Contacts of the helix formed by residues 120 - 139 (chain A) in PDB entry 4E3C
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 GLY 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A GLU* 1.3 70.3 - - - +
121A ALA* 1.3 54.8 + - - +
122A ILE 2.8 11.5 + - - -
123A LEU* 2.9 40.5 + - - +
124A THR* 4.2 0.7 + - - -
265A LEU* 4.8 9.1 + - - -
269A LEU* 6.1 1.8 - - - -
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Residues in contact with ALA 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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117A LEU* 4.4 9.4 - - + +
119A GLU* 2.7 30.3 + - + +
120A GLY* 1.3 77.7 - - - +
122A ILE* 1.3 60.1 + - - +
123A LEU 3.2 0.2 - - - -
124A THR* 2.8 28.2 + - - +
125A LEU* 3.7 5.2 + - - +
162A HIS* 4.7 2.1 + - - -
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Residues in contact with ILE 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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117A LEU* 3.4 34.8 - - + +
119A GLU 3.3 14.4 - - - +
120A GLY 2.8 1.3 - - - +
121A ALA* 1.3 78.6 - - - +
123A LEU* 1.3 68.3 + - + +
125A LEU* 3.2 7.4 + - + +
126A LEU* 2.9 40.0 + - + +
212A ALA* 5.2 0.9 - - + +
215A CYS* 3.5 17.9 - - + +
216A ILE* 3.5 47.6 - - + -
265A LEU* 4.6 13.5 - - + -
273A LEU* 5.5 1.1 - - + -
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Residues in contact with LEU 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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120A GLY* 2.9 39.2 + - - +
122A ILE* 1.3 80.0 - - + +
124A THR* 1.3 58.2 + - - +
126A LEU* 3.1 9.4 + - + -
127A SER* 2.6 38.8 + - - -
265A LEU* 6.5 1.6 - - + -
269A LEU* 4.6 29.4 - - + -
273A LEU* 6.2 0.9 - - + -
306A ILE* 5.9 0.7 - - + -
307A LEU* 3.6 43.7 - - + +
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Residues in contact with THR 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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120A GLY 4.3 0.7 + - - -
121A ALA* 2.8 22.8 + - - +
123A LEU* 1.3 77.0 - - - +
125A LEU* 1.3 63.5 + - - +
127A SER* 4.1 2.9 - - - -
128A ASP* 2.8 36.4 + - - +
159A ARG* 4.5 24.3 - - + -
160A LEU* 3.7 25.6 - - + +
162A HIS* 3.3 13.2 - - - +
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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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104A LEU* 4.1 21.1 - - + -
117A LEU* 6.3 0.7 - - + -
121A ALA 3.7 4.1 + - - +
122A ILE* 3.2 12.9 + - + +
123A LEU 3.2 0.4 - - - -
124A THR* 1.3 79.1 - - - +
126A LEU* 1.3 69.3 + - + +
129A ILE* 2.9 61.3 + - + +
151A ILE* 4.6 0.4 - - + -
162A HIS* 3.1 32.2 + - + +
208A PHE* 4.1 8.1 - - + -
211A LEU* 3.6 21.3 - - + -
212A ALA* 4.7 3.4 - - + -
215A CYS* 3.9 22.0 - - + -
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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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122A ILE* 2.9 35.6 + - + +
123A LEU* 3.5 13.0 - - + +
125A LEU* 1.3 79.2 - - + +
127A SER* 1.3 57.8 + - - +
130A ALA* 2.9 37.1 + - - +
208A PHE* 3.8 11.3 - - + -
212A ALA* 3.8 29.4 - - + -
273A LEU* 3.8 25.4 - - + -
276A TRP* 4.0 12.1 - - + -
303A LEU* 3.7 30.7 - - + -
307A LEU* 4.0 7.6 - - + -
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Residues in contact with SER 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 LEU 2.6 21.4 + - - -
124A THR* 4.1 3.6 - - - -
126A LEU* 1.3 73.8 - - - +
128A ASP* 1.3 60.5 + - - +
130A ALA* 4.0 5.3 - - - +
131A SER* 3.4 20.4 + - - -
134A ARG* 4.7 4.0 + - - +
303A LEU* 5.2 0.4 - - - -
307A LEU* 3.6 28.0 - - - +
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Residues in contact with ASP 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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72A ASN* 2.7 32.9 + - - +
124A THR* 2.8 20.7 + - - +
127A SER* 1.3 76.7 - - - +
129A ILE* 1.3 64.3 + - - +
130A ALA 2.9 5.3 + - - -
131A SER* 3.0 14.9 + - - -
132A ALA* 3.0 11.6 + - - +
160A LEU 3.6 11.5 - - - +
161A ILE* 4.6 2.6 - - - +
162A HIS* 3.1 44.1 + - + -
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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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125A LEU* 2.9 42.3 + - + +
128A ASP* 1.3 71.1 - - - +
130A ALA* 1.3 57.7 + - - +
132A ALA* 3.6 4.5 - - - -
133A LEU* 2.9 46.0 + - + +
146A LEU* 4.0 9.9 - - + -
151A ILE* 3.6 39.5 - - + -
162A HIS* 3.9 15.7 - - + +
164A ILE* 4.2 10.5 - - + -
208A PHE* 3.6 26.9 - - + -
211A LEU* 5.0 0.9 - - + -
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Residues in contact with ALA 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 LEU 2.9 22.8 + - - +
127A SER* 4.0 6.1 - - - +
129A ILE* 1.3 73.9 - - - +
131A SER* 1.3 58.5 + - - +
132A ALA 2.8 9.8 + - - -
133A LEU* 3.1 3.1 + - - +
134A ARG* 2.9 48.7 + - - +
208A PHE* 3.9 11.4 - - + -
299A CYS* 5.0 4.9 - - - +
303A LEU* 4.1 17.3 - - + -
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Residues in contact with SER 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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70A HIS* 3.3 28.1 + - - -
72A ASN* 3.8 9.1 + - - -
127A SER 3.4 12.6 + - - -
128A ASP 3.0 8.6 + - - -
130A ALA* 1.3 78.9 - - - +
132A ALA* 1.3 58.2 + - - +
134A ARG* 3.8 23.0 + - - +
135A TYR* 3.4 13.8 + - - +
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Residues in contact with ALA 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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70A HIS* 3.8 9.6 - - - -
72A ASN* 3.9 12.6 - - + +
73A VAL* 3.8 20.9 - - + -
128A ASP 3.0 10.6 + - - +
129A ILE* 3.4 14.4 - - - +
130A ALA 2.8 1.4 + - - -
131A SER* 1.3 77.0 - - - +
133A LEU* 1.3 66.2 + - - +
135A TYR* 3.1 9.4 + - - +
136A LEU* 2.9 24.6 - - - +
164A ILE* 4.0 11.7 - - + -
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Residues in contact with LEU 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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129A ILE* 2.9 33.8 + - + +
130A ALA 4.0 1.6 - - - +
132A ALA* 1.3 77.1 - - + +
134A ARG* 1.3 68.4 + - - +
135A TYR 2.8 0.7 + - - -
136A LEU* 2.9 8.9 + - + +
137A HIS* 2.8 46.1 + - + +
143A HIS* 6.0 4.3 - - + -
146A LEU* 3.8 21.8 - - + -
164A ILE* 4.7 4.5 - - + -
204A ASP* 4.2 20.0 - - + +
205A TYR* 5.2 1.8 - - + +
208A PHE* 3.8 38.8 - - + -
299A CYS* 4.6 9.2 - - - -
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Residues in contact with ARG 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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127A SER* 4.7 4.2 + - - +
130A ALA* 2.9 38.7 + - - +
131A SER* 3.8 27.3 + - - +
133A LEU* 1.3 72.2 - - - +
135A TYR* 1.3 60.2 + - - +
137A HIS* 3.9 0.8 - - - +
138A GLU* 3.0 44.4 + - - +
299A CYS* 3.6 21.5 - - - -
300A PHE* 3.7 27.5 + - + +
304A ASP* 3.6 33.9 + - - -
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Residues in contact with TYR 135 (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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68A LEU* 3.1 37.2 - - + +
69A THR* 3.1 30.8 + - - -
70A HIS* 3.8 31.2 - + + -
73A VAL* 5.6 2.7 - - + -
131A SER 3.4 14.8 + - - +
132A ALA 3.1 10.5 + - - +
133A LEU 2.8 1.4 + - - -
134A ARG* 1.3 78.3 - - - +
136A LEU* 1.3 79.7 + - + +
138A GLU* 3.3 6.2 + - - +
139A ASN* 2.9 50.7 + - + -
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Residues in contact with LEU 136 (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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73A VAL* 4.3 21.3 - - + -
132A ALA* 2.9 28.5 - - + +
133A LEU* 2.9 12.0 + - + +
135A TYR* 1.3 89.6 - - + +
137A HIS* 1.3 58.2 + - + +
139A ASN* 2.6 29.9 + - - -
140A ARG 3.0 9.4 + - - -
141A ILE* 3.1 44.5 + - + +
143A HIS* 4.8 17.5 - - + +
164A ILE* 6.0 2.7 - - + -
167A LEU* 4.3 21.5 - - + -
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Residues in contact with HIS 137 (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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133A LEU* 2.8 38.6 + - + +
134A ARG 3.9 1.6 - - - +
136A LEU* 1.3 73.9 - - + +
138A GLU* 1.3 62.1 + - - +
139A ASN 3.1 1.0 + - - -
140A ARG* 3.1 15.8 + - - -
141A ILE 3.5 12.2 + - - -
201A VAL* 3.3 32.2 - - + +
204A ASP* 3.1 37.3 - - + +
205A TYR* 3.5 35.0 - + - -
299A CYS* 5.0 1.6 - - - -
300A PHE* 3.9 22.4 - + + -
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Residues in contact with GLU 138 (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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134A ARG* 3.0 27.3 + - - +
135A TYR* 3.7 6.0 - - - +
136A LEU 3.2 1.0 - - - -
137A HIS* 1.3 74.2 - - - +
139A ASN* 1.3 60.6 + - - +
140A ARG* 3.4 5.7 - - - +
300A PHE* 3.5 30.1 - - + -
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Residues in contact with ASN 139 (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 ARG* 4.1 8.8 + - - -
68A LEU* 3.1 31.7 - - + +
135A TYR* 2.9 56.3 + - + +
136A LEU* 2.6 18.7 + - - +
138A GLU* 1.3 75.8 - - - +
140A ARG* 1.3 70.7 + - - +
141A ILE* 2.9 21.3 - - + +
172A GLU* 4.4 0.7 - - - +
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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