Contacts of the helix formed by residues 105 - 124 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E GLU* 3.3 3.6 + - - +
104F GLY* 1.3 73.0 - - - +
106F LEU* 1.3 58.3 - - - +
107F ALA 3.1 5.6 - - - -
108F LYS* 3.3 31.1 + - + +
109F HIS* 3.0 49.8 + - + -
99G LYS 4.7 0.4 - - - +
100G VAL* 4.2 13.7 - - + +
101G THR* 2.6 48.6 - - + +
103G ALA 5.4 0.5 + - - -
64H SER* 4.7 15.4 + - - -
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Residues in contact with LEU 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E TYR* 3.6 33.8 - - + +
58E LEU* 4.2 14.4 - - + -
61E GLU* 4.5 14.4 - - + +
90E ASP* 5.0 2.0 - - - +
92E GLU* 2.8 38.6 + - + +
93E LEU* 3.4 33.4 - - + -
96E LEU* 4.6 9.6 - - + -
102F LEU* 3.9 7.1 - - + +
103F PRO* 3.7 11.7 - - + +
105F GLU* 1.3 76.3 - - - +
107F ALA* 1.3 61.1 + - - +
109F HIS 4.3 0.7 - - - -
110F ALA* 3.6 16.8 + - - +
101G THR* 3.8 15.9 - - + -
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Residues in contact with ALA 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F VAL* 4.0 8.4 - - - +
99F ARG* 4.6 10.8 - - + +
102F LEU* 3.6 28.9 - - + +
103F PRO 2.8 18.3 + - - +
104F GLY* 3.9 7.2 - - - +
106F LEU* 1.3 77.7 - - - +
108F LYS* 1.3 63.8 + - + +
109F HIS 3.3 0.7 - - - -
110F ALA* 3.3 2.8 + - - +
111F VAL* 3.0 29.6 + - + +
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Residues in contact with LYS 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F ARG* 6.0 2.9 - - - +
104F GLY 4.0 14.4 - - - +
105F GLU* 3.3 28.0 + - - +
107F ALA* 1.3 78.6 - - - +
109F HIS* 1.3 63.2 + - + +
111F VAL* 3.4 8.4 + - - +
112F SER* 3.1 21.4 + - - -
68H ASP* 5.4 6.1 + - - -
71H GLU* 5.3 6.7 + - - -
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Residues in contact with HIS 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E TYR* 3.1 36.9 + + + +
105F GLU* 3.0 48.3 + - + +
106F LEU* 4.9 0.2 - - - -
107F ALA 3.3 0.6 - - - -
108F LYS* 1.3 75.5 - - + +
110F ALA* 1.3 58.7 + - - +
112F SER* 2.9 8.6 + - - -
113F GLU* 2.7 42.8 + - - +
101G THR* 6.4 0.4 - - + -
103G ALA* 4.0 24.5 - - + +
64H SER* 6.0 0.4 - - - -
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Residues in contact with ALA 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E TYR* 4.1 0.5 - - - -
54E VAL* 3.6 40.2 - - + +
57E TYR* 3.7 15.6 - - + -
98F VAL* 3.8 5.6 - - + -
102F LEU* 3.8 13.2 - - + -
106F LEU 3.6 13.2 + - - +
107F ALA 3.3 9.5 + - - +
109F HIS* 1.3 78.5 - - - +
111F VAL* 1.3 56.7 + - - +
113F GLU* 4.0 3.2 - - - +
114F GLY* 3.1 20.4 + - - -
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Residues in contact with VAL 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E TYR* 3.2 21.9 + - - +
95F GLN* 3.2 21.3 - - + +
98F VAL* 4.1 13.9 - - + -
99F ARG* 3.7 35.9 - - + +
107F ALA 3.0 18.9 + - - +
108F LYS* 3.6 8.1 - - - +
109F HIS 3.0 0.2 - - - -
110F ALA* 1.3 72.0 - - - +
112F SER* 1.3 62.4 + - - +
114F GLY 3.3 0.3 + - - -
115F THR* 2.8 36.9 + - - +
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Residues in contact with SER 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108F LYS 3.1 11.3 + - - -
109F HIS* 2.9 11.6 + - - -
111F VAL* 1.3 78.8 - - - +
113F GLU* 1.3 57.1 + - - +
115F THR* 3.1 7.2 + - - -
116F LYS* 2.7 63.0 + - - +
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Residues in contact with GLU 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E LEU* 6.2 2.5 - - + -
53E ALA* 4.0 10.7 - - + +
57E TYR* 4.1 35.7 - - + -
109F HIS* 2.7 27.3 + - - +
110F ALA 4.0 4.3 - - - +
112F SER* 1.3 75.9 + - - +
114F GLY* 1.3 56.6 + - - +
116F LYS* 3.6 18.9 - - - +
117F ALA* 2.8 31.6 + - - +
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Residues in contact with GLY 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E TYR* 3.8 23.1 - - - -
53E ALA* 3.8 16.6 - - - +
54E VAL* 5.0 0.2 - - - +
110F ALA 3.1 16.0 + - - -
111F VAL 3.7 2.7 - - - -
113F GLU* 1.3 73.9 - - - +
115F THR* 1.3 55.5 + - - +
117F ALA* 3.3 0.7 + - - +
118F VAL* 2.7 39.8 + - - +
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Residues in contact with THR 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E TYR* 3.9 5.3 - - - -
95F GLN* 3.3 21.2 + - - +
111F VAL* 2.8 27.5 + - - +
112F SER* 3.7 4.9 - - - -
114F GLY* 1.3 69.0 - - - +
116F LYS* 1.3 64.2 + - - +
118F VAL* 4.5 3.8 - - + -
119F THR* 2.6 42.7 + - - +
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Residues in contact with LYS 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F SER* 2.7 42.3 + - - +
113F GLU* 3.6 20.6 - - - +
115F THR* 1.3 72.2 - - - +
117F ALA* 1.3 64.8 + - - +
119F THR* 3.8 3.9 - - - -
120F LYS* 3.0 23.4 + - - +
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Residues in contact with ALA 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ALA* 4.0 20.4 - - - +
23E LEU* 4.2 13.5 - - + -
49E VAL* 4.3 4.7 - - + +
53E ALA* 3.5 24.2 - - + -
113F GLU 2.8 19.1 + - - +
114F GLY 3.6 1.3 - - - +
116F LYS* 1.3 75.0 - - - +
118F VAL* 1.3 65.2 + - - +
120F LYS* 3.3 4.6 + - - +
121F TYR* 3.2 22.7 + - - +
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Residues in contact with VAL 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E GLY* 3.8 16.2 - - - +
49E VAL* 3.8 14.6 - - + -
50E TYR* 3.4 41.5 - - + -
91F SER* 4.7 9.6 - - - +
114F GLY 2.7 28.8 + - - +
115F THR* 3.9 4.0 - - - +
117F ALA* 1.3 73.6 - - - +
119F THR* 1.3 61.3 + - - +
121F TYR* 3.3 3.1 + - - +
122F THR* 2.9 40.8 + - - +
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Residues in contact with THR 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F THR* 2.6 34.0 + - - +
116F LYS* 3.8 4.5 - - - -
118F VAL* 1.3 77.1 - - - +
120F LYS* 1.3 64.7 - - - +
122F THR* 3.4 6.3 + - - -
123F SER* 2.8 29.7 + - - +
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Residues in contact with LYS 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E SER 4.6 3.1 - - - -
20E ARG 3.1 16.8 - - - +
21E ALA 3.6 17.3 - - - +
22E GLY* 4.0 13.5 - - - +
116F LYS 3.0 14.4 + - - +
117F ALA* 3.3 8.2 + - - +
119F THR* 1.3 73.9 - - - +
121F TYR* 1.3 54.6 + - - +
123F SER* 2.9 7.0 + - - -
124F SER* 2.5 52.0 + - - +
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Residues in contact with TYR 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E ARG* 3.1 65.0 + - + +
20E ARG* 3.2 50.2 + - + -
21E ALA* 3.7 11.0 - - + -
27E VAL* 5.2 1.3 - - + -
45E ALA* 4.2 31.4 + - + +
46E GLY* 5.2 1.6 - - - -
49E VAL* 4.0 20.6 - - + -
117F ALA 3.2 10.3 + - - +
118F VAL 3.5 6.7 - - - +
120F LYS* 1.3 78.1 - - - +
122F THR* 1.3 68.6 + - - +
124F SER* 2.9 21.2 - - - +
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Residues in contact with THR 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E ARG* 5.1 1.0 + - - +
46E GLY* 5.8 1.2 - - - -
118F VAL* 2.9 28.3 + - - +
119F THR* 3.9 7.1 - - - -
121F TYR* 1.3 83.9 - - - +
123F SER* 1.3 62.1 + - - +
125F LYS* 3.3 20.3 - - - +
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Residues in contact with SER 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F THR* 2.8 27.4 + - - +
120F LYS* 2.9 7.8 + - - +
122F THR* 1.3 73.7 - - - +
124F SER* 1.3 59.2 + - - +
125F LYS* 2.7 25.3 + - - +
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Residues in contact with SER 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E ARG* 2.8 44.1 + - - +
120F LYS* 2.5 48.0 + - - +
121F TYR 2.9 7.4 - - - +
123F SER* 1.3 69.6 + - - +
125F LYS* 1.3 62.5 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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