Contacts of the helix formed by residues 162 - 175 (chain C) in PDB entry 3BZE
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 ASP 162 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158C ALA* 2.4 40.9 + - + +
159C TYR 3.0 2.0 + - - -
161C GLU* 1.3 103.3 - - - +
163C THR* 1.3 60.4 - - - +
164C CYS 2.9 0.2 - - - -
166C GLU* 2.2 49.8 - - + +
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Residues in contact with THR 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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158C ALA* 3.4 1.1 + - - +
159C TYR* 3.3 25.7 + - + +
162C ASP* 1.3 86.4 - - - +
164C CYS* 1.3 66.8 + - - +
166C GLU* 3.5 5.0 - - - +
167C TRP* 3.2 26.5 + - + +
1Q VAL* 3.4 31.0 - - + -
4Q PRO* 5.7 4.7 - - + +
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Residues in contact with CYS 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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5C LEU* 3.2 28.1 - - - +
100C GLY 4.0 3.8 - - - -
101C CYS* 2.0 48.5 - - - -
159C TYR* 2.5 47.7 + - + +
160C LEU* 2.9 15.9 - - - +
162C ASP 2.9 1.2 - - - -
163C THR* 1.3 73.7 - - - +
165C VAL* 1.3 50.3 + - - +
167C TRP* 2.7 26.3 + - - -
168C LEU 3.0 9.2 + - - -
1Q VAL 5.2 0.2 - - - -
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Residues in contact with VAL 165 (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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101C CYS* 3.4 17.0 - - + -
102C GLU 5.5 0.2 - - - +
103C LEU* 3.5 29.9 - - + +
107C ARG 4.6 3.4 - - - +
108C ARG* 5.1 1.3 - - - -
109C PHE* 4.4 22.7 - - + +
160C LEU 3.9 14.1 + - - +
161C GLU* 4.1 11.4 - - - +
162C ASP 3.7 0.6 + - - +
164C CYS* 1.3 76.9 - - - +
166C GLU* 1.3 80.8 + - - +
168C LEU* 3.2 5.4 + - - +
169C HIS* 3.1 24.4 + - + +
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Residues in contact with GLU 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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161C GLU 3.8 2.8 - - - +
162C ASP* 2.2 40.2 - - + +
163C THR* 3.5 7.0 - - - +
164C CYS 2.9 0.2 + - - -
165C VAL* 1.3 88.4 - - - +
167C TRP* 1.3 57.7 + - + +
169C HIS* 1.2 99.0 + - + -
170C LYS* 5.6 1.1 - - - +
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Residues in contact with TRP 167 (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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5C LEU* 4.5 1.1 - - + -
55C GLU* 3.9 15.3 - - - -
59C TYR* 3.3 37.9 - + + -
62C ARG* 3.5 21.4 - - - +
163C THR* 3.2 31.2 + - + +
164C CYS 2.7 13.6 + - - +
166C GLU* 1.3 78.0 - - + +
168C LEU* 1.3 62.1 + - - +
169C HIS* 3.1 2.9 - - - -
170C LYS* 3.4 37.1 + - + +
171C TYR* 2.8 64.9 + + + -
1Q VAL* 3.5 29.6 - - + +
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Residues in contact with LEU 168 (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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3C HIS* 3.5 17.5 - - + +
4C SER* 3.5 23.8 - - - +
5C LEU* 3.7 21.0 - - + +
28C VAL* 4.1 10.3 - - + -
101C CYS* 3.5 19.1 - - - +
103C LEU* 3.3 39.3 - - + -
164C CYS 3.0 6.1 + - - +
165C VAL* 3.2 9.6 + - - +
167C TRP* 1.3 73.6 - - - +
169C HIS* 1.3 70.4 + - - +
171C TYR* 3.5 4.6 + - + +
172C LEU* 3.1 34.1 + - + +
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Residues in contact with HIS 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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103C LEU* 5.2 5.3 - - + +
165C VAL* 3.1 9.5 + - + +
166C GLU* 1.2 112.1 + - + -
168C LEU* 1.3 82.4 - - - +
170C LYS* 1.3 106.9 + - + +
172C LEU* 2.8 15.0 + - - +
173C GLU* 2.8 29.5 + - + +
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Residues in contact with LYS 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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166C GLU* 5.6 0.8 - - - +
167C TRP* 3.4 52.6 + - + +
169C HIS* 1.3 120.7 - - + +
171C TYR* 1.3 57.9 + - + +
173C GLU* 2.9 14.7 - - - +
174C LYS* 2.8 34.6 + - + +
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Residues in contact with TYR 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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5C LEU* 3.5 30.7 - - + -
7C TYR* 4.0 1.7 + - - -
28C VAL* 4.3 11.7 - - + -
33C PHE* 3.6 14.1 - + - -
51C TRP* 3.7 19.2 - + + -
52C MET* 3.3 39.7 - - + -
55C GLU* 5.6 0.7 - - - -
59C TYR* 3.1 17.2 + - - -
167C TRP* 2.8 58.3 + + + +
168C LEU* 3.8 5.6 - - - +
169C HIS 2.9 4.2 + - - -
170C LYS* 1.3 71.2 - - + +
172C LEU* 1.3 63.2 + - - +
173C GLU 2.8 5.4 - - - -
174C LYS* 2.9 19.3 + - + +
175C GLY 3.0 10.6 + - - -
179C LEU* 3.9 1.7 - - - +
1Q VAL* 3.0 19.8 + - - -
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Residues in contact with LEU 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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3C HIS* 3.7 46.4 - - + +
28C VAL* 4.1 15.7 - - + -
29C ASP* 4.4 1.6 - - - +
103C LEU* 4.3 8.1 - - + -
107C ARG* 5.2 3.4 - - - +
168C LEU* 3.1 37.2 + - + +
169C HIS* 2.8 12.7 + - - +
171C TYR* 1.3 75.1 - - - +
173C GLU* 1.3 62.5 + - - +
175C GLY 4.0 0.4 - - - -
176C LYS* 3.2 30.0 + - - +
179C LEU* 4.0 16.6 - - + -
180C LEU* 4.0 21.7 - - + +
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Residues in contact with GLU 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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169C HIS* 2.8 35.8 - - + +
170C LYS* 2.9 21.1 - - - +
172C LEU* 1.3 82.7 - - - +
174C LYS* 1.3 55.9 + - - +
175C GLY 2.9 9.7 + - - -
176C LYS* 3.4 15.2 + - - +
177C GLU* 4.6 3.1 - - - +
180C LEU* 5.7 2.1 - - - +
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Residues in contact with LYS 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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51C TRP* 2.7 42.5 - - + +
52C MET* 4.6 6.7 - - - -
54C GLN* 1.0 80.2 - - + +
55C GLU* 2.3 46.8 + - + +
167C TRP* 6.5 0.2 - - + -
170C LYS* 2.8 23.5 + - + +
171C TYR* 2.9 12.3 + - + +
173C GLU* 1.3 70.6 - - - +
175C GLY* 1.3 48.6 + - - +
177C GLU* 5.3 1.9 - - - +
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Residues in contact with GLY 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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51C TRP* 3.5 25.1 - - - -
171C TYR 3.0 8.3 + - - -
172C LEU 3.8 3.1 - - - -
174C LYS* 1.3 80.3 - - - +
176C LYS* 1.3 59.7 + - - +
177C GLU* 3.3 5.4 - - - -
178C THR* 2.9 10.7 + - - -
179C LEU* 2.8 32.4 + - - +
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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