 + - - -
140A MET* 4.7 13.9 - - - +
142A LYS* 3.7 27.9 + - + +
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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