Contacts of the helix formed by residues 127 - 136 (chain B) in PDB entry 3E8E
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 GLU 127 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B LEU 4.9 2.4 - - - +
126B GLY* 1.3 73.4 - - - -
128B MET* 1.3 64.5 + - - +
129B PHE* 3.8 8.4 - - + +
130B SER* 2.7 30.5 + - - +
131B HIS* 3.2 8.3 - - - -
169B PRO 4.0 1.8 - - - +
170B GLU* 3.4 33.0 - - - +
172B LEU 3.6 5.4 - - - -
173B LEU* 3.6 13.9 - - + -
326B ASN 4.6 0.8 + - - -
327B PHE* 4.5 12.0 - - + -
330B TYR* 4.8 2.6 + - - -
351B G98 4.3 16.6 - - - +
18C ARG* 2.3 45.9 + - - -
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Residues in contact with MET 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B GLY 3.9 1.2 + - - -
127B GLU* 1.3 71.2 - - - +
129B PHE* 1.3 53.6 + - - +
131B HIS* 3.2 11.3 + - - +
132B LEU* 2.7 34.7 + - + +
138B PHE* 3.6 19.7 - - + -
146B TYR* 3.5 29.4 - - + -
169B PRO* 3.5 19.7 + - + +
172B LEU* 2.8 37.1 + - + +
174B ILE* 4.2 8.6 - - + +
180B ILE* 3.4 28.5 - - + -
227B LEU* 4.4 1.3 - - + -
231B MET* 3.7 27.4 - - - +
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Residues in contact with PHE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B GLU* 3.8 5.2 - - - +
128B MET* 1.3 78.1 - - - +
130B SER* 1.3 62.9 + - - +
132B LEU* 3.8 2.9 - - - +
133B ARG* 2.9 73.9 + - + +
169B PRO* 3.2 14.3 + - + -
170B GLU* 3.5 48.7 - - + +
328B ASP* 5.7 0.7 - - - -
16C THR 3.6 8.5 - - - -
17C GLY* 3.4 15.3 - - - -
18C ARG* 3.2 53.2 - - - -
19C ARG* 4.3 3.8 - - - -
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Residues in contact with SER 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B GLU* 2.7 26.7 + - - +
129B PHE* 1.3 86.9 - - - +
131B HIS* 1.3 67.6 + - - +
133B ARG* 3.5 3.9 + - - +
134B ARG* 3.1 32.7 + - - +
326B ASN 3.8 19.7 + - - -
328B ASP* 5.0 11.4 - - - -
18C ARG* 5.4 4.3 - - - -
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Residues in contact with HIS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B GLY 2.6 29.2 + - - -
127B GLU 3.2 21.7 + - - -
128B MET* 3.2 6.2 + - - +
130B SER* 1.3 81.2 + - - +
132B LEU* 1.3 60.0 + - - +
134B ARG* 3.0 36.9 + - - +
135B ILE* 3.2 31.2 + - + +
138B PHE* 4.2 12.3 - - + -
146B TYR* 6.0 0.4 - - - +
174B ILE* 3.9 20.6 - - + -
314B PHE* 3.5 29.5 - + + -
316B PRO* 4.1 6.9 - - + +
317B LYS 5.9 0.2 - - - -
326B ASN* 4.1 17.0 - - + +
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Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B MET 2.7 19.9 + - - +
129B PHE* 3.8 4.0 - - - +
131B HIS* 1.3 69.5 - - - +
133B ARG* 1.3 70.9 + - - +
135B ILE* 4.2 0.2 - - - -
136B GLY 2.9 50.0 + - - +
137B ARG* 3.7 7.9 - - - -
138B PHE* 3.7 24.2 - - + +
169B PRO* 4.3 15.3 - - + -
230B GLU* 3.9 37.0 - - + +
231B MET* 3.7 37.2 - - + +
234B GLY* 4.5 0.2 - - - -
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Residues in contact with ARG 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B PHE* 2.9 62.6 + - + +
130B SER* 3.9 5.4 - - - +
132B LEU* 1.3 86.9 - - - +
134B ARG* 1.3 61.1 + - - +
136B GLY* 3.9 4.5 + - - -
230B GLU* 2.8 32.8 + - - +
234B GLY 2.8 28.4 + - - -
7C TYR* 4.3 15.7 + - - -
10C PHE* 3.7 22.3 - - - -
15C ARG 5.0 0.4 + - - -
16C THR* 3.3 28.9 + - - -
19C ARG* 4.2 6.7 - - - +
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Residues in contact with ARG 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B SER* 3.1 27.8 + - - +
131B HIS* 3.0 43.4 + - - +
132B LEU 3.2 0.2 - - - -
133B ARG* 1.3 79.7 - - - +
135B ILE* 1.3 70.0 + - + +
136B GLY 3.8 0.3 + - - -
314B PHE* 3.9 16.2 - - - -
326B ASN* 5.4 2.4 + - - -
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Residues in contact with ILE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B HIS* 3.2 14.5 + - + +
132B LEU 3.8 4.3 - - - +
134B ARG* 1.3 94.5 - - + +
136B GLY* 1.3 58.6 + - - +
137B ARG* 3.2 21.0 + - - +
138B PHE* 2.9 42.2 - - + -
142B HIS* 4.8 7.0 - - + +
314B PHE* 6.0 6.1 - - + -
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Residues in contact with GLY 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B LEU* 2.9 19.1 + - - +
133B ARG 3.9 2.1 + - - -
134B ARG 3.4 3.0 + - - -
135B ILE* 1.3 74.8 - - - +
137B ARG* 1.3 59.7 + - - -
234B GLY* 3.1 25.3 - - - +
7C TYR* 3.9 23.1 + - - -
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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