Contacts of the helix formed by residues 168 - 180 (chain B) in PDB entry 3CB4
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 GLY 168 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B VAL* 3.4 1.6 - - - +
160B ARG 3.7 11.0 - - - -
161B CYS* 3.6 12.3 - - - -
166B GLY 3.6 0.2 + - - -
167B VAL* 1.3 73.6 - - - +
169B VAL* 1.3 53.3 + - - +
170B GLN 3.2 3.1 - - - +
171B ASP* 3.0 18.3 + - - +
172B VAL* 2.8 36.7 + - - +
535F HIS* 3.4 15.9 - - - +
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Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 3.9 21.1 - - + -
23B ARG* 4.1 24.9 - - + +
24B ILE* 4.0 31.4 - - + +
27B ILE* 3.7 21.6 - - + +
161B CYS* 4.0 11.2 - - + -
162B SER 4.2 1.8 - - - +
166B GLY* 3.4 20.8 + - - +
167B VAL 3.2 1.2 + - - -
168B GLY* 1.3 74.1 - - - +
170B GLN* 1.3 63.3 + - - +
172B VAL* 3.3 9.1 + - - +
173B LEU* 3.2 20.8 + - - +
505F GLN* 5.9 0.2 - - - +
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Residues in contact with GLN 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ILE* 3.9 11.7 - - + +
63B TYR* 3.3 32.2 + - + +
64B LYS 5.4 0.8 + - - -
66B SER* 5.7 6.1 - - - +
166B GLY 4.5 2.2 + - - -
168B GLY 4.4 0.4 - - - +
169B VAL* 1.3 78.5 - - - +
171B ASP* 1.3 62.2 + - - +
173B LEU* 3.2 6.4 + - - +
174B GLU* 3.0 31.4 + - + +
534F THR* 3.7 5.8 + - - +
535F HIS* 3.6 12.5 - - + -
536F ILE* 2.7 71.0 + - + +
539F ARG* 4.9 0.6 - - - +
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Residues in contact with ASP 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B VAL* 3.6 20.4 - - + +
168B GLY* 3.0 14.3 + - - +
170B GLN* 1.3 82.3 - - - +
172B VAL* 1.3 57.2 + - - +
174B GLU* 3.7 12.5 - - - +
175B ARG* 3.1 27.2 + - - +
534F THR* 6.1 0.9 - - - +
535F HIS* 2.9 32.7 + - - -
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 4.4 8.1 - - + -
24B ILE* 5.3 0.4 - - + -
99B LEU* 3.6 34.2 - - + +
127B VAL* 5.7 1.1 - - + -
129B VAL* 3.7 34.1 - - + -
159B VAL* 3.6 19.1 - - + -
161B CYS* 4.1 6.3 - - - -
168B GLY 2.8 20.9 + - - +
169B VAL* 3.4 14.4 - - - +
170B GLN 3.2 0.4 - - - -
171B ASP* 1.3 77.2 - - - +
173B LEU* 1.3 57.4 + - + +
175B ARG* 3.3 3.6 + - - +
176B LEU* 2.8 35.2 + - - +
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Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 3.7 39.3 - - + -
27B ILE* 3.7 26.2 - - + -
28B CYS* 3.7 25.8 - - - -
63B TYR* 3.8 26.0 - - + -
73B LEU* 3.8 15.3 - - + -
169B VAL 3.2 7.8 + - - +
170B GLN 3.2 9.7 + - - +
172B VAL* 1.3 77.4 - - + +
174B GLU* 1.3 64.4 + - - +
176B LEU* 3.4 17.6 - - + +
177B VAL* 3.1 31.1 + - - +
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Residues in contact with GLU 174 (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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63B TYR* 2.7 33.6 + - - +
65B ALA* 3.5 5.7 - - - +
66B SER* 2.7 40.4 + - - -
170B GLN* 3.0 23.4 + - + +
171B ASP* 3.7 15.9 - - - +
173B LEU* 1.3 73.8 - - - +
175B ARG* 1.3 65.3 + - - +
177B VAL* 3.2 8.0 + - - +
178B ARG* 3.1 22.2 + - - +
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Residues in contact with ARG 175 (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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127B VAL* 3.8 23.8 - - + -
157B ASP* 3.0 54.8 + - - +
158B ALA* 4.2 2.2 - - - +
159B VAL* 3.7 28.4 - - + +
171B ASP 3.1 17.9 + - - +
172B VAL* 3.6 4.9 - - - +
174B GLU* 1.3 75.5 - - - +
176B LEU* 1.3 63.7 + - - +
178B ARG* 3.1 42.1 + - - +
179B ASP* 3.0 31.3 + - - +
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Residues in contact with LEU 176 (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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5B ARG* 3.7 29.3 + - + -
7B PHE* 3.5 41.3 - - + -
73B LEU* 4.0 11.9 - - + -
99B LEU* 4.3 15.5 - - + -
127B VAL* 4.8 7.5 - - - +
172B VAL 2.8 17.8 + - - +
173B LEU* 3.4 28.7 - - + +
175B ARG* 1.3 71.9 - - - +
177B VAL* 1.3 61.7 + - - +
180B ILE* 3.1 51.8 + - + +
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Residues in contact with VAL 177 (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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5B ARG* 2.9 49.9 + - + +
63B TYR* 4.5 10.1 - - + -
65B ALA* 5.1 4.3 - - + -
67B ASP* 5.2 1.6 - - - +
71B TYR* 3.7 44.4 - - + +
73B LEU* 4.4 18.6 - - + -
173B LEU 3.1 18.5 + - - +
174B GLU* 3.2 7.2 + - - +
176B LEU* 1.3 79.2 - - - +
178B ARG* 1.3 61.6 + - - +
180B ILE 3.7 2.1 - - - +
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Residues in contact with ARG 178 (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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157B ASP* 4.2 9.3 + - - -
174B GLU 3.1 13.3 + - - +
175B ARG* 3.1 42.8 + - - +
177B VAL* 1.3 80.4 - - - +
179B ASP* 1.3 91.1 + - - +
180B ILE 4.7 0.5 - - - +
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Residues in contact with ASP 179 (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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125B GLU* 3.2 35.4 - - - +
127B VAL* 4.5 11.5 - - + +
175B ARG* 3.0 19.8 + - - +
178B ARG* 1.3 124.6 + - - +
180B ILE* 1.3 65.3 + - - +
181B PRO* 3.4 4.2 - - - +
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Residues in contact with ILE 180 (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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5B ARG* 3.0 38.6 + - + -
6B ASN 4.4 6.7 - - - +
7B PHE* 3.7 26.0 - - + -
96B GLU* 3.9 2.7 - - + -
97B GLY* 3.8 33.9 - - - +
98B ALA 4.0 8.7 - - - +
99B LEU* 4.8 1.1 - - + -
125B GLU* 3.9 4.7 - - + +
127B VAL* 3.9 22.9 - - + -
176B LEU* 3.1 29.9 + - + +
177B VAL 3.7 4.7 - - - +
178B ARG 4.6 0.7 - - - +
179B ASP* 1.3 74.3 - - - +
181B PRO* 1.3 76.4 - - + +
182B PRO* 4.3 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