Contacts of the helix formed by residues 159 - 172 (chain B) in PDB entry 4B94
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 VAL 159 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B LEU* 4.1 22.0 - - + -
157B GLY* 3.2 15.9 + - - +
158B ASN* 1.3 68.5 - - - +
160B LYS* 1.3 64.7 + - - +
162B SER* 3.4 8.6 + - - -
163B LYS* 3.1 23.3 + - + +
187B LEU* 4.2 21.8 - - + +
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Residues in contact with LYS 160 (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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158B ASN 3.4 0.4 - - - -
159B VAL* 1.3 77.4 - - - +
161B LYS* 1.4 54.9 - - - +
163B LYS* 3.4 7.5 + - - +
164B GLN* 3.0 58.6 + - + +
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Residues in contact with LYS 161 (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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133B GLN* 5.5 2.7 + - - +
136B ARG* 5.0 1.0 - - - +
149B PHE* 4.8 10.7 - - - -
153B GLU* 3.8 24.5 - - + +
158B ASN* 3.5 20.2 + - + +
160B LYS* 1.4 74.8 - - - +
162B SER* 1.4 59.5 + - - +
164B GLN* 3.3 21.5 + - + +
165B LEU* 2.9 52.0 + - + +
129D ARG* 5.8 0.8 - - - +
130D ASP* 3.8 29.5 + - - +
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Residues in contact with SER 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ALA* 2.7 40.2 + - - +
153B GLU* 4.0 4.6 - - - +
154B LEU* 3.7 17.1 - - - +
158B ASN 3.0 14.4 + - - -
159B VAL* 3.5 11.2 - - - -
161B LYS* 1.4 76.5 - - - +
163B LYS* 1.4 60.6 + - - +
165B LEU 3.5 0.7 + - - -
166B LEU* 3.2 24.8 + - - +
187B LEU* 3.8 14.3 - - - +
194B LEU* 4.1 3.8 - - - +
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Residues in contact with LYS 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B VAL* 3.1 13.6 + - + +
160B LYS* 3.7 9.6 - - - +
161B LYS 3.3 0.2 - - - -
162B SER* 1.4 73.3 - - - +
164B GLN* 1.4 58.7 + - + +
166B LEU* 3.3 5.4 + - - +
167B GLN* 2.9 63.1 + - - +
184B LEU* 4.3 12.6 - - + -
187B LEU* 3.5 28.2 - - + +
188B ASN* 4.4 14.7 + - - -
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Residues in contact with GLN 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* 3.0 46.6 + - + +
161B LYS* 3.3 29.3 + - + +
163B LYS* 1.4 74.2 - - + +
165B LEU* 1.3 56.3 + - - +
167B GLN* 3.4 13.7 + - - +
168B LYS* 2.9 32.2 + - - +
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Residues in contact with LEU 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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136B ARG* 3.5 30.2 + - - +
146B HIS* 4.5 13.6 + - + +
149B PHE* 3.7 49.4 - - + -
150B ALA* 3.9 17.0 - - + +
153B GLU* 3.7 18.2 - - + -
161B LYS* 2.9 38.6 + - + +
162B SER 3.6 5.2 - - - +
163B LYS 3.3 0.2 - - - -
164B GLN* 1.3 76.4 - - - +
166B LEU* 1.3 60.0 + - - +
168B LYS* 3.5 4.8 + - - +
169B ALA* 3.1 23.2 + - - +
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Residues in contact with LEU 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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146B HIS 4.6 2.0 - - - +
147B ILE* 3.8 30.3 - - + -
150B ALA* 3.7 17.5 - - + -
162B SER 3.2 9.0 + - - +
163B LYS 3.3 6.5 + - - +
165B LEU* 1.3 73.2 - - - +
167B GLN* 1.3 65.0 + - - +
169B ALA* 3.4 6.9 + - - +
170B VAL* 3.2 27.3 + - - +
180B LEU* 4.4 9.1 - - + +
183B ALA* 3.9 34.1 - - + +
184B LEU* 3.8 17.9 - - + +
187B LEU* 3.9 27.8 - - + -
194B LEU* 4.1 8.5 - - + -
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Residues in contact with GLN 167 (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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163B LYS* 2.9 52.4 + - - +
164B GLN* 3.9 11.5 + - - +
166B LEU* 1.3 71.7 - - - +
168B LYS* 1.3 59.4 + - - +
170B VAL* 3.3 9.9 + - - +
171B GLU* 3.0 29.5 + - - +
184B LEU* 4.2 16.2 - - + +
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Residues in contact with LYS 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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136B ARG* 3.6 11.6 - - - +
146B HIS* 5.5 0.9 - - - +
164B GLN 2.9 19.2 + - - +
165B LEU* 3.8 5.4 - - - +
166B LEU 3.4 0.2 - - - -
167B GLN* 1.3 74.6 - - - +
169B ALA* 1.4 57.2 + - - +
171B GLU* 3.3 12.8 + - - +
172B ARG* 2.8 68.3 + - + +
1199B MLI 3.4 24.7 + - - +
126D ASP 4.9 2.2 + - - -
127D ASP* 4.6 13.7 + - - +
129D ARG* 6.0 2.0 - - - +
130D ASP* 3.2 29.4 + - - +
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Residues in contact with ALA 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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146B HIS* 3.6 38.1 + - + -
165B LEU 3.1 12.2 + - - +
166B LEU 3.5 9.4 - - - +
167B GLN 3.3 0.2 - - - -
168B LYS* 1.4 76.3 - - - +
170B VAL* 1.4 59.8 + - - +
172B ARG* 3.5 1.0 + - - -
173B GLY 3.1 4.9 + - - -
174B ALA* 3.0 31.7 + - + +
180B LEU* 3.7 23.1 - - + +
1200B GOL 4.9 1.8 - - - -
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Residues in contact with VAL 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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166B LEU 3.2 15.4 + - - +
167B GLN* 3.3 8.3 + - - +
169B ALA* 1.4 75.5 - - - +
171B GLU* 1.3 62.4 + - - +
173B GLY* 3.2 13.4 + - - -
177B LEU* 4.1 23.5 - - + +
180B LEU* 3.8 28.9 - - + -
181B GLU* 4.6 6.7 - - - +
184B LEU* 3.9 19.7 - - + -
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Residues in contact with GLU 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 GLN 3.0 16.8 + - - +
168B LYS* 3.5 13.7 - - - +
170B VAL* 1.3 79.5 - - - +
172B ARG* 1.3 96.8 + - - +
173B GLY 3.5 0.5 + - - -
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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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168B LYS* 2.8 52.1 + - + +
169B ALA* 4.4 0.7 - - - +
171B GLU* 1.3 98.6 + - - +
173B GLY* 1.3 58.4 + - - +
174B ALA 3.6 0.9 - - - -
1199B MLI 4.8 4.0 - - - +
1200B GOL 3.1 44.6 - - - +
126D ASP* 3.5 21.0 + - - +
127D ASP* 2.8 48.3 + - - +
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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