Contacts of the helix formed by residues 114 - 134 (chain A) in PDB entry 2A11
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 LYS 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A GLU* 4.4 9.9 - - - +
109A THR 6.0 0.7 - - - +
110A GLY 3.4 5.2 + - - +
111A GLY* 3.0 18.6 + - - +
113A ASP* 1.3 76.2 - - - +
115A SER* 1.3 57.2 + - - +
116A SER* 3.0 29.9 + - - +
117A ILE* 2.7 43.3 + - + +
118A LEU* 2.9 11.5 + - - +
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Residues in contact with SER 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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81A THR* 4.2 10.9 - - - +
82A GLN* 3.9 20.3 + - - -
85A ALA* 3.6 13.0 - - - +
89A ARG* 3.2 27.1 - - - +
113A ASP 2.9 5.9 + - - -
114A LYS* 1.3 70.0 - - - +
116A SER* 1.3 61.8 + - - +
118A LEU* 3.1 3.7 + - - +
119A ALA* 2.7 38.5 + - - +
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Residues in contact with SER 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A THR* 4.1 12.8 - - - -
114A LYS* 3.7 30.9 + - - +
115A SER* 1.3 84.6 + - - +
117A ILE* 1.3 63.5 + - - +
119A ALA* 3.5 1.9 + - - +
120A ASP* 3.1 34.9 + - - +
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Residues in contact with ILE 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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27A HIS* 3.6 36.3 - - + +
100A VAL* 4.2 16.7 - - + +
102A LEU* 4.0 13.9 - - + -
106A GLU* 3.4 39.5 - - + +
111A GLY 3.6 20.9 - - - +
112A ALA* 5.9 0.7 - - - -
114A LYS* 2.7 26.0 + - + +
116A SER* 1.3 75.8 - - - +
118A LEU* 1.3 58.4 + - + +
120A ASP* 3.4 7.4 + - - +
121A GLY* 2.9 26.9 + - - -
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Residues in contact with LEU 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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85A ALA* 3.9 11.4 - - + +
88A ALA* 3.7 18.1 - - + +
89A ARG* 2.9 59.0 - - + +
96A LEU* 4.0 6.3 - - + +
97A GLY* 3.3 39.0 - - - +
100A VAL* 5.1 4.7 - - + -
112A ALA 4.2 6.7 - - - +
113A ASP* 4.1 5.6 - - - +
114A LYS 2.9 11.7 + - - +
115A SER 3.5 6.5 - - - +
117A ILE* 1.3 79.6 - - + +
119A ALA* 1.3 57.5 + - - +
121A GLY* 3.7 1.4 - - - -
122A MET* 2.9 29.5 + - - +
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Residues in contact with ALA 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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81A THR* 3.7 24.0 - - + +
84A LEU* 3.7 35.0 - - + +
85A ALA* 4.1 2.2 - - - +
115A SER 2.7 19.2 + - - +
116A SER 3.8 4.3 - - - +
118A LEU* 1.3 71.6 - - - +
120A ASP* 1.3 69.6 + - - +
122A MET* 3.2 4.3 + - - +
123A GLU* 3.0 25.6 + - - +
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Residues in contact with ASP 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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27A HIS* 5.7 7.0 + - + -
40A ASN* 5.0 5.8 - - - +
44A GLU* 3.5 38.0 - - + +
116A SER* 3.1 24.2 + - - +
117A ILE* 3.7 6.6 - - - +
119A ALA* 1.3 79.4 - - - +
121A GLY* 1.3 57.2 + - - +
123A GLU* 3.2 6.8 + - - +
124A SER* 2.9 30.8 + - - -
1001A CA 3.5 7.8 - - - -
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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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24A ALA 4.8 2.3 - - - +
25A LEU* 6.4 1.6 - - - -
40A ASN* 4.4 9.8 - - - +
96A LEU* 3.9 13.9 - - - -
100A VAL* 5.5 6.3 - - - -
117A ILE 2.9 16.5 + - - -
118A LEU 3.7 1.8 - - - -
119A ALA 3.2 0.2 - - - -
120A ASP* 1.3 73.8 - - - +
122A MET* 1.3 64.5 + - - +
124A SER* 3.0 18.9 + - - -
125A LEU* 3.1 16.8 + - - +
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Residues in contact with MET 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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12A LEU* 4.8 4.5 - - + -
84A LEU* 4.1 22.4 - - + +
87A VAL* 4.2 14.6 - - + -
88A ALA* 4.1 22.0 - - + -
91A LEU* 4.1 20.9 - - + -
96A LEU* 3.7 5.8 - - - +
118A LEU 2.9 18.0 + - - +
119A ALA* 3.5 6.1 - - - +
121A GLY* 1.3 75.5 - - - +
123A GLU* 1.3 62.4 + - - +
125A LEU* 3.3 14.8 + - + +
126A LEU* 3.2 42.3 + - + +
145A LEU* 3.8 23.1 - - + -
146A PHE* 4.9 11.2 - - + -
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Residues in contact with GLU 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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44A GLU* 3.8 17.0 - - + +
47A GLY* 3.3 13.0 - - - -
48A ASP* 2.5 36.0 - - - +
51A LEU* 4.2 14.8 - - + +
79A VAL* 5.0 2.3 - - - +
84A LEU* 3.3 30.6 - - + +
119A ALA 3.0 15.7 + - - +
120A ASP* 3.5 10.1 - - - +
122A MET* 1.3 78.7 - - - +
124A SER* 1.3 56.6 + - - +
126A LEU* 3.3 7.9 + - + +
127A GLY 2.9 23.2 + - - -
1001A CA 2.8 27.0 - - - -
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Residues in contact with SER 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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24A ALA* 3.5 23.8 - - - -
40A ASN* 3.1 35.3 + - - -
43A LEU* 3.8 8.8 - - - +
44A GLU* 3.6 14.6 - - - +
120A ASP 2.9 16.7 + - - -
121A GLY 3.0 9.2 + - - -
123A GLU* 1.3 77.1 - - - +
125A LEU* 1.3 57.6 + - - +
127A GLY* 3.1 2.3 + - - -
128A ALA* 2.8 28.2 + - - +
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Residues in contact with LEU 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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8A LEU* 4.3 6.7 - - + -
12A LEU* 4.5 18.2 - - + -
16A LEU* 4.9 3.1 - - + +
21A LEU* 3.9 27.4 - - + -
24A ALA* 4.0 13.7 - - + +
25A LEU* 4.2 10.8 - - + -
91A LEU* 4.2 17.5 - - + -
96A LEU* 3.8 32.1 - - + -
121A GLY 3.1 13.7 + - - +
122A MET* 3.6 16.2 - - + +
124A SER* 1.3 74.0 - - - +
126A LEU* 1.3 55.3 + - - +
128A ALA* 3.0 5.3 + - - +
129A ILE* 2.8 40.6 + - + +
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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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47A GLY* 4.2 9.4 - - - +
50A VAL* 4.9 2.7 - - + +
51A LEU* 4.0 35.9 - - + -
122A MET* 3.2 32.0 + - + +
123A GLU* 3.3 12.5 + - + +
125A LEU* 1.3 76.4 - - - +
127A GLY* 1.3 62.2 + - - +
129A ILE* 3.4 18.2 + - + +
130A TYR* 3.0 25.1 + - - +
138A ALA* 4.8 3.3 - - + +
141A VAL* 4.7 9.9 - - + -
142A ILE* 3.7 28.7 - - + -
145A LEU* 5.1 1.8 - - + -
146A PHE* 4.1 17.0 - - + -
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Residues in contact with GLY 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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43A LEU* 3.7 12.3 - - - -
46A LEU* 3.7 10.7 - - - +
47A GLY* 3.5 23.9 - - - -
123A GLU 2.9 10.7 + - - -
124A SER 3.4 4.5 - - - -
125A LEU 3.1 0.4 - - - -
126A LEU* 1.3 78.4 - - - +
128A ALA* 1.3 61.1 + - - +
130A TYR* 3.4 3.4 + - - +
131A LEU* 3.0 23.6 + - - +
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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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16A LEU* 4.1 15.9 - - + -
20A LEU* 3.7 30.7 - - + +
24A ALA* 4.2 13.7 - - + -
43A LEU* 4.1 7.1 - - + +
124A SER 2.8 16.2 + - - +
125A LEU* 3.0 7.4 + - - +
127A GLY* 1.3 73.5 - - - +
129A ILE* 1.3 56.9 + - - +
131A LEU* 3.1 5.4 + - - +
132A GLN* 2.8 31.9 + - - +
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Residues in contact with ILE 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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12A LEU* 3.8 28.3 - - + -
14A VAL* 3.8 20.6 - - + -
16A LEU* 4.1 15.7 - - + -
125A LEU* 2.8 26.6 + - + +
126A LEU* 3.7 13.5 - - + +
128A ALA* 1.3 72.7 - - - +
130A TYR* 1.3 53.7 + - - +
132A GLN 3.3 0.2 + - - -
133A HIS* 2.8 47.6 + - + +
137A LYS* 4.5 1.6 - - + -
138A ALA* 4.0 26.7 - - + +
141A VAL* 4.1 24.9 - - + -
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Residues in contact with TYR 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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46A LEU* 4.0 22.9 - - + -
50A VAL* 3.4 37.7 - - + -
126A LEU 3.0 17.2 + - - +
127A GLY* 3.7 2.9 - - - +
129A ILE* 1.3 78.1 - - - +
131A LEU* 1.3 66.8 + - + +
134A GLY* 2.9 25.7 + - - +
135A MET* 3.7 49.6 - - + +
138A ALA* 4.0 12.1 - - + +
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Residues in contact with LEU 131 (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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20A LEU* 4.4 16.2 - - + -
43A LEU* 4.2 20.0 - - + -
46A LEU* 4.3 15.0 - - + -
127A GLY 3.0 17.7 + - - +
128A ALA* 3.5 5.6 - - - +
130A TYR* 1.3 86.8 - - + +
132A GLN* 1.3 62.4 + - - +
134A GLY 4.8 0.3 + - - -
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Residues in contact with GLN 132 (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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15A ASP 4.2 0.4 - - - +
16A LEU* 3.8 12.8 - - + -
17A PRO* 3.7 34.7 - - + +
20A LEU* 3.7 15.1 - - + +
128A ALA 2.8 15.4 + - - +
129A ILE 3.9 1.1 - - - +
131A LEU* 1.3 80.8 - - - +
133A HIS* 1.3 80.5 + - + +
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Residues in contact with HIS 133 (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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14A VAL* 3.6 32.6 - - + +
15A ASP* 2.9 32.6 + - + -
16A LEU* 4.2 0.4 - - - +
129A ILE* 2.8 31.5 + - + +
131A LEU 5.1 0.2 - - - -
132A GLN* 1.3 96.1 + - + +
134A GLY* 1.3 57.2 + - - +
137A LYS* 3.8 25.2 - - + +
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Residues in contact with GLY 134 (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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130A TYR* 2.9 29.1 + - - -
131A LEU 4.8 0.2 + - - -
132A GLN 4.0 0.2 - - - -
133A HIS* 1.3 76.1 - - - +
135A MET* 1.3 63.9 + - - -
136A GLU 3.4 2.8 + - - -
137A LYS* 3.5 3.3 + - - +
138A ALA* 3.2 21.3 + - - +
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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