Contacts of the helix formed by residues 70 - 82 (chain A) in PDB entry 4XXL
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 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A LYS* 4.0 14.4 - - - +
69A ALA* 1.3 76.1 + - + +
71A ALA* 1.3 66.9 + - - +
72A GLU 3.3 2.0 - - - -
73A ALA* 3.3 14.5 + - + +
74A LYS* 2.9 54.4 + - + +
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Residues in contact with ALA 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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65A TYR* 4.0 32.9 - - + +
68A LYS* 3.1 18.0 + - + +
69A ALA 3.4 1.2 - - - -
70A ASP* 1.3 80.1 + - - +
72A GLU* 1.3 65.0 + - - +
74A LYS* 3.3 2.8 + - - +
75A LEU* 3.0 29.1 + - - +
115A LEU* 3.9 22.9 - - + -
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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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69A ALA 5.1 1.2 + - - -
70A ASP 3.3 0.4 - - - -
71A ALA* 1.3 79.3 - - - +
73A ALA* 1.3 64.6 + - - +
75A LEU 3.3 0.2 + - - -
76A ILE* 2.9 43.6 + - + +
108A LYS* 3.0 39.1 + - + +
111A VAL* 3.7 7.9 - - + +
112A ASP* 2.5 30.1 - - - +
115A LEU* 3.7 13.3 - - + +
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Residues in contact with ALA 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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70A ASP* 3.3 16.5 + - + +
72A GLU* 1.3 79.9 + - - +
74A LYS* 1.4 58.9 + - + +
76A ILE* 3.4 9.4 + - - +
77A HIS* 2.9 30.0 + - - +
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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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65A TYR* 4.1 28.5 - - + +
68A LYS* 6.0 2.9 - - - -
70A ASP* 2.9 52.4 + - + +
71A ALA 3.7 3.8 - - - +
72A GLU 3.2 0.2 - - - -
73A ALA* 1.4 78.7 - - + +
75A LEU* 1.3 58.9 + - - +
77A HIS* 3.5 12.0 + - + +
78A HIS* 2.9 25.3 + - - +
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Residues in contact with LEU 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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61A VAL* 4.0 16.4 - - + -
65A TYR* 3.7 30.5 - - + +
71A ALA 3.0 14.6 + - - +
74A LYS* 1.3 75.6 - - - +
76A ILE* 1.3 68.4 + - - +
77A HIS 3.2 0.4 - - - -
78A HIS* 3.5 6.7 + - + +
79A VAL* 3.0 26.5 + - - +
111A VAL* 3.6 24.5 - - + +
114A ILE* 4.1 9.9 - - + -
115A LEU* 3.6 32.3 - - + -
201A HEC 3.9 37.4 - - + +
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Residues in contact with ILE 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 GLU* 2.9 41.3 + - + +
73A ALA* 3.8 7.6 - - - +
75A LEU* 1.3 78.1 - - - +
77A HIS* 1.4 55.2 + - - +
79A VAL* 3.4 3.1 + - - +
80A THR* 2.7 41.6 + - + +
107A ILE* 4.5 15.3 - - + -
108A LYS* 4.2 23.3 - - + +
111A VAL* 3.9 19.7 - - + -
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Residues in contact with HIS 77 (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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73A ALA 2.9 18.9 + - - +
74A LYS* 3.5 11.0 - - + +
76A ILE* 1.4 75.6 - - - +
78A HIS* 1.3 68.9 + - - +
80A THR* 3.2 7.2 + - - -
81A SER* 2.9 39.7 + - - -
83A GLU* 3.0 37.5 + - - -
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Residues in contact with HIS 78 (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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74A LYS 2.9 18.0 + - - +
75A LEU* 3.2 13.6 + - + +
77A HIS* 1.3 82.3 - - + +
79A VAL* 1.3 63.4 + - - +
80A THR 3.5 0.5 + - - -
81A SER* 3.7 11.8 + - - -
82A GLY 4.4 4.5 + - - -
83A GLU* 5.2 11.7 + - + -
84A LYS 5.7 3.6 + - - -
85A ALA* 5.7 0.6 - - - +
95A HIS* 3.4 40.2 + + + +
201A HEC 3.3 75.8 - + + +
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Residues in contact with VAL 79 (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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75A LEU 3.0 15.7 + - - +
76A ILE* 3.5 14.1 - - - +
78A HIS* 1.3 81.0 - - - +
80A THR* 1.3 59.1 + - + +
81A SER 3.7 0.7 - - - -
95A HIS* 4.7 2.7 - - + -
96A LYS 4.2 10.8 - - - +
97A ASN* 3.4 3.3 - - - -
98A ILE* 2.8 45.0 + - + +
107A ILE* 3.9 25.1 - - + -
110A LEU* 5.7 1.3 - - + -
111A VAL* 4.7 6.5 - - + -
201A HEC 3.8 40.6 - - + -
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Residues in contact with THR 80 (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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76A ILE* 2.7 31.2 + - + +
77A HIS* 3.2 7.7 + - - -
79A VAL* 1.3 89.7 - - + +
81A SER* 1.3 54.4 + - - +
97A ASN* 3.2 21.1 + - - +
98A ILE 4.7 0.2 - - - -
99A ASN* 3.6 42.3 + - - +
107A ILE* 4.2 20.4 - - + -
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Residues in contact with SER 81 (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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77A HIS* 2.9 35.7 + - - -
78A HIS* 3.7 6.4 + - - -
79A VAL 3.7 0.2 - - - -
80A THR* 1.3 78.8 - - - +
82A GLY* 1.3 65.7 + - - +
83A GLU* 3.5 29.8 + - - +
97A ASN* 3.7 9.0 + - - +
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Residues in contact with GLY 82 (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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78A HIS 4.4 4.4 + - - -
81A SER* 1.3 79.8 + - - +
83A GLU* 1.3 65.9 + - - +
94A GLU* 3.3 24.9 - - - +
95A HIS* 3.4 25.3 + - - -
96A LYS 5.0 0.2 + - - -
97A ASN* 3.8 12.7 - - - +
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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