Contacts of the helix formed by residues 108 - 129 (chain A) in PDB entry 4IM0
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 108 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A SER 5.6 0.9 - - - +
103A ASN* 3.5 17.7 - - - +
106A GLY 3.9 1.1 - - - +
107A LEU* 1.3 88.8 - - + +
109A GLU* 1.3 66.6 + - - +
110A SER* 4.4 12.1 - - - +
111A GLU* 3.0 15.0 + - + -
112A PHE* 3.0 19.2 + - - +
268A SER* 4.4 6.1 - - - +
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Residues in contact with GLU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU 3.6 1.8 + - - -
108A PRO* 1.3 71.1 - - - +
110A SER* 1.3 62.2 + - - +
112A PHE* 3.3 2.3 + - - +
113A LEU* 3.1 31.2 + - + +
268A SER* 4.1 6.7 + - - +
269A LEU* 3.6 17.1 - - + +
270A SER* 2.7 49.4 + - - -
273A LEU* 3.3 20.7 - - + +
323A LYS* 3.7 26.0 + - - +
325A TYR* 2.5 28.4 + - - +
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Residues in contact with SER 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PRO* 4.4 9.2 - - - +
109A GLU* 1.3 78.6 - - - +
111A GLU* 1.3 65.4 + - - +
113A LEU* 3.4 12.1 + - - +
114A ILE* 3.3 26.7 + - - +
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Residues in contact with GLU 111 (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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97A VAL* 5.3 2.9 - - + +
107A LEU* 4.2 17.9 - - + -
108A PRO* 3.0 24.1 + - + +
110A SER* 1.3 81.0 + - - +
112A PHE* 1.3 65.8 + - - +
114A ILE* 3.1 13.1 + - - +
115A VAL* 3.0 22.0 + - - +
143A ARG* 3.9 3.7 + - - -
151A SER* 2.7 36.0 + - - -
153A TYR* 2.7 26.9 + - - +
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Residues in contact with PHE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 4.0 13.8 - - + +
108A PRO 3.0 12.3 + - - +
109A GLU 3.3 7.2 + - - +
111A GLU* 1.3 76.8 - - - +
113A LEU* 1.3 61.4 + - + +
115A VAL* 3.3 4.4 + - + +
116A LEU* 2.9 41.2 + - + +
211A PHE* 3.2 40.8 - + + -
214A ALA* 3.9 13.9 - - + -
215A ALA* 3.6 25.1 - - + -
269A LEU* 4.2 19.7 - - + -
273A LEU* 4.2 15.5 - - + -
277A LEU* 3.4 39.9 - - + -
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Residues in contact with LEU 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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109A GLU* 3.1 24.7 + - + +
110A SER* 3.7 9.4 - - - +
111A GLU 3.1 0.4 - - - -
112A PHE* 1.3 75.0 - - + +
114A ILE* 1.3 61.6 + - + +
116A LEU* 3.5 19.0 + - + +
117A ARG* 2.9 29.0 + - - +
273A LEU* 3.9 30.5 - - + -
305A ILE* 4.6 7.2 - - + +
306A LEU* 3.7 10.9 - - + +
310A VAL* 5.7 2.7 - - + -
325A TYR* 3.7 26.0 - - + +
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Residues in contact with ILE 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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110A SER* 3.3 15.9 - - - +
111A GLU* 3.1 17.4 + - - +
113A LEU* 1.3 75.9 - - + +
115A VAL* 1.3 59.1 + - - +
117A ARG* 3.5 31.4 - - - +
118A ASP* 2.8 45.7 + - - +
150A GLN* 3.9 28.9 - - + +
151A SER* 3.4 29.8 - - - +
153A TYR* 3.9 13.5 - - + -
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Residues in contact with VAL 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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94A LEU* 4.2 21.8 - - + -
107A LEU* 3.7 17.5 - - + -
111A GLU 3.0 16.3 + - - +
112A PHE* 3.4 10.3 - - + +
114A ILE* 1.3 76.2 - - - +
116A LEU* 1.3 63.5 + - - +
119A VAL* 2.9 39.5 + - + +
153A TYR* 3.5 37.7 - - + -
210A THR* 5.5 0.2 - - + -
211A PHE* 4.0 20.9 - - + -
214A ALA* 4.6 8.7 - - + -
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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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112A PHE* 2.9 32.2 + - + +
113A LEU* 3.6 13.9 - - + +
115A VAL* 1.3 76.9 - - - +
117A ARG* 1.3 64.0 + - - +
119A VAL* 4.1 0.5 - - - +
120A VAL* 3.1 40.0 + - + +
211A PHE* 3.5 36.8 - - + -
273A LEU* 5.7 0.9 - - + -
277A LEU* 5.5 5.4 - - + -
280A VAL* 6.4 0.2 - - + -
302A THR* 4.3 13.9 - - + +
305A ILE* 4.1 29.4 - - + -
306A LEU* 3.8 22.9 - - + -
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Residues in contact with ARG 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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65A LYS* 4.8 15.0 - - - +
66A ASN* 4.8 0.4 - - - +
113A LEU 2.9 17.9 + - - +
114A ILE* 3.5 41.1 + - - +
116A LEU* 1.3 78.4 - - - +
118A ASP* 1.3 74.2 + - - +
120A VAL* 3.7 2.1 - - - +
121A GLY* 2.9 26.0 + - - -
150A GLN* 5.3 10.1 + - - +
151A SER 4.2 5.9 + - - -
152A VAL* 5.9 1.0 - - - +
306A LEU* 3.6 26.0 - - + +
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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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65A LYS* 5.5 2.1 + - - -
66A ASN* 3.3 35.5 + - - +
114A ILE* 2.8 30.1 + - - +
115A VAL 4.2 0.2 - - - +
117A ARG* 1.3 96.2 + - - +
119A VAL* 1.3 60.6 + - - +
122A GLY* 2.9 25.3 + - - -
151A SER 4.1 0.2 - - - +
152A VAL* 3.4 11.1 - - - +
153A TYR* 2.7 41.5 + - + +
155A LEU* 5.2 1.3 - - - +
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Residues in contact with VAL 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 2.9 27.7 + - + +
118A ASP* 1.3 76.4 - - + +
120A VAL* 1.3 58.0 + - + +
122A GLY* 3.7 0.3 - - - -
123A MET* 2.8 47.0 + - + +
136A ILE* 5.0 9.6 - - + -
141A ILE* 3.9 34.8 - - + -
153A TYR* 5.2 0.9 - - + +
155A LEU* 4.4 11.5 - - + +
207A ILE* 4.7 12.8 - - + -
210A THR* 6.1 0.9 - - + -
211A PHE* 3.6 31.0 - - + -
298A PHE* 6.5 0.2 - - + -
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Residues in contact with VAL 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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116A LEU* 3.1 38.3 + - + +
117A ARG 3.7 3.6 - - - +
119A VAL* 1.3 78.1 - - - +
121A GLY* 1.3 57.6 + - - +
123A MET* 3.6 6.3 - - - +
124A ASN* 3.0 28.8 + - - +
211A PHE* 4.5 3.8 - - + -
295A PHE* 4.8 0.3 - - - -
298A PHE* 4.1 20.0 - - + -
299A PHE* 3.6 31.1 - - + -
302A THR* 3.8 23.8 - - - +
303A SER* 5.0 1.6 - - - +
306A LEU* 4.6 10.5 - - + -
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Residues in contact with GLY 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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64A HIS* 3.6 9.9 + - - -
66A ASN* 3.9 13.9 - - - -
117A ARG 2.9 16.7 + - - -
118A ASP 3.9 0.7 - - - -
120A VAL* 1.3 77.8 - - - +
122A GLY* 1.3 60.7 + - - +
124A ASN* 4.0 6.5 + - - +
125A HIS* 3.1 23.6 + - - +
299A PHE* 5.3 2.0 - - - -
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Residues in contact with GLY 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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64A HIS* 4.7 0.2 - - - -
66A ASN* 3.6 17.8 - - - +
67A ILE* 3.8 5.4 - - - +
118A ASP 2.9 16.8 + - - -
119A VAL 3.7 0.7 - - - -
121A GLY* 1.3 74.6 - - - +
123A MET* 1.3 63.5 - - - +
125A HIS* 3.2 5.7 + - - +
126A LEU* 3.1 25.5 + - - +
155A LEU* 3.5 16.8 - - - -
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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 VAL* 2.8 31.2 + - + +
120A VAL* 3.6 6.5 - - - +
122A GLY* 1.3 71.0 - - - +
124A ASN* 1.3 62.6 + - - +
126A LEU* 3.0 30.6 + - + +
127A ARG* 3.1 13.7 + - - +
133A HIS* 4.1 5.4 - - + -
136A ILE* 3.5 33.2 - - + -
155A LEU* 3.5 24.4 - - + +
203A ASP* 4.5 8.5 - - - +
207A ILE* 3.5 33.7 - - + -
295A PHE* 3.9 20.1 - - + -
298A PHE* 5.6 1.8 - - + -
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Residues in contact with ASN 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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64A HIS* 6.2 0.2 + - - -
120A VAL 3.0 15.7 + - - +
121A GLY* 4.0 5.4 + - - +
123A MET* 1.3 79.3 - - - +
125A HIS* 1.3 58.5 + - - +
127A ARG* 3.3 8.1 + - - +
128A GLU* 2.8 67.5 + - - +
295A PHE* 3.6 25.2 - - + -
299A PHE* 3.8 31.3 - - + -
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Residues in contact with HIS 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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62A LEU* 4.0 21.4 - - + +
63A ASN 4.0 14.6 + - - -
64A HIS* 3.2 48.1 - + + +
67A ILE* 4.0 12.8 - - + -
121A GLY 3.1 18.7 + - - +
122A GLY* 3.5 6.3 - - - +
123A MET 3.2 0.2 - - - -
124A ASN* 1.3 78.9 - - - +
126A LEU* 1.3 57.9 + - - +
128A GLU* 3.4 17.0 + - - +
129A ASN* 2.3 54.3 + - - -
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Residues in contact with LEU 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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62A LEU* 4.1 21.5 - - + -
67A ILE* 3.7 20.9 - - + -
122A GLY 3.1 10.8 + - - +
123A MET* 3.0 21.7 + - + +
125A HIS* 1.3 75.9 - - - +
127A ARG* 1.3 56.0 - - - +
129A ASN* 2.8 21.0 + - - +
130A GLY 2.9 10.6 + - - -
131A ILE* 3.0 39.0 + - + +
132A VAL* 5.5 0.2 - - - -
133A HIS* 3.7 32.5 - - + +
155A LEU* 4.2 7.9 - - + -
158A PHE* 4.2 13.9 - - + -
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Residues in contact with ARG 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 3.1 8.8 + - - +
124A ASN* 3.5 13.8 + - - +
126A LEU* 1.3 77.4 - - - +
128A GLU* 1.3 58.1 + - - +
129A ASN 2.8 0.2 + - - -
130A GLY* 2.7 24.7 + - - +
131A ILE 3.8 9.8 + - - +
132A VAL* 6.0 3.4 - - + -
200A ALA 5.8 7.6 - - - +
295A PHE* 3.3 57.4 - - + +
296A ASP* 3.5 27.0 + - - -
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Residues in contact with GLU 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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124A ASN* 2.8 50.5 + - - +
125A HIS* 3.5 21.6 + - - +
126A LEU 3.3 0.2 - - - -
127A ARG* 1.3 73.2 - - + +
129A ASN* 1.3 63.3 + - - +
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Residues in contact with ASN 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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62A LEU* 4.1 18.4 - - + +
125A HIS* 2.3 55.6 + - - +
126A LEU* 2.8 6.0 + - - +
128A GLU* 1.3 84.7 - - - +
130A GLY* 1.3 56.8 + - - +
131A ILE* 3.3 29.3 - - + +
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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