Contacts of the helix formed by residues 152 - 163 (chain A) in PDB entry 1EBF
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 ILE 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A GLU* 3.2 4.9 + - - +
146A VAL* 3.8 31.4 - - + +
147A GLY* 3.9 9.4 - - - -
150A LEU* 2.9 36.3 + - + +
151A PRO* 1.3 77.5 - - - +
153A ILE* 1.3 66.2 + - + +
154A SER 3.4 0.7 - - - -
155A PHE* 3.2 5.8 + - - +
156A LEU* 2.9 39.8 + - + +
173A PHE* 6.0 1.8 - - + -
227A VAL* 5.7 0.7 - - + -
319A ASN* 6.2 0.9 - - + -
320A VAL* 6.0 0.7 - - - -
321A ILE* 3.7 50.7 - - + +
323A ILE* 4.9 2.1 - - + +
334A ILE* 4.4 7.6 - - + +
2104A NA 4.4 0.2 - - - -
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Residues in contact with ILE 153 (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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142A HIS* 3.4 27.1 - - + +
143A GLU* 3.1 23.7 + - - +
145A THR* 3.4 14.1 - - - +
146A VAL* 3.4 33.2 - - + +
152A ILE* 1.3 83.3 - - + +
154A SER* 1.3 67.1 + - - +
156A LEU* 3.2 8.5 + - + +
157A ARG* 2.9 49.7 + - - +
227A VAL* 5.7 0.9 - - + -
230A ILE* 3.9 20.2 - - + -
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Residues in contact with SER 154 (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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141A TYR* 6.3 1.8 - - - -
143A GLU* 2.9 20.9 + - - -
151A PRO* 4.2 15.2 - - - +
153A ILE* 1.3 78.7 - - - +
155A PHE* 1.3 59.4 + - - +
157A ARG* 3.4 6.9 + - - +
158A GLU* 2.9 31.6 + - - +
354A LYS* 4.5 20.9 + - - -
151B PRO* 5.9 0.5 - - - +
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Residues in contact with PHE 155 (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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151A PRO 3.7 15.0 - - - +
152A ILE 3.2 8.2 + - - +
153A ILE 3.2 0.4 - - - -
154A SER* 1.3 83.5 + - - +
156A LEU* 1.3 65.6 + - + +
158A GLU* 3.7 10.4 - - - +
159A ILE* 3.0 57.0 + - + +
323A ILE* 4.4 21.8 - - + -
328A TYR* 4.0 22.2 - + - -
332A VAL* 3.7 30.7 - - + -
334A ILE* 4.6 4.9 - - + -
149B GLY 3.5 23.3 - - - -
150B LEU* 4.8 1.1 - - - -
151B PRO* 3.5 33.4 - - + -
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Residues in contact with LEU 156 (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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152A ILE* 2.9 31.0 + - + +
153A ILE* 3.2 11.9 + - + +
155A PHE* 1.3 78.6 - - + +
157A ARG* 1.3 57.6 + - - +
159A ILE* 3.3 7.6 + - + +
160A ILE* 2.9 36.2 + - + +
166A VAL* 4.3 14.8 - - + -
169A ILE* 4.2 10.8 - - + -
227A VAL* 4.3 23.1 - - + +
230A ILE* 3.8 28.0 - - + -
231A SER* 5.3 0.2 - - - +
321A ILE* 5.0 0.4 - - + -
323A ILE* 3.8 37.2 - - + -
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Residues in contact with ARG 157 (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 TRP* 4.0 10.9 - - - -
131A PHE* 3.1 39.6 - - - +
141A TYR* 6.5 1.1 - - - -
142A HIS* 2.9 30.7 + - - -
153A ILE* 2.9 37.3 + - + +
154A SER* 3.9 6.1 - - - +
156A LEU* 1.3 76.2 - - - +
158A GLU* 1.3 63.3 + - - +
160A ILE* 3.9 6.4 - - - +
161A GLN* 3.0 40.1 + - - +
230A ILE* 4.2 19.7 - - + +
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Residues in contact with GLU 158 (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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154A SER 2.9 19.0 + - - +
155A PHE* 3.7 10.0 - - - +
157A ARG* 1.3 75.8 - - - +
159A ILE* 1.3 72.9 + - - +
161A GLN* 3.1 22.7 + - - +
162A THR* 3.1 20.4 + - + +
143B GLU* 6.0 3.2 - - - +
149B GLY 4.2 15.1 - - - +
346B ALA 4.3 6.3 - - - +
347B GLY* 4.8 3.5 - - - +
350B GLY* 3.7 27.5 - - - +
351B ASP* 5.4 0.2 - - - +
353B ILE* 5.0 3.8 - - + +
354B LYS* 2.7 32.4 + - - +
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Residues in contact with ILE 159 (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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155A PHE* 3.0 59.6 + - + +
156A LEU* 3.5 7.0 - - + +
158A GLU* 1.3 84.5 - - - +
160A ILE* 1.3 71.9 + - + +
162A THR* 2.7 21.8 + - - +
164A ASP* 3.1 44.9 + - + +
166A VAL* 5.7 0.7 - - + -
325A THR* 4.6 11.0 - - + -
328A TYR* 4.1 16.6 - - + +
149B GLY* 5.0 2.2 - - - +
346B ALA* 4.6 19.3 - - + +
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Residues in contact with ILE 160 (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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156A LEU* 2.9 29.1 + - - +
157A ARG* 3.9 6.3 - - - +
159A ILE* 1.3 78.8 - - + +
161A GLN* 1.3 64.4 + - + +
163A GLY* 3.1 13.7 + - - -
164A ASP 3.6 19.8 - - - +
165A GLU* 4.5 0.4 - - - -
166A VAL* 3.5 36.1 - - + +
230A ILE* 4.5 19.5 - - + +
231A SER* 5.6 1.1 - - - -
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Residues in contact with GLN 161 (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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157A ARG* 3.0 37.5 + - - +
158A GLU* 3.1 12.8 + - - +
160A ILE* 1.3 78.7 - - + +
162A THR* 1.3 60.2 + - - +
163A GLY* 3.3 1.2 + - - -
27B MET* 3.3 29.2 - - + +
28B LYS 5.0 3.9 + - - +
29B SER* 5.4 6.1 + - - -
353B ILE* 3.6 39.0 - - + +
357B GLN* 4.7 7.6 + - - +
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Residues in contact with THR 162 (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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158A GLU* 3.1 13.6 + - + +
159A ILE* 2.7 20.9 + - + -
161A GLN* 1.3 75.6 - - - +
163A GLY* 1.3 55.5 + - - +
327A ARG* 2.8 30.0 + - - -
23B GLN* 3.6 33.0 - - - +
26B ALA* 6.0 0.7 - - - +
27B MET* 5.3 2.0 - - - -
346B ALA* 3.7 26.3 - - + +
349B LEU* 3.9 29.6 - - + -
350B GLY* 4.3 4.9 - - - +
353B ILE* 4.4 5.8 - - + -
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Residues in contact with GLY 163 (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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160A ILE 3.1 11.3 + - - -
161A GLN 3.1 2.3 + - - -
162A THR* 1.3 79.4 - - - +
164A ASP* 1.3 66.6 + - - +
165A GLU* 3.8 5.1 - - - +
326A LYS* 3.2 20.4 + - - -
327A ARG* 3.4 8.4 + - - -
27B MET* 6.5 0.2 - - - -
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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