Contacts of the helix formed by residues 110 - 127 (chain X) in PDB entry 5XTD
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 LEU 110 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90X TYR* 4.3 4.7 - - + -
92X LYS* 3.7 27.6 - - + -
93X ILE* 4.3 9.4 - - + -
104X PHE* 3.5 41.3 + - + +
108X LEU* 3.2 30.5 + - + -
109X GLY* 1.3 78.1 - - - +
111X ASP* 1.3 72.2 + - - +
114X ASP* 3.0 41.2 - - + +
115X GLN 5.1 2.2 - - - +
118X ILE* 3.8 16.4 - - + -
45p ARG* 4.9 1.2 + - - -
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Residues in contact with ASP 111 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104X PHE* 4.8 4.0 + - - +
105X MET* 5.2 8.3 - - - +
108X LEU 5.1 0.2 + - - -
109X GLY* 3.2 17.2 - - - +
110X LEU* 1.3 86.1 - - - +
112X SER* 1.3 69.8 + - - +
113X LEU* 5.1 2.5 - - + +
114X ASP* 5.4 0.2 - - + -
115X GLN* 3.6 10.4 + - - +
52p LYS* 4.5 14.4 + - - +
201p 8Q1 4.1 8.5 - - - +
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Residues in contact with SER 112 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111X ASP* 1.3 72.6 - - - +
113X LEU* 1.3 55.5 + - - -
115X GLN* 2.8 35.3 + - - +
116X VAL* 3.5 5.3 + - - +
13p GLN* 4.7 2.0 - - - +
17p LEU* 4.8 4.0 - - - -
201p 8Q1 2.1 40.1 + - - -
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Residues in contact with LEU 113 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111X ASP* 6.1 2.0 - - + -
112X SER* 1.3 72.8 - - - +
114X ASP* 1.3 72.6 + - + +
116X VAL* 2.9 29.4 + - - +
117X GLU* 3.0 10.2 + - - +
16p VAL* 6.3 0.7 - - + -
17p LEU* 4.1 15.1 - - + +
20p TYR* 3.9 23.2 - - + +
45p ARG* 3.3 43.5 - - + +
48p PHE* 4.8 22.0 - - + -
49p GLU* 5.2 11.7 - - + +
52p LYS* 5.7 6.7 - - + -
201p 8Q1 2.6 30.4 + - + +
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Residues in contact with ASP 114 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90X TYR* 2.4 40.5 + - - -
92X LYS* 3.9 6.9 + - - +
110X LEU* 3.0 45.4 + - - +
112X SER 3.0 0.2 + - - -
113X LEU* 1.3 82.6 - - - +
115X GLN* 1.3 60.5 + - - +
117X GLU* 3.2 7.5 + - - +
118X ILE* 3.0 23.2 + - - +
45p ARG* 3.4 26.9 + - - +
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Residues in contact with GLN 115 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104X PHE* 5.0 15.9 - - + +
110X LEU* 5.1 1.7 - - - +
111X ASP 3.6 8.1 + - - +
112X SER* 2.8 15.9 + - - +
114X ASP* 1.3 78.3 - - - +
116X VAL* 1.3 65.7 + - + +
118X ILE* 2.9 15.8 + - + +
119X ILE* 2.9 32.9 + - + +
135X ALA 3.3 12.5 + - - -
136X GLU 4.5 1.6 + - - +
137X LYS 2.8 28.7 + - - -
138X LEU 3.3 13.3 + - - +
139X MET* 3.1 32.4 - - - +
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Residues in contact with VAL 116 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112X SER 4.0 3.4 - - - +
113X LEU* 2.9 24.1 + - - +
115X GLN* 1.3 78.9 - - + +
117X GLU* 1.3 64.5 + - - +
119X ILE* 3.2 8.2 + - + +
120X MET* 2.9 49.0 + - + +
135X ALA 6.2 0.2 - - - +
17p LEU* 3.9 29.8 - - + +
20p TYR* 4.0 15.3 - - + -
21p LYS* 4.4 14.1 - - + -
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Residues in contact with GLU 117 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113X LEU 3.0 9.9 + - - +
114X ASP* 3.6 8.0 - - - +
115X GLN 3.1 0.4 - - - -
116X VAL* 1.3 77.5 - - - +
118X ILE* 1.3 63.4 + - - +
120X MET* 3.5 12.0 + - + +
121X ALA* 3.0 17.2 + - - +
44Z PRO* 5.2 1.0 - - - +
45Z TRP* 3.1 47.3 + - + +
20p TYR* 3.4 21.5 + - + +
24p LEU* 4.8 9.3 - - + +
38p ARG* 3.7 10.1 + - - +
41p ALA* 5.6 4.0 - - - +
42p CYS* 6.1 1.2 - - - -
45p ARG* 2.8 32.3 + - - +
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Residues in contact with ILE 118 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87X LEU* 4.0 26.7 - - + -
90X TYR* 4.9 4.5 - - + -
93X ILE* 4.9 3.4 - - + -
104X PHE* 4.1 21.3 - - + -
110X LEU* 3.8 28.9 - - + -
114X ASP* 3.0 24.7 + - - +
115X GLN* 2.9 15.8 + - + +
117X GLU* 1.3 79.9 - - - +
119X ILE* 1.3 63.3 + - + +
121X ALA* 2.8 20.6 + - - +
122X MET* 2.9 24.2 + - + +
144X ILE* 5.4 2.7 - - + -
45Z TRP* 3.6 20.9 - - + -
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Residues in contact with ILE 119 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104X PHE* 6.5 1.1 - - + -
115X GLN* 2.9 38.9 + - + +
116X VAL* 3.8 6.5 - - - +
118X ILE* 1.3 79.3 - - + +
120X MET* 1.3 65.6 + - + +
122X MET* 3.0 9.0 + - + +
123X GLU* 2.9 26.0 + - - +
130X ILE* 3.8 28.0 - - + +
135X ALA* 3.4 45.5 - - + +
138X LEU* 3.8 21.5 - - + +
144X ILE* 5.3 5.2 - - + -
21p LYS* 6.1 1.1 - - - +
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Residues in contact with MET 120 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116X VAL* 2.9 35.6 + - + +
117X GLU* 3.6 6.7 - - + +
118X ILE 3.1 0.2 - - - -
119X ILE* 1.3 78.0 - - + +
121X ALA* 1.3 63.4 + - - +
123X GLU* 3.2 12.6 - - - +
124X ASP* 3.0 21.2 + - - +
21p LYS* 3.7 27.6 - - + +
24p LEU* 3.5 43.1 - - + -
25p ARG* 3.1 50.4 + - + +
37p TYR* 5.0 3.4 - - - +
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Residues in contact with ALA 121 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86X VAL* 4.8 6.0 - - + +
117X GLU 3.0 7.2 + - - +
118X ILE 2.8 10.3 + - - +
120X MET* 1.3 77.9 - - - +
122X MET* 1.3 63.0 + - - +
124X ASP* 3.0 12.7 + - - +
125X GLU* 3.0 22.9 + - - +
45Z TRP* 3.5 36.3 - - + -
48Z ASN* 4.6 10.6 + - - +
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Residues in contact with MET 122 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83X VAL* 3.5 50.0 - - + +
86X VAL* 3.7 31.6 - - + -
87X LEU* 5.1 3.8 - - - -
118X ILE* 2.9 33.5 + - + +
119X ILE* 3.0 9.6 + - - +
121X ALA* 1.3 76.6 - - - +
123X GLU* 1.3 60.6 + - - +
125X GLU* 2.9 19.9 + - - +
126X PHE* 3.0 34.2 + - + -
130X ILE* 5.1 7.4 - - + -
144X ILE* 4.9 19.1 - - + -
148X ILE* 6.1 0.2 - - + -
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Residues in contact with GLU 123 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119X ILE* 2.9 15.6 + - - +
120X MET* 3.2 18.7 - - - +
122X MET* 1.3 77.3 - - - +
124X ASP* 1.3 58.5 + - - +
126X PHE* 4.4 5.2 - - - +
127X GLY* 2.7 28.5 + - - +
128X PHE* 3.1 21.2 + - - +
129X GLU* 3.3 7.5 - - - +
130X ILE* 2.4 54.3 + - + +
21p LYS* 3.6 21.0 + - - -
25p ARG* 2.9 29.2 + - - +
82p PHE* 4.8 3.8 - - + -
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Residues in contact with ASP 124 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120X MET* 3.0 19.0 + - - +
121X ALA* 3.0 13.7 + - - +
123X GLU* 1.3 79.8 - - - +
125X GLU* 1.3 63.4 + - + +
127X GLY* 3.7 6.7 + - - -
358l LYS* 5.7 8.3 + - - +
438l PRO* 4.3 13.2 - - - +
25p ARG* 3.2 24.7 + - - -
28p GLU* 4.1 20.2 - - - +
34p ARG* 4.9 9.8 + - - +
37p TYR* 6.2 0.2 - - - -
82p PHE* 3.7 16.2 - - - -
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Residues in contact with GLU 125 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82X ARG* 3.3 32.5 + - - +
85X TYR* 5.2 0.7 - - - -
86X VAL* 3.1 35.9 - - + +
121X ALA 3.0 11.4 + - - +
122X MET 2.9 10.7 + - - +
124X ASP* 1.3 75.9 - - + +
126X PHE* 1.3 68.1 + - + +
127X GLY* 3.0 6.0 + - - -
44Y TYR* 4.5 1.8 + - - -
45Y ARG* 2.6 31.0 + - - +
48Z ASN* 4.4 6.4 - - - +
438l PRO* 4.7 7.3 - - - +
439l THR* 3.7 31.5 + - + +
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Residues in contact with PHE 126 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74X LEU* 5.2 6.1 - - + -
79X ILE* 4.1 24.2 - - + -
82X ARG* 3.3 44.6 - - + +
83X VAL* 3.6 21.8 - - + -
122X MET* 3.0 52.9 + - + +
123X GLU* 4.6 2.5 - - - +
125X GLU* 1.3 80.0 - - - +
127X GLY* 1.3 63.4 + - - +
128X PHE* 3.4 30.2 + + + -
130X ILE* 6.5 0.4 - - + -
148X ILE* 4.5 26.7 - - + -
152X LYS* 5.0 7.6 + - + -
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Residues in contact with GLY 127 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123X GLU 2.7 14.3 + - - -
124X ASP* 4.1 7.4 - - - -
125X GLU 3.0 3.9 - - - -
126X PHE* 1.3 79.9 - - - +
128X PHE* 1.3 58.6 + - - +
152X LYS* 5.7 0.6 + - - -
438l PRO* 6.0 3.4 - - - -
82p PHE* 4.4 21.0 - - - +
83p PRO* 5.2 4.0 - - - +
84p ASP* 4.3 8.5 - - - +
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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
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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