Contacts of the helix formed by residues 86 - 110 (chain A) in PDB entry 5XA0
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 ALA 86 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ASP* 1.3 71.7 - - - +
87A VAL* 1.3 61.0 + - + +
89A LEU* 3.0 20.8 + - - +
90A ASN* 2.3 26.8 + - - +
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ASP* 3.3 6.7 - - + -
86A ALA* 1.3 77.0 - - + +
88A LEU* 1.3 67.1 + - + +
90A ASN* 2.6 28.9 + - + +
91A LYS* 3.0 44.9 + - + +
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ASP* 3.0 45.5 - - + +
86A ALA 3.2 0.4 - - - -
87A VAL* 1.3 79.1 - - + +
89A LEU* 1.3 55.8 + - + +
91A LYS* 3.8 11.9 - - + +
92A LEU* 2.9 37.4 + - + +
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 3.9 30.3 - - + -
76A ALA* 6.4 0.2 - - + -
85A ASP 3.4 21.4 + - - +
86A ALA* 3.0 12.5 + - - +
88A LEU* 1.3 77.3 - - + +
90A ASN* 1.3 54.1 + - - +
92A LEU* 5.8 1.3 - - + -
93A HIS* 2.7 38.6 + - - +
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Residues in contact with ASN 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ALA 2.3 33.7 + - - +
87A VAL* 2.6 27.6 + - + +
89A LEU* 1.3 73.3 - - - +
91A LYS* 1.3 58.5 + - + +
93A HIS* 3.4 5.6 + - - +
94A HIS* 2.8 28.2 + - - +
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Residues in contact with LYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A VAL* 3.0 48.6 + - + +
88A LEU* 3.8 11.4 - - + +
90A ASN* 1.3 74.8 - - + +
92A LEU* 1.3 58.3 + - - +
94A HIS* 2.6 29.6 + - - +
95A ALA* 2.9 10.9 + - - +
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Residues in contact with LEU 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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68A ALA 3.1 15.9 - - - +
71A GLN* 3.0 29.8 - - + +
72A PHE* 2.7 62.3 - - + +
75A ALA* 5.7 5.4 - - + -
88A LEU* 2.9 22.6 + - + +
89A LEU* 5.8 1.3 - - + -
91A LYS* 1.3 72.4 - - - +
93A HIS* 1.3 61.1 + - - +
95A ALA* 3.2 10.8 - - + +
96A ALA* 3.0 16.5 + - - +
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Residues in contact with HIS 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 3.5 16.0 - + + -
89A LEU 2.7 24.8 + - - +
90A ASN* 3.5 7.4 + - - +
92A LEU* 1.3 77.5 - - - +
94A HIS* 1.3 54.7 + - - +
96A ALA* 2.7 33.2 + - + +
97A ASP* 3.0 21.4 + - + +
100A LYS* 5.8 4.2 + - - -
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Residues in contact with HIS 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 ASN 2.8 13.9 + - - +
91A LYS* 2.6 20.5 + - - +
93A HIS* 1.3 72.1 + - - +
95A ALA* 1.3 57.7 + - - +
97A ASP* 3.6 7.1 + - + +
98A LEU* 2.8 65.6 + - + +
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Residues in contact with ALA 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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68A ALA* 2.8 44.5 - - + +
69A GLN 4.3 0.9 - - - -
91A LYS 2.9 8.8 + - - +
92A LEU* 3.2 15.3 - - + +
94A HIS* 1.3 76.3 - - - +
96A ALA* 1.3 61.9 + - - +
98A LEU* 3.3 12.9 + - - +
99A GLU* 3.0 24.3 + - - +
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Residues in contact with ALA 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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69A GLN* 2.3 50.6 + - - +
72A PHE* 5.1 6.7 - - + -
92A LEU 3.0 9.7 + - - +
93A HIS* 2.7 34.2 + - + +
95A ALA* 1.3 71.8 - - - +
97A ASP* 1.3 55.2 + - - +
99A GLU 3.3 0.2 + - - -
100A LYS* 2.8 24.0 + - + +
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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 HIS* 3.0 21.1 + - + +
94A HIS* 3.6 9.2 + - + +
96A ALA* 1.3 78.0 - - - +
98A LEU* 1.4 56.2 + - + +
100A LYS* 4.1 9.0 - - + -
101A LYS* 2.8 41.5 + - + +
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Residues in contact with LEU 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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68A ALA* 5.9 1.8 - - + -
94A HIS* 2.8 62.8 + - + +
95A ALA* 3.3 10.3 + - - +
97A ASP* 1.4 78.6 - - + +
99A GLU* 1.3 50.9 + - + +
101A LYS* 5.0 0.4 - - - -
102A GLN* 2.5 63.0 + - - +
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Residues in contact with GLU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ARG* 2.1 63.4 + - - +
66A TYR* 2.5 15.9 + - + -
67A SER* 2.5 25.4 + - - -
68A ALA* 3.1 15.3 + - + +
69A GLN* 2.4 37.4 - - + +
95A ALA 3.0 8.5 + - - +
96A ALA 3.3 0.2 + - - -
98A LEU* 1.3 76.4 - - + +
100A LYS* 1.3 53.0 + - - +
102A GLN* 4.0 5.6 - - - +
103A ASN* 2.2 19.3 + - - -
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Residues in contact with LYS 100 (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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66A TYR* 2.8 29.6 - - + +
69A GLN* 3.1 0.8 - - - +
93A HIS* 5.8 4.2 + - - -
96A ALA* 2.8 31.0 + - + +
97A ASP* 4.1 6.7 - - + -
99A GLU* 1.3 74.2 - - - +
101A LYS* 1.3 56.9 + - - +
103A ASN* 3.1 12.2 - - - +
104A GLU* 3.1 23.0 + - - +
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Residues in contact with LYS 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASP* 2.8 23.5 + - + +
98A LEU* 4.6 0.4 - - - +
100A LYS* 1.3 74.2 - - - +
102A GLN* 1.4 60.2 + - - +
103A ASN 3.2 0.9 - - - -
104A GLU* 2.9 28.7 - - + +
105A THR* 3.2 9.4 + - - -
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Residues in contact with GLN 102 (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 ARG* 2.8 27.3 + - - +
98A LEU* 2.5 58.5 + - - +
99A GLU* 3.8 11.4 - - - +
101A LYS* 1.4 68.0 - - - +
103A ASN* 1.3 68.3 + - - +
105A THR* 3.3 8.8 + - - -
106A GLU* 2.9 18.3 + - + +
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Residues in contact with ASN 103 (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 ASN* 2.6 50.9 + - - +
65A ARG* 2.6 31.9 + - - +
66A TYR* 3.9 6.1 - - - -
99A GLU 2.2 30.4 + - - -
100A LYS* 3.1 14.2 - - - +
102A GLN* 1.3 69.1 - - - +
104A GLU* 1.3 78.1 - - - +
106A GLU 2.7 11.4 + - - -
107A ASN* 2.6 23.4 + - - +
131A TYR* 5.8 0.2 - - - +
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Residues in contact with GLU 104 (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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100A LYS 3.1 8.6 + - - +
101A LYS* 2.9 18.6 - - + +
103A ASN* 1.3 83.3 - - - +
105A THR* 1.3 54.7 + - - +
107A ASN* 2.9 10.0 - - - +
108A ARG* 2.4 55.1 + - - +
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Residues in contact with THR 105 (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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101A LYS 3.2 9.6 + - - -
102A GLN* 3.6 10.3 - - - -
103A ASN 2.8 3.6 + - - -
104A GLU* 1.3 69.4 - - - +
106A GLU* 1.3 55.3 + - - +
108A ARG* 1.9 39.6 + - - +
109A LYS* 2.5 34.7 + - + +
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Residues in contact with GLU 106 (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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62A PRO* 5.5 5.6 - - + -
63A MET 5.5 5.4 - - - +
65A ARG* 3.6 22.2 - - - +
102A GLN* 2.9 12.4 + - + +
103A ASN* 2.7 8.2 + - - +
105A THR* 1.3 78.1 - - - +
107A ASN* 1.3 67.0 + - - +
109A LYS* 2.5 50.8 + - - +
110A LEU* 3.1 13.2 + - - +
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Residues in contact with ASN 107 (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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59A LYS* 5.4 9.4 - - - +
61A CYS* 3.7 29.1 - - - -
62A PRO* 4.6 3.9 - - + +
63A MET 5.6 0.5 - - - +
64A ASN* 4.7 3.3 + - - +
103A ASN* 2.6 54.3 + - - +
104A GLU* 2.9 12.3 + - - +
106A GLU* 1.3 74.1 - - - +
108A ARG* 1.4 56.1 + - - +
110A LEU* 2.6 40.2 + - + +
111A LEU* 4.1 1.9 + - - +
131A TYR* 5.3 4.0 + - - -
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Residues in contact with ARG 108 (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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104A GLU* 2.4 41.6 + - - +
105A THR* 1.9 49.0 + - - +
107A ASN* 1.4 73.3 - - - +
109A LYS* 1.4 78.9 + - - +
110A LEU 3.0 5.2 + - - -
111A LEU* 3.9 12.6 + - - +
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Residues in contact with LYS 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A THR* 2.5 36.5 + - + +
106A GLU* 2.5 54.8 + - - +
107A ASN 3.2 0.6 - - - -
108A ARG* 1.4 90.7 - - - +
110A LEU* 1.3 62.1 + - - +
111A LEU 3.5 3.6 + - - +
113A THR* 5.6 0.3 - - - +
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Residues in contact with LEU 110 (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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11A ILE* 2.9 31.3 - - + +
12A GLY* 4.0 7.4 - - - +
60A LEU 4.4 0.2 - - - +
61A CYS* 4.3 2.5 - - - -
62A PRO* 2.9 45.3 - - + -
106A GLU 3.1 11.8 + - - +
107A ASN* 2.6 23.9 + - + +
109A LYS* 1.3 73.1 - - - +
111A LEU* 1.3 62.4 + - - +
112A GLY 3.5 0.3 + - - -
113A THR* 3.1 47.4 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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