Contacts of the helix formed by residues 85 - 98 (chain A) in PDB entry 2XGZ
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 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A ASP* 2.9 26.4 + - + +
83A VAL 4.1 1.6 - - - -
84A LYS* 1.3 75.6 - - - +
86A GLN* 1.3 61.3 + - - +
87A LYS* 3.5 11.6 + - - +
88A ALA* 3.0 31.4 + - + +
89A VAL* 3.0 22.3 + - - +
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Residues in contact with GLN 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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83A VAL 4.3 4.8 - - - +
84A LYS 3.2 5.3 + - - -
85A ASP* 1.3 74.7 + - - +
87A LYS* 1.3 59.8 + - + +
89A VAL* 3.2 13.1 + - - +
90A ASP* 2.9 47.6 + - - +
114A SER* 3.0 29.3 + - - +
117A ALA* 4.3 2.1 - - - +
118A SER* 3.4 29.1 + - - -
132A HIS* 4.9 0.4 + - - +
136A LEU* 3.6 34.0 - - + +
352A LEU* 3.7 18.8 - - + +
353A SER* 3.2 18.3 + - - +
356A ILE* 5.3 1.3 - - + -
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Residues in contact with LYS 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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85A ASP* 3.2 8.4 + - - +
86A GLN* 1.3 78.6 - - + +
88A ALA* 1.3 56.5 + - - +
90A ASP* 3.8 0.9 - - - +
91A ASP* 2.8 43.2 + - - +
136A LEU 5.8 3.7 + - - -
138A LYS* 6.2 2.6 - - - +
353A SER* 3.5 18.8 - - - +
360A GLN* 5.8 2.4 + - - +
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Residues in contact with ALA 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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81A ILE* 4.5 13.1 - - + +
82A ASP 5.9 0.4 - - - +
85A ASP* 3.0 35.7 + - + +
87A LYS* 1.3 72.3 - - - +
89A VAL* 1.3 66.1 + - - +
91A ASP* 3.8 7.8 - - - +
92A PHE* 3.0 24.8 + - - +
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Residues in contact with VAL 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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76A PHE* 3.8 20.8 - - + -
81A ILE* 3.7 24.6 - - + +
83A VAL* 4.0 21.1 - - - +
85A ASP 3.0 17.8 + - - +
86A GLN* 3.2 14.3 + - - +
88A ALA* 1.3 76.8 - - - +
90A ASP* 1.3 63.3 + - - +
92A PHE* 3.4 3.8 + - - +
93A LEU* 3.1 39.6 + - + +
113A VAL 4.8 0.2 - - - +
114A SER* 4.5 1.8 - - - -
117A ALA* 3.8 26.9 - - + -
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Residues in contact with ASP 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLN* 2.9 26.3 + - - +
87A LYS 4.1 0.9 - - - +
89A VAL* 1.3 75.4 - - - +
91A ASP* 1.3 60.7 + - - +
93A LEU* 3.7 8.5 - - - +
94A ILE* 2.9 41.1 + - + +
114A SER* 2.6 29.2 + - - -
351A THR* 3.5 19.5 - - + +
353A SER* 2.7 45.7 + - - +
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Residues in contact with ASP 91 (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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87A LYS* 2.8 29.1 + - - +
88A ALA* 3.4 8.0 + - - +
90A ASP* 1.3 75.4 - - - +
92A PHE* 1.3 61.4 + - - +
94A ILE* 4.0 10.1 - - - +
95A SER* 3.1 25.5 + - - -
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Residues in contact with PHE 92 (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 ALA* 3.5 30.1 - - + -
76A PHE* 3.8 29.8 - + + -
79A ALA* 3.5 19.5 - - + -
81A ILE* 3.6 21.1 - - + -
88A ALA 3.0 13.4 + - - +
89A VAL 3.5 8.3 - - - +
90A ASP 3.2 0.2 - - - -
91A ASP* 1.3 76.5 - - - +
93A LEU* 1.3 66.1 + - + +
95A SER* 2.9 24.0 + - - -
96A LEU* 3.2 35.5 + - + +
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Residues in contact with LEU 93 (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 ILE* 3.7 38.8 - - + -
76A PHE* 4.0 10.5 - - + -
89A VAL* 3.1 26.9 + - + +
90A ASP* 3.3 24.8 + - - +
92A PHE* 1.3 78.7 - - + +
94A ILE* 1.3 62.8 + - - +
96A LEU* 3.2 16.6 + - + +
97A ASP* 3.2 13.5 + - - +
105A LEU* 4.6 2.0 - - - +
110A ILE* 3.9 31.3 - - + +
113A VAL* 3.9 12.3 - - + -
114A SER* 3.8 24.5 - - - +
351A THR* 5.1 0.4 - - + -
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Residues in contact with ILE 94 (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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90A ASP* 2.9 27.2 + - + +
91A ASP* 4.0 11.2 - - - +
93A LEU* 1.3 75.4 - - - +
95A SER* 1.3 58.5 + - - +
97A ASP* 3.4 6.2 + - - +
98A GLY* 3.0 26.3 + - - -
99A THR 4.9 6.0 + - - +
102A LYS* 4.4 13.0 - - + +
110A ILE* 5.4 2.5 - - + -
351A THR* 4.2 18.2 - - + +
353A SER* 6.2 0.4 - - - -
354A GLU* 3.8 32.5 - - + +
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Residues in contact with SER 95 (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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91A ASP 3.1 16.9 + - - -
92A PHE* 2.9 22.9 + - - -
93A LEU 3.2 0.2 - - - -
94A ILE* 1.3 74.7 - - - +
96A LEU* 1.3 68.5 + - - +
98A GLY* 3.8 9.1 + - - +
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Residues in contact with LEU 96 (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 VAL* 4.6 8.3 - - + +
72A ILE* 4.1 34.8 - - + +
75A ALA* 4.1 13.2 - - + -
92A PHE* 3.2 45.5 + - + +
93A LEU* 3.2 10.7 + - - +
95A SER* 1.3 86.6 + - - +
97A ASP* 1.3 63.2 + - - +
98A GLY* 4.5 0.3 - - - -
104A LYS* 5.0 3.3 - - - +
105A LEU* 4.1 10.7 - - + +
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Residues in contact with ASP 97 (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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93A LEU 3.2 3.5 + - - +
94A ILE* 3.9 7.4 - - - +
96A LEU* 1.3 82.4 - - - +
98A GLY* 1.3 60.6 + - - +
99A THR* 2.7 45.6 + - - +
102A LYS* 3.3 17.0 - - + +
104A LYS* 3.2 27.1 + - - +
105A LEU* 2.9 41.0 + - + +
110A ILE* 3.7 22.2 - - + +
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Residues in contact with GLY 98 (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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94A ILE* 3.0 15.9 + - - -
95A SER* 4.2 9.0 - - - -
96A LEU 3.4 1.8 - - - -
97A ASP* 1.3 74.5 - - - +
99A THR* 1.3 62.2 + - - +
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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