Contacts of the helix formed by residues 105 - 124 (chain J) in PDB entry 2XQL
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 GLU 105 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A LYS 4.3 0.6 + - - +
100A VAL* 4.2 13.8 - - + +
101A THR* 2.6 48.7 - - + +
103A ALA 5.4 0.3 + - - -
64B SER* 4.7 15.5 + - - -
92I GLU* 3.3 3.6 + - - -
104J GLY* 1.3 72.1 - - - +
106J LEU* 1.3 59.2 + - - +
107J ALA 3.1 4.7 - - - -
108J LYS* 3.3 30.7 + - + +
109J HIS* 3.0 50.4 + - + -
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Residues in contact with LEU 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A THR* 3.8 15.0 - - + -
57I TYR* 3.6 33.0 - - + +
58I LEU* 4.2 14.6 - - + -
61I GLU* 4.5 15.5 - - + +
90I ASP* 5.0 2.0 - - - +
92I GLU* 2.8 38.0 + - + +
93I LEU* 3.4 33.9 - - + +
96I LEU* 4.6 9.6 - - + -
102J LEU* 3.9 6.5 - - + +
103J PRO* 3.7 11.2 - - + +
105J GLU* 1.3 75.9 - - - +
107J ALA* 1.3 59.6 + - - +
109J HIS* 4.3 1.1 - - - -
110J ALA* 3.6 17.2 + - - +
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Residues in contact with ALA 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98J VAL* 4.0 8.6 - - - +
99J ARG* 4.6 10.5 - - + +
102J LEU* 3.6 28.7 - - + +
103J PRO 2.8 18.1 + - - +
104J GLY* 3.9 6.3 - - - +
105J GLU 3.1 0.2 - - - -
106J LEU* 1.3 77.5 - - - +
108J LYS* 1.3 64.9 + - + +
109J HIS 3.3 0.7 - - - -
110J ALA* 3.3 3.0 + - - +
111J VAL* 3.0 30.0 + - + +
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Residues in contact with LYS 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ASP* 5.4 6.1 + - - -
71B GLU* 5.3 6.7 + - - -
99J ARG* 6.0 2.5 - - - +
104J GLY 4.0 15.7 - - - +
105J GLU* 3.3 28.3 + - + +
107J ALA* 1.3 79.3 - - - +
109J HIS* 1.3 63.7 + - + +
111J VAL* 3.4 8.0 + - - +
112J SER* 3.1 21.1 + - - -
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Residues in contact with HIS 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ALA* 4.0 23.8 - - + +
57I TYR* 3.1 37.4 + + + +
105J GLU* 3.0 48.9 + - + +
106J LEU* 4.3 0.6 - - - +
107J ALA 3.3 0.4 - - - -
108J LYS* 1.3 74.8 - - + +
110J ALA* 1.3 59.4 + - - +
112J SER* 2.9 10.0 + - - -
113J GLU* 2.7 42.7 + - - +
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Residues in contact with ALA 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I TYR* 4.1 0.3 - - - -
54I VAL* 3.6 40.3 - - + +
57I TYR* 3.7 15.3 - - + -
98J VAL* 3.8 6.5 - - + -
102J LEU* 3.8 12.6 - - + -
106J LEU 3.6 14.3 + - - +
107J ALA 3.3 8.7 + - - +
109J HIS* 1.3 78.0 - - - +
111J VAL* 1.3 57.8 + - - +
113J GLU* 4.0 3.4 - - - +
114J GLY* 3.1 20.8 + - - -
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Residues in contact with VAL 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I TYR* 3.2 22.6 + - - +
95J GLN* 3.2 21.3 - - + +
98J VAL* 4.1 14.4 - - + -
99J ARG* 3.7 35.7 - - + +
107J ALA 3.0 18.4 + - - +
108J LYS* 3.6 8.1 - - - +
109J HIS 3.0 0.2 - - - -
110J ALA* 1.3 73.9 - - - +
112J SER* 1.3 61.8 + - - +
114J GLY 3.3 0.5 + - - -
115J THR* 2.8 37.6 + - - +
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Residues in contact with SER 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108J LYS 3.1 10.5 + - - -
109J HIS* 2.9 12.5 + - - -
111J VAL* 1.3 78.4 - - - +
113J GLU* 1.3 57.2 + - - +
115J THR* 3.1 6.4 + - - -
116J LYS* 2.7 64.0 + - - +
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Residues in contact with GLU 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I LEU* 6.2 2.7 - - + -
53I ALA* 4.0 10.7 - - + +
57I TYR* 4.1 36.8 - - + -
109J HIS* 2.7 25.6 + - - +
110J ALA 4.0 3.8 - - - +
112J SER* 1.3 77.1 + - - +
114J GLY* 1.3 57.8 + - - +
116J LYS* 3.6 17.7 - - - +
117J ALA* 2.8 31.1 + - - +
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Residues in contact with GLY 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I TYR* 3.8 22.4 - - - -
53I ALA* 3.8 17.0 - - - +
54I VAL* 4.8 0.2 - - - -
110J ALA 3.1 17.1 + - - -
111J VAL 3.7 2.5 - - - -
113J GLU* 1.3 73.6 - - - +
115J THR* 1.3 56.1 + - - +
117J ALA* 3.3 0.7 + - - +
118J VAL* 2.7 40.0 + - - +
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Residues in contact with THR 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I TYR* 3.9 5.2 - - - -
95J GLN* 3.3 21.4 + - - +
111J VAL* 2.8 25.6 + - - +
112J SER* 3.7 5.2 - - - -
114J GLY* 1.3 69.8 - - - -
116J LYS* 1.3 64.6 + - - +
118J VAL* 3.9 3.7 - - + +
119J THR* 2.6 43.1 + - - +
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Residues in contact with LYS 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112J SER* 2.7 43.1 + - - +
113J GLU* 3.6 21.5 - - - +
115J THR* 1.3 71.8 - - - +
117J ALA* 1.3 61.9 + - - +
119J THR* 3.8 4.4 - - - -
120J LYS* 3.0 24.7 + - - +
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Residues in contact with ALA 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I ALA* 4.0 20.0 - - - +
23I LEU* 4.2 13.5 - - + -
49I VAL* 4.3 4.7 - - + +
53I ALA* 3.5 25.6 - - + -
113J GLU 2.8 19.2 + - - +
114J GLY 3.6 0.7 - - - +
116J LYS* 1.3 74.2 - - - +
118J VAL* 1.3 65.9 + - - +
120J LYS* 3.3 4.8 + - - +
121J TYR* 3.2 22.3 + - - +
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Residues in contact with VAL 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I GLY* 3.8 17.3 - - - +
49I VAL* 3.8 15.0 - - + -
50I TYR* 3.4 41.3 - - + -
91J SER* 4.7 9.4 - - - +
114J GLY 2.7 28.5 + - - +
115J THR* 3.9 4.7 - - + +
117J ALA* 1.3 72.4 - - - +
119J THR* 1.3 60.8 + - - +
121J TYR* 3.3 3.3 + - - +
122J THR* 2.9 41.2 + - - +
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Residues in contact with THR 119 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115J THR* 2.6 34.8 + - - +
116J LYS* 3.8 4.9 - - - -
118J VAL* 1.3 76.4 - - - +
120J LYS* 1.3 65.7 + - - +
122J THR* 3.9 5.9 - - - -
123J SER* 2.8 29.8 + - - +
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Residues in contact with LYS 120 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I SER 4.6 3.8 - - - -
20I ARG 3.1 16.8 - - - +
21I ALA 3.6 17.5 - - - +
22I GLY* 3.6 13.1 - - - +
116J LYS 3.0 14.8 + - - +
117J ALA* 3.7 7.6 - - - +
119J THR* 1.3 74.0 - - - +
121J TYR* 1.3 53.7 + - - +
123J SER* 2.9 6.8 + - - -
124J SER* 2.5 52.5 + - - +
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Residues in contact with TYR 121 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I ARG* 3.1 63.3 + - + +
20I ARG* 3.2 51.4 + - + -
21I ALA* 3.7 11.9 - - + -
27I VAL* 5.2 1.1 - - + -
45I ALA* 4.2 30.7 + - + +
46I GLY* 5.2 2.0 - - - -
49I VAL* 4.0 21.3 - - + -
117J ALA 3.2 9.6 + - - +
118J VAL 3.3 7.2 + - - +
120J LYS* 1.3 78.8 - - - +
122J THR* 1.3 69.5 + - - +
124J SER* 2.9 21.6 - - - +
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Residues in contact with THR 122 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I ARG* 5.1 0.8 + - - +
46I GLY* 5.8 0.9 - - - -
118J VAL* 2.9 28.8 + - - +
119J THR* 3.9 6.5 - - - -
121J TYR* 1.3 85.5 - - - +
123J SER* 1.3 61.7 + - - +
125J LYS* 3.3 20.8 - - - +
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Residues in contact with SER 123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119J THR* 2.8 26.6 + - - +
120J LYS* 2.9 7.6 + - - -
122J THR* 1.3 74.8 - - - +
124J SER* 1.3 59.8 + - - +
125J LYS* 2.7 26.1 + - - +
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Residues in contact with SER 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I ARG* 2.8 43.7 + - - -
120J LYS* 2.5 49.2 + - - +
121J TYR 2.9 7.6 - - - +
123J SER* 1.3 69.4 + - - +
125J LYS* 1.3 62.8 + - - +
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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
------------------------------------------------------------
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