Contacts of the helix formed by residues 154 - 165 (chain B) in PDB entry 4CYM
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 SER 154 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A TRP* 4.5 10.3 - - - -
190A GLU* 2.2 38.1 + - - -
149B LYS* 5.2 0.2 - - - -
152B SER 4.3 0.2 + - - -
153B GLN* 1.3 75.8 - - - +
155B PRO* 1.3 73.2 - - - +
156B SER* 3.3 5.0 + - - -
157B GLN* 3.0 34.7 + - - +
158B VAL* 3.2 14.3 + - - +
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Residues in contact with PRO 155 (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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69A TRP* 5.3 22.9 - - + +
186A ARG* 3.2 28.9 - - - +
149B LYS* 4.7 8.9 - - - +
153B GLN 3.9 4.7 - - - +
154B SER* 1.3 83.7 - - - +
156B SER* 1.3 56.4 + - - +
158B VAL* 3.2 3.9 + - + +
159B ASP* 2.8 35.4 + - - +
170B TRP* 3.7 28.7 - - + -
172B GLU* 5.4 4.7 - - - +
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Residues in contact with SER 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TRP* 4.9 2.2 - - - -
183A GLU 5.1 0.2 + - - -
186A ARG* 4.1 16.0 - - - +
187A PHE* 3.3 25.3 + - - +
190A GLU* 3.4 32.6 + - - -
154B SER* 3.0 3.5 - - - -
155B PRO* 1.3 78.1 - - - +
157B GLN* 1.3 57.7 + - - +
159B ASP* 3.3 11.6 + - - +
160B GLN* 2.9 43.6 + - - -
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Residues in contact with GLN 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A GLU* 3.6 11.8 + - - +
152B SER 4.6 4.0 + - - -
153B GLN* 3.9 19.3 - - + +
154B SER* 3.0 40.7 + - - +
156B SER* 1.3 72.4 - - - +
158B VAL* 1.3 61.9 + - - +
160B GLN* 3.2 16.4 + - - +
161B PHE* 2.9 29.4 + - - +
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Residues in contact with VAL 158 (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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106B PHE* 5.5 6.1 - - + -
114B PHE* 4.9 6.3 - - + -
140B LEU* 4.5 11.2 - - + -
149B LYS* 5.8 3.1 - - - +
153B GLN* 3.4 28.7 - - + +
154B SER 3.2 13.0 + - - +
155B PRO* 3.5 8.1 - - + +
157B GLN* 1.3 74.0 - - - +
159B ASP* 1.3 64.2 + - - +
161B PHE* 3.3 8.2 - - - +
162B CYS* 3.0 27.0 + - - -
170B TRP* 3.2 49.4 - - + -
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Residues in contact with ASP 159 (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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171A PHE* 6.2 1.8 - - + -
183A GLU* 3.5 29.9 - - + +
186A ARG* 2.1 36.3 + - - +
155B PRO 2.8 23.4 + - - +
156B SER* 3.3 13.7 - - - +
157B GLN 3.3 0.2 - - - -
158B VAL* 1.3 70.9 - - - +
160B GLN* 1.3 68.6 + - - +
162B CYS* 3.5 4.0 + - - +
163B LYS* 3.3 21.5 + - - +
170B TRP* 2.8 28.3 + - - +
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Residues in contact with GLN 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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171A PHE* 5.6 2.0 - - - -
187A PHE* 3.5 36.3 - - + +
190A GLU* 5.0 4.7 - - - +
156B SER* 2.9 35.5 + - - +
157B GLN* 3.2 21.2 + - - +
159B ASP* 1.3 73.2 - - - +
161B PHE* 1.3 69.7 + - - +
163B LYS* 2.9 10.6 + - - +
164B GLU* 2.9 27.6 + - - +
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Residues in contact with PHE 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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114B PHE* 3.7 34.5 - + + -
117B VAL* 3.7 32.1 - - + -
118B LEU* 3.9 27.4 - - + -
140B LEU* 4.1 17.5 - - + -
157B GLN 2.9 10.4 + - - +
158B VAL* 3.3 12.8 - - - +
160B GLN* 1.3 78.3 - - - +
162B CYS* 1.3 66.3 + - - +
164B GLU* 3.0 5.2 + - - -
165B HIS* 3.0 52.4 + + - +
167B PHE* 4.0 15.7 - + - -
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Residues in contact with CYS 162 (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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140B LEU* 4.1 14.1 - - - -
158B VAL 3.0 20.9 + - - +
159B ASP* 3.8 7.0 - - - +
160B GLN 3.2 0.2 - - - -
161B PHE* 1.3 75.1 - - - +
163B LYS* 1.3 63.6 + - - +
165B HIS 3.3 0.5 + - - -
166B GLY* 3.1 5.7 + - - -
167B PHE* 2.9 53.0 + - + +
169B GLY* 3.5 24.5 - - - +
170B TRP* 3.7 24.2 - - + -
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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
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170A TRP 4.4 8.3 + - - -
171A PHE* 3.8 33.3 - - - +
172A GLU 5.0 1.8 - - - +
180A ASN* 3.9 25.8 - - - +
183A GLU* 6.0 1.6 - - - -
159B ASP 3.3 10.2 + - - +
160B GLN* 2.9 11.2 + - - +
162B CYS* 1.3 80.0 - - - +
164B GLU* 1.3 63.1 + - - +
165B HIS 3.3 0.3 + - - -
166B GLY* 3.9 5.9 + - - -
167B PHE 5.1 1.6 - - - -
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Residues in contact with GLU 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 GLN* 2.9 16.4 + - - +
161B PHE* 3.0 11.2 + - - +
163B LYS* 1.3 78.0 - - - +
165B HIS* 1.3 81.6 + - + +
166B GLY 3.7 0.2 - - - -
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Residues in contact with HIS 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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118B LEU* 3.4 30.2 - - + +
121B LYS* 3.2 23.3 + - + +
161B PHE* 3.0 55.5 + + - +
162B CYS 3.6 0.4 - - - -
163B LYS 3.2 0.2 - - - -
164B GLU* 1.3 105.5 + - + +
166B GLY* 1.3 63.7 + - - +
167B PHE* 3.3 18.0 + - + -
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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