Contacts of the helix formed by residues 109 - 130 (chain A) in PDB entry 4ASQ
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 PRO 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A LYS* 4.7 4.3 - - - +
107A ALA 3.8 0.9 - - - +
108A LEU* 1.4 87.5 - - + +
110A GLU* 1.3 67.0 + - - +
111A ASP* 3.3 2.5 - - + +
112A ASP* 3.0 31.4 + - - +
113A TYR* 2.9 19.9 + - - +
190A LYS* 4.5 9.2 - - - +
194A LEU* 3.9 16.8 - - + -
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Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ALA* 6.0 5.5 - - + +
71A LYS* 4.5 19.5 - - + -
74A LYS* 4.6 6.3 - - - +
108A LEU 3.6 2.1 + - - -
109A PRO* 1.3 71.9 - - - +
111A ASP* 1.3 70.7 + - - +
113A TYR* 3.5 6.0 + - - +
114A ALA* 3.1 23.6 + - + +
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Residues in contact with ASP 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PRO* 3.3 3.2 - - + +
110A GLU* 1.3 83.7 - - - +
112A ASP* 1.3 64.5 + - - +
114A ALA* 3.4 7.4 + - - +
115A GLU* 3.0 28.3 + - - +
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Residues in contact with ASP 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LEU* 4.0 13.5 - - + +
109A PRO* 3.0 27.4 + - + +
111A ASP* 1.3 77.7 - - - +
113A TYR* 1.3 60.6 + - - +
115A GLU* 3.4 15.0 + - - +
116A LEU* 3.0 28.4 + - - +
183A ARG* 4.4 4.8 + - - -
187A LEU* 4.0 16.3 - - + +
190A LYS* 2.6 37.2 + - - -
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Residues in contact with TYR 113 (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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43A GLU* 4.7 4.3 + - - -
66A SER* 3.6 19.9 + - - -
67A ALA* 3.7 10.5 - - + -
70A ALA* 3.5 26.0 - - + +
74A LYS* 5.4 1.3 - - - +
105A TYR* 3.2 48.2 - + + -
106A ALA* 3.9 6.8 - - - +
108A LEU* 3.9 16.7 - - + +
109A PRO 2.9 14.3 + - - +
110A GLU* 3.7 6.7 - - - +
112A ASP* 1.3 75.8 - - - +
114A ALA* 1.3 63.8 + - - +
116A LEU* 3.4 5.0 + - + +
117A LEU* 3.1 62.1 + - + +
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Residues in contact with ALA 114 (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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67A ALA* 5.7 7.4 - - + -
110A GLU* 3.1 17.5 + - + +
111A ASP* 3.6 8.3 - - - +
112A ASP 3.3 0.2 - - - -
113A TYR* 1.3 78.3 - - - +
115A GLU* 1.3 55.5 + - - +
117A LEU* 3.5 12.4 + - - +
118A ASP* 3.1 36.2 + - - +
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Residues in contact with GLU 115 (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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111A ASP 3.0 17.2 + - - +
112A ASP* 3.7 12.0 - - - +
114A ALA* 1.3 74.3 - - - +
116A LEU* 1.3 59.2 + - - +
118A ASP* 3.2 10.5 + - + +
119A THR* 2.8 36.7 + - - +
183A ARG* 2.8 50.4 + - - +
187A LEU* 4.1 5.6 - - + +
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Residues in contact with LEU 116 (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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105A TYR* 3.6 43.7 - - + -
108A LEU* 3.7 18.8 - - + -
112A ASP 3.0 18.0 + - - +
113A TYR* 3.7 7.4 - - + +
115A GLU* 1.3 76.5 - - - +
117A LEU* 1.3 58.1 + - + +
119A THR* 3.1 4.9 + - - -
120A LEU* 2.8 52.5 + - + +
184A TYR* 4.1 27.8 - - + +
187A LEU* 3.7 29.1 - - + +
188A ASN 4.8 0.7 - - - +
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Residues in contact with LEU 117 (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 LYS* 6.0 3.4 - - - +
63A ASN* 3.3 51.5 + - + +
66A SER* 3.8 13.9 - - - +
67A ALA* 4.1 2.7 - - + +
105A TYR* 6.4 1.3 - - + -
113A TYR* 3.1 63.6 + - + +
114A ALA* 3.7 7.2 - - - +
115A GLU 3.3 0.2 - - - -
116A LEU* 1.3 77.3 - - + +
118A ASP* 1.3 56.8 + - - +
120A LEU* 3.5 15.8 + - + +
121A SER* 2.9 30.8 + - - -
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Residues in contact with ASP 118 (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 GLU* 4.3 7.4 - - - +
63A ASN* 3.6 16.5 + - - +
114A ALA* 3.1 24.1 + - - +
115A GLU* 3.2 12.1 + - + +
117A LEU* 1.3 74.8 - - - +
119A THR* 1.3 58.6 + - - +
121A SER* 3.3 6.7 + - - -
122A ALA* 3.1 27.9 + - - +
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Residues in contact with THR 119 (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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115A GLU* 2.8 22.0 + - - +
116A LEU* 3.4 13.4 - - + -
118A ASP* 1.3 74.8 - - - +
120A LEU* 1.3 64.7 + - - +
122A ALA* 3.3 6.7 + - - +
123A MET* 3.1 25.1 + - + +
180A GLN* 3.1 40.2 - - + +
183A ARG* 4.2 15.8 - - + +
184A TYR* 3.9 20.0 - - + +
187A LEU* 4.7 0.6 - - - +
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Residues in contact with LEU 120 (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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105A TYR* 4.2 19.1 - - + -
116A LEU* 2.8 39.5 + - + +
117A LEU* 3.9 15.3 - - + +
119A THR* 1.3 73.7 - - - +
121A SER* 1.3 56.7 + - - +
123A MET* 3.3 12.8 + - + +
124A GLU* 3.0 29.3 + - - +
184A TYR* 3.7 24.5 - - + -
499A SER 4.3 2.8 - - - +
500A ALA* 5.4 1.2 - - - -
501A ASP* 3.6 31.4 - - + +
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Residues in contact with SER 121 (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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50A TYR* 3.6 14.0 + - - -
59A GLU* 2.7 40.4 + - - -
62A LYS* 5.0 6.5 - - - +
63A ASN* 3.3 11.0 + - - -
117A LEU 2.9 19.5 + - - -
118A ASP 3.3 5.4 + - - -
120A LEU* 1.3 74.7 - - - +
122A ALA* 1.3 58.9 + - - +
124A GLU* 4.5 4.9 - - - +
125A SER* 2.8 35.6 + - - -
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Residues in contact with ALA 122 (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 GLU* 4.5 2.4 + - - +
118A ASP 3.1 19.0 + - - +
119A THR* 3.5 7.9 - - - +
120A LEU 3.3 0.2 - - - -
121A SER* 1.3 76.9 + - - +
123A MET* 1.3 56.9 + - - +
125A SER* 3.2 7.0 + - - -
126A ASN* 3.1 28.2 + - - +
177A VAL* 4.5 2.6 - - - +
180A GLN* 4.3 21.9 + - + +
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Residues in contact with MET 123 (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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119A THR 3.1 15.6 + - - +
120A LEU* 3.8 18.6 - - + +
121A SER 3.3 0.2 - - - -
122A ALA* 1.3 75.0 - - - +
124A GLU* 1.3 64.8 + - - +
126A ASN* 3.5 3.1 + - - +
127A PHE* 3.2 22.9 + - - +
177A VAL* 3.8 22.5 - - + +
180A GLN* 3.8 17.5 - - + -
181A PHE* 3.7 39.7 - - + -
184A TYR* 3.8 35.0 - - + -
498A ILE 4.8 1.3 - - - +
499A SER* 3.4 31.1 + - - +
501A ASP* 5.5 0.2 - - + -
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Residues in contact with GLU 124 (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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50A TYR* 4.5 16.5 - - + -
54A ILE* 6.2 0.2 - - + -
62A LYS* 5.3 6.8 + - - -
120A LEU 3.0 16.3 + - - +
121A SER* 4.2 5.3 - - - +
123A MET* 1.3 76.8 - - - +
125A SER* 1.3 58.1 + - - +
127A PHE* 3.5 6.4 + - - +
128A ALA* 3.0 26.7 + - - +
335A VAL* 4.0 23.2 - - + +
496A TYR* 2.9 33.0 + - + -
499A SER 3.9 10.0 + - - +
500A ALA* 3.9 17.0 - - + +
1P ARG* 4.4 4.2 + - - -
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Residues in contact with SER 125 (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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50A TYR* 3.3 18.3 + - - -
54A ILE* 4.2 17.7 - - - -
59A GLU* 5.4 3.4 + - - -
121A SER 2.8 23.0 + - - -
122A ALA* 3.2 9.9 + - - -
124A GLU* 1.3 73.8 - - - +
126A ASN* 1.3 62.4 + - - +
128A ALA* 3.8 5.5 - - - +
129A LYS* 2.9 41.9 + - - +
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Residues in contact with ASN 126 (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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122A ALA 3.1 15.9 + - - +
123A MET 3.6 6.0 - - - +
124A GLU 3.4 0.4 - - - -
125A SER* 1.3 81.4 + - - +
127A PHE* 1.3 62.9 + - - +
129A LYS* 3.2 12.2 + - - +
130A VAL* 3.2 19.3 + - - +
172A LYS 3.2 25.2 + - - +
173A ALA* 3.9 10.7 - - - +
176A ALA* 4.2 12.3 + - - +
177A VAL* 3.7 24.4 - - + +
499A SER* 5.7 0.2 + - - -
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Residues in contact with PHE 127 (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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123A MET 3.2 11.3 + - - +
124A GLU* 3.6 9.2 - - - +
125A SER 3.3 0.2 - - - -
126A ASN* 1.3 82.0 + - - +
128A ALA* 1.3 66.6 + - + +
129A LYS 3.3 0.5 + - - -
130A VAL* 3.4 20.5 + - - +
145A LEU* 3.7 32.3 - - + +
169A PHE* 3.8 9.2 - + - -
173A ALA* 4.2 10.3 - - + +
263A TRP* 4.6 2.9 - + - -
335A VAL* 6.3 0.7 - - + -
337A HIS* 5.5 4.3 - - + -
493A PRO 3.7 16.4 - - - -
494A ALA 3.2 25.6 - - - -
496A TYR* 3.5 52.9 - + + -
499A SER* 4.1 10.3 - - - +
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Residues in contact with ALA 128 (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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54A ILE* 3.6 22.4 - - + -
124A GLU 3.0 18.4 + - - +
125A SER 3.9 1.3 - - - +
126A ASN 3.3 0.2 - - - -
127A PHE* 1.3 82.1 - - + +
129A LYS* 1.3 59.5 + - - +
130A VAL 3.4 2.8 + - - +
131A LYS* 5.0 4.7 + - - -
144A ALA* 5.7 2.8 - - - +
333A ASP* 4.9 3.2 - - - +
334A LEU 3.5 28.7 + - - +
335A VAL* 4.2 10.3 - - + -
336A CYS 6.0 0.4 - - - +
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Residues in contact with LYS 129 (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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54A ILE* 4.0 26.8 + - + +
55A THR* 6.1 0.8 - - - +
56A ASP* 5.5 4.9 + - - -
125A SER* 2.9 26.1 + - - +
126A ASN* 3.2 5.4 + - - +
127A PHE 3.2 0.4 - - - -
128A ALA* 1.3 79.5 - - + +
130A VAL* 1.3 63.6 + - - +
131A LYS* 3.2 16.9 + - - +
333A ASP* 3.5 42.5 + - + +
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Residues in contact with VAL 130 (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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126A ASN* 3.2 18.1 + - - +
127A PHE* 3.6 12.5 - - - +
128A ALA 3.4 3.8 - - - +
129A LYS* 1.3 76.4 - - - +
131A LYS* 1.3 65.6 + - - +
132A VAL* 4.4 5.4 - - + -
144A ALA* 3.7 19.2 - - - +
145A LEU* 4.4 2.6 + - + +
149A ILE* 5.0 2.0 - - + -
169A PHE* 3.7 30.5 - - + -
172A LYS* 3.9 31.6 - - + +
173A ALA* 3.9 28.9 - - + -
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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
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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