Contacts of the helix formed by residues 75 - 89 (chain A) in PDB entry 2XZ0
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 GLY 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A SER* 2.7 16.8 + - - -
74A ASP* 1.3 73.5 - - - +
76A PHE* 1.3 56.8 + - - -
77A ASP 3.4 2.2 - - - -
78A GLU* 3.4 20.3 - - - +
79A GLN* 2.9 44.9 + - - +
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Residues in contact with PHE 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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69A PRO* 3.9 12.1 - - + -
70A ASP 3.3 15.2 + - - +
71A PRO* 3.4 30.7 - - + -
73A SER 2.8 11.2 + - - +
74A ASP 3.3 1.0 - - - -
75A GLY* 1.3 76.0 - - - +
77A ASP* 1.3 77.1 + - - +
79A GLN* 3.2 12.1 + - - +
80A VAL* 2.9 50.7 + - + +
156A LEU* 5.3 0.2 - - + -
80B VAL* 4.1 9.6 - - + -
84B ARG* 3.5 43.1 - - - +
155B TYR* 4.0 12.6 - + - -
156B LEU* 4.3 22.4 - - + -
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Residues in contact with ASP 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASP 4.8 3.9 + - - +
75A GLY 3.4 0.4 - - - -
76A PHE* 1.3 93.5 - - - +
78A GLU* 1.3 64.4 + - - +
80A VAL* 3.2 4.8 + - - +
81A ARG* 2.8 34.9 + - - +
80B VAL* 5.8 1.4 - - - +
84B ARG* 4.9 4.5 + - - -
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Residues in contact with GLU 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 ASP 5.3 1.5 + - - +
75A GLY* 3.4 25.9 - - - +
77A ASP* 1.3 78.5 - - - +
79A GLN* 1.3 60.5 + - + +
81A ARG* 3.3 31.6 + - - +
82A GLU* 2.8 39.3 + - + +
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Residues in contact with GLN 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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69A PRO* 3.8 17.5 - - + +
70A ASP* 2.8 34.6 + - - +
73A SER* 4.4 6.3 + - - -
75A GLY* 2.9 31.1 + - - +
76A PHE* 3.3 9.1 - - - +
78A GLU* 1.3 83.7 + - + +
80A VAL* 1.3 57.4 + - - +
82A GLU* 3.3 6.4 + - - +
83A LEU* 2.9 28.1 + - - +
217A LYS* 5.8 5.2 - - - +
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PRO* 3.8 15.3 - - + -
76A PHE* 2.9 47.3 + - + +
77A ASP* 3.7 6.1 - - - +
79A GLN* 1.3 69.8 - - - +
81A ARG* 1.3 67.9 + - - +
82A GLU 3.2 0.2 + - - -
83A LEU* 3.3 4.9 + - - +
84A ARG* 3.1 41.0 + - + +
156A LEU* 4.2 19.1 - - + -
76B PHE* 4.2 17.3 - - + -
77B ASP* 5.6 2.2 - - - +
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Residues in contact with ARG 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ASP* 2.8 28.9 + - - +
78A GLU* 3.3 39.8 + - - +
80A VAL* 1.3 75.6 - - - +
82A GLU* 1.3 63.2 + - + +
84A ARG* 3.2 9.4 + - - +
85A GLU* 3.0 36.9 + - - +
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Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU* 2.8 24.2 + - + +
79A GLN* 3.4 10.1 - - - +
81A ARG* 1.3 69.4 - - + +
83A LEU* 1.3 67.5 + - - +
84A ARG 2.9 3.0 + - - -
85A GLU* 3.1 8.0 + - - +
86A ARG* 2.9 62.4 + - + +
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Residues in contact with LEU 83 (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 PHE 5.9 1.1 - - - +
68A LEU* 5.0 2.5 - - + -
69A PRO* 3.9 27.1 - - + -
79A GLN 2.9 15.2 + - - +
80A VAL* 3.5 10.3 - - - +
82A GLU* 1.3 72.1 - - - +
84A ARG* 1.3 57.2 + - + +
86A ARG* 3.6 8.1 - - - +
87A ALA* 3.0 23.7 + - - +
153A TYR* 3.6 41.1 + - + -
156A LEU* 4.0 19.3 - - + +
157A SER* 3.8 29.8 - - - +
215A ASP* 4.7 0.8 - - - +
221A ILE* 6.2 0.2 - - + -
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Residues in contact with ARG 84 (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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80A VAL* 3.1 29.8 + - + +
81A ARG* 3.5 10.5 - - - +
82A GLU 2.9 1.0 - - - -
83A LEU* 1.3 78.1 - - + +
85A GLU* 1.3 65.1 + - - +
87A ALA* 3.1 17.0 + - - +
88A LYS* 3.3 21.1 + - - +
156A LEU 2.9 26.4 + - - +
157A SER 3.8 9.9 - - - +
158A GLY* 4.0 2.8 - - - -
159A ARG* 5.5 0.2 - - - -
71B PRO* 2.3 42.0 + - - +
73B SER 5.7 0.6 + - - -
76B PHE* 3.3 31.8 - - - +
77B ASP* 5.0 6.0 + - - -
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Residues in contact with GLU 85 (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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81A ARG* 3.0 29.6 + - - +
82A GLU* 3.5 10.5 - - - +
84A ARG* 1.3 73.1 - - - +
86A ARG* 1.3 78.7 + - - +
88A LYS* 3.2 48.1 + - + +
89A GLU* 3.9 7.8 + - - +
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Residues in contact with ARG 86 (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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82A GLU* 2.9 43.5 + - + +
83A LEU* 3.6 10.1 - - - +
85A GLU* 1.3 92.1 - - - +
87A ALA* 1.3 65.1 + - - +
89A GLU* 3.2 23.5 + - - +
90A ILE* 3.7 8.5 + - - +
213A HIS 5.3 0.5 - - - +
214A GLY 3.9 21.3 + - - -
215A ASP* 3.2 31.7 - - + +
217A LYS* 6.6 0.2 - - + -
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Residues in contact with ALA 87 (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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83A LEU 3.0 16.5 + - - +
84A ARG* 3.1 12.7 + - - +
86A ARG* 1.3 76.0 - - - +
88A LYS* 1.3 58.5 + - - +
90A ILE* 2.8 36.6 + - - +
95A PHE* 3.7 2.1 - - + -
153A TYR* 4.2 7.0 - - - +
157A SER* 4.1 18.4 - - - +
159A ARG* 3.2 30.8 + - + -
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Residues in contact with LYS 88 (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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84A ARG* 3.5 17.0 - - - +
85A GLU* 3.5 32.7 + - + +
86A ARG 3.2 0.4 - - - -
87A ALA* 1.3 76.0 - - - +
89A GLU* 1.3 66.1 + - + +
90A ILE 3.3 8.0 + - - +
159A ARG* 3.9 19.8 + - - +
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Residues in contact with GLU 89 (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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85A GLU 4.2 8.5 - - - +
86A ARG* 3.2 15.5 + - - +
88A LYS* 1.3 78.8 - - + +
90A ILE* 1.3 61.2 + - - +
91A PRO* 3.7 6.6 - - - +
213A HIS* 4.2 24.6 + - - +
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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