Contacts of the helix formed by residues 140 - 155 (chain E) in PDB entry 3EXF
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 ALA 140 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E ASN* 5.7 3.4 - - + +
137E ILE* 2.7 37.8 + - + +
138E VAL 3.2 0.2 - - - -
139E GLY* 1.3 70.2 - - - +
141E GLN* 1.3 61.7 + - - +
142E VAL 3.0 1.7 + - - -
143E PRO* 3.5 5.5 - - - +
144E LEU* 3.5 19.6 + - + +
174E GLN* 3.0 17.8 - - - +
91F ASP* 4.1 8.3 - - - +
92F GLN* 3.8 18.7 + - - +
96F SER* 4.2 12.1 - - - +
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Residues in contact with GLN 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E ILE* 3.8 18.8 - - + +
87E THR 3.5 32.8 - - - +
88E ALA* 3.9 18.4 - - - +
135E ASN* 3.9 12.7 - - - +
137E ILE 3.7 4.0 - - - +
138E VAL* 4.7 0.9 - - - +
139E GLY 3.2 23.9 + - - +
140E ALA* 1.3 73.8 + - - +
142E VAL* 1.3 64.4 + - + +
144E LEU* 3.4 13.4 - - - +
145E GLY* 3.0 19.9 + - - -
163E THR* 3.6 6.5 - - + +
164E LEU 3.0 24.2 + - - +
165E TYR* 3.7 18.0 - - - +
166E GLY 4.9 0.8 - - - +
169E ALA* 5.5 0.4 - - - +
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Residues in contact with VAL 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139E GLY 2.8 18.4 + - - +
140E ALA 3.0 0.4 + - - -
141E GLN* 1.3 72.5 - - - +
143E PRO* 1.3 77.7 - - + +
144E LEU 3.0 0.9 + - - -
145E GLY* 3.2 1.0 + - - -
146E ALA* 3.1 15.9 + - - +
163E THR* 3.6 9.3 - - + +
165E TYR* 3.7 30.7 - - + -
175E ILE* 3.3 35.0 - - + -
178E ALA* 3.5 13.5 - - + -
191E PHE* 3.4 35.3 - - + -
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Residues in contact with PRO 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E GLY 3.5 3.1 - - - +
140E ALA 3.6 4.0 - - - +
142E VAL* 1.3 91.1 - - + +
144E LEU* 1.3 65.3 + - - +
146E ALA* 3.0 6.0 + - + +
147E GLY 2.9 16.6 + - - -
174E GLN* 3.3 50.0 - - + +
178E ALA* 4.1 11.0 - - + -
60F MET 4.6 1.1 - - - +
61F GLY* 3.9 17.0 - - - +
64F GLY* 3.6 27.6 - - - -
65F ILE* 3.8 7.5 - - + +
92F GLN* 4.5 0.4 - - - +
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Residues in contact with LEU 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E ILE* 3.7 18.4 - - + -
132E TYR 5.4 0.2 - - - +
135E ASN* 3.7 23.1 - - - +
140E ALA* 3.5 12.0 + - + +
141E GLN* 3.3 11.2 + - - +
142E VAL 3.0 1.0 + - - -
143E PRO* 1.3 74.8 - - - +
145E GLY* 1.3 51.8 + - - +
147E GLY* 2.6 23.6 + - - -
148E ILE* 2.7 21.1 + - + +
64F GLY 3.3 20.2 - - - +
67F VAL* 3.6 24.5 - - + -
68F GLY* 3.4 10.0 - - - +
71F MET* 4.4 19.5 - - + -
92F GLN* 3.8 13.7 - - - +
96F SER* 4.3 11.9 - - - +
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Residues in contact with GLY 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E ILE* 3.7 16.1 - - - +
141E GLN 3.0 7.7 + - - -
142E VAL 3.8 1.1 - - - -
144E LEU* 1.3 79.1 - - - +
146E ALA* 1.3 55.5 + - - +
148E ILE* 3.2 3.8 + - - -
149E ALA* 2.8 24.8 + - - +
161E CYS* 3.4 15.1 - - - -
163E THR* 3.3 24.7 - - - -
189E CYS* 4.6 1.3 - - - -
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Residues in contact with ALA 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E VAL 3.1 10.0 + - - +
143E PRO* 3.0 12.4 + - + +
145E GLY* 1.3 73.9 - - - +
147E GLY* 1.3 58.4 + - - +
149E ALA* 3.0 10.6 + - - +
150E LEU* 2.9 22.9 + - - +
163E THR* 4.3 0.6 + - - -
178E ALA* 4.5 14.4 - - + +
182E ALA* 4.9 1.8 - - + -
187E LEU* 3.3 14.6 - - + +
189E CYS* 4.4 6.8 - - - -
191E PHE* 4.7 9.2 - - + -
65F ILE* 4.0 20.9 - - + -
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Residues in contact with GLY 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E PRO 2.9 7.0 + - - -
144E LEU 2.6 10.3 + - - -
146E ALA* 1.3 72.7 - - - +
148E ILE* 1.3 61.1 + - - -
149E ALA 2.8 5.0 + - - -
150E LEU* 3.0 6.8 + - - +
151E ALA 2.8 20.4 + - - -
65F ILE* 3.2 33.6 - - - +
69F ALA* 3.6 12.4 - - - -
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Residues in contact with ILE 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E HIS* 3.6 42.0 - - + +
86E ILE* 4.2 10.1 - - + -
132E TYR* 3.6 40.6 - - + +
144E LEU* 2.7 25.9 + - + +
145E GLY* 3.5 17.5 - - - +
147E GLY* 1.3 71.8 - - - +
149E ALA* 1.3 61.4 + - - +
151E ALA* 3.3 8.1 - - - +
152E CYS* 3.1 15.8 - - - -
161E CYS* 3.8 6.1 - - + -
68F GLY* 3.5 20.4 - - - +
71F MET* 5.2 2.5 - - + -
72F ALA* 4.1 13.2 - - + -
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Residues in contact with ALA 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E GLY 2.8 12.5 + - - +
146E ALA 3.1 13.0 - - - +
147E GLY 2.8 0.8 - - - -
148E ILE* 1.3 76.4 - - - +
150E LEU* 1.3 64.7 + - - +
152E CYS* 2.8 19.0 + - - +
153E LYS* 3.0 12.0 + - - +
161E CYS* 4.4 7.9 - - + -
187E LEU* 4.0 10.5 - - + -
188E PRO* 3.9 16.5 - - - +
189E CYS* 3.6 28.0 - - + -
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Residues in contact with LEU 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E ALA 2.9 12.1 + - - +
147E GLY* 3.4 9.6 - - - +
149E ALA* 1.3 75.1 - - - +
151E ALA* 1.3 63.2 + - - +
153E LYS* 3.3 11.7 + - + +
154E TYR* 2.9 36.3 + - + +
185E TRP* 4.5 18.2 - - + -
187E LEU* 3.8 25.1 - - + +
24F PHE* 4.6 25.6 - - + -
26F LEU* 5.4 2.0 - - + -
50F LYS 6.1 0.2 - - - +
53F ILE* 4.6 16.4 - - + -
65F ILE* 4.1 21.3 - - + -
69F ALA* 5.2 3.4 - - + -
74F LEU* 5.0 1.1 - - + -
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Residues in contact with ALA 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E HIS* 6.2 0.9 - - + -
147E GLY 2.8 12.6 + - - +
148E ILE 3.3 8.5 - - - +
150E LEU* 1.3 69.6 - - - +
152E CYS* 1.3 53.7 + - - +
154E TYR* 2.9 6.1 + - - +
155E ASN* 2.8 44.4 + - - +
69F ALA* 4.7 1.5 - - - +
72F ALA* 3.3 37.7 - - + +
74F LEU* 3.9 21.6 - - + +
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Residues in contact with CYS 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E HIS* 3.4 39.0 - - - -
148E ILE* 3.1 22.0 - - - -
149E ALA* 2.8 11.7 + - - +
151E ALA* 1.3 77.4 - - - +
153E LYS* 1.3 61.3 + - - +
155E ASN* 3.6 5.0 + - - +
156E GLY* 3.4 20.3 + - - -
157E LYS* 3.6 8.0 + - - +
158E ASP* 4.3 3.5 + - - -
159E GLU* 3.9 34.0 + - + +
160E VAL 4.4 8.1 - - - -
188E PRO* 4.5 5.2 - - + -
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Residues in contact with LYS 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E ALA 3.0 10.0 + - - +
150E LEU* 3.7 17.3 - - + +
152E CYS* 1.3 79.0 - - - +
154E TYR* 1.3 61.6 + - - +
156E GLY* 3.3 12.8 + - - -
185E TRP* 2.3 37.0 + - - +
186E LYS* 3.7 9.3 - - - +
187E LEU* 4.0 10.8 - - + +
188E PRO* 4.1 22.1 - - + +
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Residues in contact with TYR 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E LEU* 2.9 27.4 + - + +
151E ALA 3.3 4.5 - - - +
153E LYS* 1.3 77.4 - - - +
155E ASN* 1.3 70.4 + - - +
156E GLY 3.2 2.8 + - - -
21F GLU* 2.5 35.8 + - + -
22F LYS* 3.7 8.7 - - + -
23F VAL 3.4 9.0 + - - -
24F PHE* 4.1 20.6 - + + -
50F LYS* 3.6 62.8 + - + +
51F ARG* 3.2 18.2 + - - -
74F LEU* 3.9 24.2 - - + -
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Residues in contact with ASN 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E ALA* 2.8 27.5 + - - +
152E CYS* 3.6 5.9 + - - +
153E LYS 3.3 0.2 - - - -
154E TYR* 1.3 88.0 - - - +
156E GLY* 1.3 52.7 + - - +
157E LYS* 2.6 47.8 + - + +
22F LYS* 3.0 30.0 + - - +
72F ALA 5.0 6.7 + - - -
73F GLY* 6.3 0.2 - - - -
74F LEU* 4.1 9.8 - - - +
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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