Contacts of the helix formed by residues 162 - 175 (chain C) in PDB entry 4BEJ
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 162 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60C ARG* 3.6 27.1 - - - +
124C GLY* 3.3 35.4 - - - +
125C VAL* 3.5 18.6 - - + -
160C LYS 2.7 4.5 + - - -
161C ASP* 1.3 100.9 + - - +
163C GLU* 1.3 73.7 + - + +
164C LEU 3.4 2.0 - - - -
165C GLN* 3.0 19.2 + - - +
166C ILE* 2.9 31.2 + - + +
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Residues in contact with GLU 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C MET* 3.2 19.1 - - - +
151C THR* 3.1 40.4 + - - +
153C VAL* 5.2 5.7 - - + +
159C PRO* 4.1 15.6 + - + +
160C LYS 4.3 0.2 + - - -
161C ASP* 3.4 3.0 + - - +
162C ILE* 1.3 85.0 - - + +
164C LEU* 1.3 59.8 + - + +
166C ILE* 2.9 19.7 - - + +
167C ARG* 2.6 58.3 + - - +
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Residues in contact with LEU 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C GLN* 4.2 9.0 - - + +
159C PRO 3.0 31.2 - - - +
160C LYS* 3.2 30.5 + - + +
162C ILE 3.4 0.8 - - - -
163C GLU* 1.3 75.9 - - + +
165C GLN* 1.3 57.5 + - - +
166C ILE 3.0 1.6 - - - -
167C ARG* 3.4 26.4 - - + +
168C GLU* 2.7 39.5 + - + +
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Residues in contact with GLN 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C GLY* 3.1 20.5 + - - +
125C VAL* 2.6 51.1 + - + +
160C LYS 4.7 3.8 + - - +
161C ASP 5.9 0.7 - - - -
162C ILE* 3.0 21.6 + - - +
164C LEU* 1.3 78.2 - - - +
166C ILE* 1.3 60.3 + - - +
168C GLU* 3.3 8.7 + - + +
169C LEU* 3.1 21.7 + - - +
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Residues in contact with ILE 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ARG* 3.6 34.8 - - - +
125C VAL* 3.8 18.4 - - + -
148C PRO* 3.7 31.0 - - + +
149C GLY 4.3 13.9 - - - +
150C MET* 5.0 4.9 - - + +
162C ILE* 2.9 15.3 + - + +
163C GLU* 2.9 31.2 - - + +
165C GLN* 1.3 74.0 - - - +
167C ARG* 1.3 58.7 + - - +
169C LEU* 2.9 9.1 + - - +
170C ILE* 2.8 37.7 + - + +
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Residues in contact with ARG 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C MET* 3.9 31.5 - - - +
151C THR 4.5 3.2 + - - -
163C GLU* 2.6 50.1 + - - +
164C LEU* 3.0 31.5 + - + +
166C ILE* 1.3 72.6 - - - +
168C GLU* 1.3 58.7 + - + +
170C ILE* 3.3 5.7 + - - +
171C LEU* 2.9 41.6 + - + +
195C GLU* 3.2 28.1 + - - +
198C LYS* 5.9 4.4 - - - +
199C ILE* 4.0 19.6 - - + +
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Residues in contact with GLU 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C LEU* 2.7 25.6 + - + +
165C GLN* 3.6 8.5 - - - +
166C ILE 3.2 0.2 - - - -
167C ARG* 1.3 74.4 - - + +
169C LEU* 1.3 56.9 + - - +
171C LEU* 3.4 8.9 + - + +
172C ARG* 2.9 28.8 + - - +
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Residues in contact with LEU 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ARG 4.5 2.0 - - - +
62C PRO* 3.8 14.4 - - + -
125C VAL* 3.7 23.1 - - + -
126C SER 3.6 27.6 - - - +
127C PRO* 4.2 8.3 - - + -
147C LEU* 3.7 26.2 - - + -
148C PRO* 4.0 16.2 - - + -
165C GLN 3.1 12.4 + - - +
166C ILE* 2.9 10.4 + - + +
168C GLU* 1.3 74.0 - - - +
170C ILE* 1.3 69.4 + - + +
172C ARG* 3.2 19.1 + - - +
173C PHE* 3.1 30.4 - - + -
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Residues in contact with ILE 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C VAL* 3.9 30.5 - - + -
32C GLY 5.8 0.9 - - - +
147C LEU* 4.1 23.1 - - + +
148C PRO 3.4 26.5 - - - +
149C GLY* 5.4 0.2 - - - -
150C MET* 3.6 26.5 - - + -
166C ILE* 2.8 31.4 + - + +
167C ARG* 3.8 4.7 - - - +
169C LEU* 1.3 74.3 - - + +
171C LEU* 1.3 59.0 + - - +
173C PHE* 3.1 5.4 + - - +
174C ILE* 2.8 35.1 + - + +
199C ILE* 3.9 19.1 - - + -
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Residues in contact with LEU 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C ARG* 2.9 28.1 + - + +
168C GLU* 3.7 8.3 - - + +
170C ILE* 1.3 73.9 - - - +
172C ARG* 1.3 58.3 + - - +
174C ILE* 3.5 12.8 - - + -
175C SER* 2.8 41.1 + - - +
199C ILE* 3.6 25.8 - - + +
202C GLU* 3.2 32.8 - - - +
203C VAL* 3.9 13.9 - - + -
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Residues in contact with ARG 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C GLY 3.9 18.2 + - - -
20C ALA* 4.9 1.4 - - - +
21C ASP* 4.6 17.1 - - - +
127C PRO* 3.1 42.7 + - - +
168C GLU 2.9 13.6 + - - +
169C LEU* 3.2 16.7 + - - +
171C LEU* 1.3 76.7 - - - +
173C PHE* 1.3 96.3 + - - +
175C SER* 4.2 7.9 + - - -
176C ASN* 4.4 4.7 + - - +
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Residues in contact with PHE 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ASP* 5.8 8.1 - - + -
27C GLN* 4.5 14.9 + - - -
29C VAL* 4.0 27.8 - - + -
62C PRO* 3.8 29.8 - - + -
64C ILE* 5.9 2.0 - - + -
127C PRO 4.3 4.3 - - - -
129C PRO* 5.1 8.5 - - + -
145C VAL* 4.1 15.7 - - + -
147C LEU* 3.8 15.3 - - + -
169C LEU* 3.1 24.0 + - + -
170C ILE 3.1 6.4 + - - +
171C LEU 3.1 0.2 - - - -
172C ARG* 1.3 112.0 - - - +
174C ILE* 1.3 58.5 + - - +
175C SER 3.1 4.0 - - - -
176C ASN* 3.0 29.2 + - - +
179C SER* 3.6 6.9 + - - -
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Residues in contact with ILE 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C VAL* 4.6 13.0 - - + -
31C VAL* 4.5 10.3 - - + -
147C LEU* 5.8 0.2 - - + -
170C ILE* 2.8 33.8 + - + +
171C LEU* 3.5 27.4 - - + -
173C PHE* 1.3 69.5 - - + +
175C SER* 1.3 58.4 + - - +
176C ASN 3.1 10.7 + - - +
179C SER* 5.0 2.7 - - - +
181C ILE* 3.4 50.0 - - + +
199C ILE* 4.4 5.6 - - + +
200C SER* 3.7 27.1 - - - +
203C VAL* 3.4 16.2 - - + +
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Residues in contact with SER 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C LEU* 2.8 25.4 + - - +
172C ARG* 4.4 6.1 - - - -
173C PHE 3.1 0.4 - - - -
174C ILE* 1.3 75.7 - - - +
176C ASN* 1.3 62.5 + - - +
177C PRO* 3.4 9.5 - - - +
203C VAL* 3.5 28.2 - - - +
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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