Contacts of the helix formed by residues 104 - 121 (chain O) in PDB entry 5A31
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 104 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100O MET 4.2 0.2 - - - +
103O GLY* 1.3 76.7 - - - +
105O LEU* 1.3 68.5 + - - +
106O LYS* 3.1 19.6 - - + +
107O ASP* 2.6 28.9 + - - +
108O MET 3.8 1.7 + - - -
155O TYR* 3.9 6.2 - - - -
314P SER* 2.7 46.5 + - - +
315P GLU* 5.0 0.2 - - - -
317P SER* 4.0 10.8 - - - -
318P TYR* 3.6 31.1 - - + +
321P HIS* 5.4 4.3 - - + +
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Residues in contact with LEU 105 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104O GLU* 1.3 75.5 - - - +
106O LYS* 1.3 62.7 + - - +
108O MET* 3.1 11.5 + - + +
109O GLU* 3.0 21.9 + - + +
148O PHE* 3.8 31.9 - - + -
151O VAL* 3.3 26.7 - - + -
152O PHE* 3.9 29.4 - - + -
155O TYR* 3.8 41.0 - - + -
317P SER* 4.8 6.7 - - - +
321P HIS* 4.2 11.3 + - + +
340P TYR* 3.9 10.5 - - + +
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Residues in contact with LYS 106 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104O GLU* 3.9 11.4 - - + +
105O LEU* 1.3 76.9 - - - +
107O ASP* 1.3 88.8 + - - +
109O GLU* 3.1 4.3 + - - +
110O GLN* 2.7 47.2 + - - +
313P LYS* 4.2 34.7 - - + +
314P SER* 4.4 23.0 - - - +
317P SER* 3.4 23.9 + - - +
340P TYR* 3.9 12.7 + - - +
344P ARG* 4.6 5.2 - - - +
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Residues in contact with ASP 107 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99O LEU* 5.1 12.3 - - + +
100O MET* 4.3 21.3 - - + +
103O GLY* 3.1 8.1 - - - -
104O GLU* 2.6 38.4 + - - +
106O LYS* 1.3 107.2 + - - +
108O MET* 1.3 52.1 + - - +
110O GLN* 3.3 12.7 + - - +
111O PHE* 2.7 33.6 + - - +
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Residues in contact with MET 108 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35O ILE* 4.7 4.3 - - + -
100O MET* 4.0 21.3 - - + +
104O GLU 3.8 1.4 + - - -
105O LEU* 3.1 14.0 + - + +
107O ASP* 1.3 79.3 - - - +
109O GLU* 1.3 63.5 + - - +
111O PHE* 3.1 12.2 + - + +
112O PHE* 3.1 31.3 + - + -
143O TYR* 4.4 8.3 - - - -
151O VAL* 4.1 4.0 - - - +
154O LEU* 3.7 27.4 - - + -
155O TYR* 3.1 60.3 - - + +
158O LEU* 4.3 18.6 - - + -
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Residues in contact with GLU 109 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105O LEU* 3.0 22.1 + - + +
106O LYS 3.5 5.4 - - - +
108O MET* 1.3 75.8 - - - +
110O GLN* 1.3 57.6 - - - +
112O PHE* 3.5 3.1 + - - +
113O ASP* 3.1 31.4 + - - +
143O TYR* 3.0 29.9 + - + +
148O PHE* 4.4 1.6 - - - -
151O VAL* 3.9 16.2 - - + +
340P TYR* 3.1 32.2 + - - +
341P TYR* 3.4 28.0 + - - -
344P ARG* 2.5 43.1 + - - +
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Residues in contact with GLN 110 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106O LYS* 2.7 35.3 + - - +
107O ASP* 3.5 9.8 + - - +
109O GLU* 1.3 71.2 - - - +
111O PHE* 1.3 55.5 + - - +
113O ASP* 3.2 3.6 + - + +
114O ASP* 2.8 61.5 + - - +
313P LYS* 5.3 8.7 + - - -
344P ARG* 4.2 12.7 - - - +
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Residues in contact with PHE 111 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35O ILE* 3.7 35.7 - - + -
38O LEU* 4.1 12.3 - - + -
39O VAL* 3.7 33.9 - - + -
42O SER* 4.3 15.7 - - - -
96O ARG* 3.4 31.6 - - - +
100O MET* 3.5 29.6 - - + -
107O ASP 2.7 17.6 + - - +
108O MET* 3.1 9.4 + - + +
110O GLN* 1.3 74.2 - - - +
112O PHE* 1.3 63.9 + + - +
114O ASP* 3.5 7.5 + - + +
115O LEU* 3.1 33.7 + - + +
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Residues in contact with PHE 112 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30O VAL* 3.9 15.7 - - + -
35O ILE* 3.1 35.0 - - + -
38O LEU* 3.9 19.1 - - + -
108O MET* 3.1 26.1 + - - -
109O GLU 3.7 7.2 - - - +
110O GLN 3.4 0.2 - - - -
111O PHE* 1.3 81.2 - + - +
113O ASP* 1.3 60.8 + - - +
115O LEU* 3.2 17.7 - - + +
116O SER* 3.2 20.8 + - - -
139O MET 3.9 11.9 - - - -
140O ILE* 4.6 9.6 - - - +
143O TYR* 3.5 61.7 - + + -
154O LEU* 4.4 2.7 - - + -
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Residues in contact with ASP 113 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109O GLU 3.1 12.6 + - - +
110O GLN* 3.2 7.6 + - + +
112O PHE* 1.3 77.2 - - - +
114O ASP* 1.3 56.4 + - - +
116O SER* 2.8 21.3 + - - +
117O ASP* 2.6 22.6 + - - +
143O TYR* 4.3 7.6 - - - -
344P ARG* 3.0 37.3 + - - +
346P GLN* 3.8 12.7 + - - +
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Residues in contact with ASP 114 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42O SER* 5.7 1.3 + - - -
96O ARG* 4.3 16.4 + - - +
110O GLN* 2.8 55.0 + - - +
111O PHE* 3.5 10.1 - - + +
113O ASP* 1.3 66.6 - - - +
115O LEU* 1.3 60.6 + - - +
117O ASP* 2.3 35.0 - - - +
118O SER* 3.5 7.1 + - - -
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Residues in contact with LEU 115 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38O LEU* 3.3 50.7 - - + -
42O SER* 4.1 28.0 - - - +
111O PHE* 3.1 23.0 + - + +
112O PHE* 3.2 25.6 - - + +
114O ASP* 1.3 77.3 - - - +
116O SER* 1.3 56.9 + - - +
118O SER* 3.1 27.3 - - - -
119O PHE 4.4 0.7 + - - -
136O LEU* 4.0 20.8 - - + +
140O ILE* 4.1 18.6 - - + +
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Residues in contact with SER 116 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112O PHE 3.2 9.8 + - - -
113O ASP* 2.8 26.9 + - - +
115O LEU* 1.3 74.2 - - - +
117O ASP* 1.3 63.9 + - - +
118O SER 3.1 2.6 + - - -
119O PHE* 3.5 15.0 + - - +
120O SER* 3.7 8.3 + - - -
140O ILE* 3.5 30.9 - - - +
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Residues in contact with ASP 117 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113O ASP 2.6 15.0 + - - +
114O ASP* 2.3 46.1 - - - +
116O SER* 1.3 70.0 + - - +
118O SER* 1.3 64.3 + - - +
119O PHE 3.3 0.2 - - - -
120O SER* 2.8 28.9 + - - +
121O GLY* 3.1 9.5 + - - -
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Residues in contact with SER 118 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42O SER* 6.1 0.7 - - - -
114O ASP 3.5 8.5 + - - -
115O LEU* 3.1 21.6 + - - -
116O SER 3.1 0.4 - - - -
117O ASP* 1.3 77.1 - - - +
119O PHE* 1.3 68.1 + - - +
121O GLY* 3.5 9.5 + - - -
122O THR 4.4 1.2 + - - -
124O PRO 5.2 0.2 - - - -
125O GLU* 3.4 42.8 + - - +
126O VAL* 3.5 16.0 - - - +
136O LEU* 5.1 2.9 - - - -
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Residues in contact with PHE 119 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115O LEU 4.7 1.6 - - - -
116O SER 3.5 8.4 + - - +
117O ASP 3.3 0.6 - - - -
118O SER* 1.3 84.4 - - - +
120O SER* 1.3 64.0 + - - +
121O GLY 3.2 1.2 + - - -
122O THR* 3.2 14.0 + - - -
124O PRO* 4.9 4.8 - - - +
125O GLU 4.5 3.6 - - - -
126O VAL* 3.6 24.2 - - + -
128O LYS* 3.5 45.8 - - + -
133O GLY 3.7 9.9 - - - -
136O LEU* 3.2 48.7 - - + -
137O ARG* 3.6 24.7 - - + -
140O ILE* 5.5 3.1 - - + -
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Residues in contact with SER 120 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116O SER 3.7 4.0 + - - -
117O ASP* 2.8 34.3 + - - +
119O PHE* 1.3 76.4 - - - +
121O GLY* 1.3 64.5 + - - +
122O THR* 3.3 6.5 + - - -
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Residues in contact with GLY 121 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117O ASP 3.1 13.5 + - - -
118O SER 3.5 6.0 + - - -
119O PHE 3.1 1.2 - - - -
120O SER* 1.3 78.0 + - - +
122O THR* 1.3 66.6 + - - +
123O GLU* 3.2 6.0 + - - -
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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