Contacts of the helix formed by residues 162 - 175 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58B VAL* 6.3 3.6 - - + -
124B GLY* 5.0 13.0 - - - +
125B VAL* 4.4 5.1 - - + +
160B LYS 5.4 1.3 - - - +
161B ASP* 1.3 99.8 + - - +
163B GLU* 1.3 74.3 + - + +
164B LEU 3.1 2.0 - - - -
165B GLN* 2.8 39.6 + - - +
166B ILE* 2.9 25.2 + - + +
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Residues in contact with GLU 163 (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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150B MET* 3.8 17.7 - - - +
151B THR* 2.8 44.0 + - - +
152B LYS 4.8 2.4 - - - -
160B LYS* 4.6 17.0 - - + +
161B ASP 3.8 0.2 - - - -
162B ILE* 1.3 84.7 - - + +
164B LEU* 1.3 59.9 + - + +
166B ILE* 3.2 17.9 - - + +
167B ARG* 2.4 59.8 + - - +
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Residues in contact with LEU 164 (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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160B LYS 3.7 17.2 + - - +
161B ASP* 5.0 4.5 - - - +
162B ILE 3.1 0.6 - - - -
163B GLU* 1.3 76.5 - - + +
165B GLN* 1.3 63.6 + - + +
166B ILE 3.1 0.2 - - - -
167B ARG* 3.7 13.8 - - + +
168B GLU* 2.9 34.2 + - + +
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Residues in contact with GLN 165 (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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124B GLY* 4.0 9.1 - - - -
125B VAL* 3.5 38.5 + - + +
161B ASP 3.6 18.7 + - - +
162B ILE* 2.8 29.2 + - - +
164B LEU* 1.3 82.5 - - + +
166B ILE* 1.3 54.8 + - - +
168B GLU* 3.4 8.9 + - - +
169B LEU* 3.0 28.8 + - - +
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Residues in contact with ILE 166 (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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34B GLN* 5.7 1.6 - - - +
125B VAL* 3.6 21.8 - - + -
148B PRO* 3.6 39.7 - - + +
149B GLY 3.7 21.3 - - - +
150B MET* 4.6 4.3 - - + -
151B THR* 5.6 2.7 - - - +
162B ILE* 2.9 20.6 + - + +
163B GLU* 3.2 26.5 - - + +
165B GLN* 1.3 74.3 - - - +
167B ARG* 1.3 61.3 + - - +
169B LEU* 3.0 8.5 + - - +
170B ILE* 2.8 38.2 + - + +
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Residues in contact with ARG 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B MET* 4.4 16.0 - - + +
152B LYS* 4.8 4.4 - - - +
163B GLU* 2.4 56.6 + - - +
164B LEU* 3.3 16.7 + - + +
166B ILE* 1.3 76.0 - - - +
168B GLU* 1.3 57.5 + - - +
170B ILE* 3.3 4.9 + - - +
171B LEU* 2.9 30.2 + - - +
195B GLU* 2.8 40.8 + - - +
199B ILE* 3.8 28.0 - - + +
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Residues in contact with GLU 168 (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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164B LEU* 2.9 22.4 + - + +
165B GLN* 3.7 8.3 - - - +
167B ARG* 1.3 77.5 - - - +
169B LEU* 1.3 66.1 + - - +
171B LEU* 3.3 11.3 + - + +
172B ARG* 3.1 54.0 + - - +
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Residues in contact with LEU 169 (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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62B PRO* 4.5 3.1 - - + -
125B VAL* 3.5 25.8 - - + -
126B SER* 3.5 25.4 - - - +
127B PRO* 3.9 11.4 - - + -
147B LEU* 3.9 16.2 - - + -
148B PRO* 4.2 17.7 - - + -
165B GLN 3.0 14.8 + - - +
166B ILE* 3.4 9.0 - - - +
168B GLU* 1.3 81.3 + - - +
170B ILE* 1.3 68.3 + - + +
172B ARG* 3.1 28.7 + - - +
173B PHE* 3.3 33.4 - - + -
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Residues in contact with ILE 170 (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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31B VAL* 3.8 30.5 - - + -
32B GLY 5.7 0.4 - - - +
147B LEU* 4.1 27.5 - - + +
148B PRO 3.8 18.6 - - - +
150B MET* 3.9 29.2 - - + -
166B ILE* 2.8 32.1 + - + +
167B ARG* 3.6 6.7 - - - +
169B LEU* 1.3 74.0 - - + +
171B LEU* 1.3 59.1 + - - +
173B PHE* 3.1 5.7 + - - +
174B ILE* 2.9 35.3 + - + +
199B ILE* 3.6 18.6 - - + -
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Residues in contact with LEU 171 (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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167B ARG 2.9 17.4 + - - +
168B GLU* 3.5 10.1 - - + +
169B LEU 3.1 0.2 - - - -
170B ILE* 1.3 78.3 - - - +
172B ARG* 1.3 58.9 + - + +
174B ILE* 3.6 9.6 - - + -
175B SER* 2.8 49.3 + - - +
199B ILE* 4.7 4.5 - - + +
202B GLU* 3.2 34.3 - - - +
203B VAL* 4.2 13.2 - - + -
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Residues in contact with ARG 172 (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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21B ASP* 4.3 23.6 + - - +
127B PRO* 3.2 42.7 + - - +
168B GLU* 3.1 43.1 + - - +
169B LEU* 3.1 18.9 + - - +
171B LEU* 1.3 79.9 - - + +
173B PHE* 1.3 67.0 + - + +
175B SER* 3.2 15.4 + - - -
176B ASN* 4.7 2.3 + - - +
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Residues in contact with PHE 173 (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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27B GLN* 4.5 16.7 + - - -
29B VAL* 3.9 25.4 - - + +
62B PRO* 3.8 23.8 - - + -
64B ILE* 5.9 2.5 - - + -
127B PRO* 4.2 13.9 - - + -
129B PRO* 5.1 9.0 - - + -
145B VAL* 4.5 11.2 - - + -
147B LEU* 3.6 21.3 - - + -
169B LEU* 3.3 40.8 + - + -
170B ILE 3.1 6.6 + - - +
172B ARG* 1.3 85.0 - - + +
174B ILE* 1.3 57.6 + - - +
175B SER 3.2 3.8 - - - -
176B ASN* 3.2 28.9 + - - +
179B SER* 3.9 4.7 + - - -
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Residues in contact with ILE 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 4.4 12.3 - - + -
31B VAL* 4.5 10.3 - - + -
147B LEU* 5.8 0.2 - - + -
170B ILE* 2.9 39.5 + - + +
171B LEU* 3.6 13.5 - - - -
173B PHE* 1.3 69.0 - - - +
175B SER* 1.3 57.8 + - - +
176B ASN 3.1 5.9 + - - -
179B SER* 3.5 11.3 + - - +
181B ILE* 3.4 49.1 - - + -
199B ILE* 4.3 8.5 - - + +
200B SER* 3.7 24.7 - - - +
203B VAL* 3.2 22.9 - - + +
209B ARG* 3.5 4.5 + - - -
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Residues in contact with SER 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LEU* 2.8 35.0 + - - +
172B ARG* 3.2 14.9 + - - -
173B PHE 3.2 0.2 - - - -
174B ILE* 1.3 76.1 - - - +
176B ASN* 1.3 63.3 + - - +
177B PRO* 3.4 8.0 - - - +
203B VAL* 3.4 21.9 - - - +
209B ARG* 4.2 1.9 + - - -
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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