Contacts of the strand formed by residues 168 - 172 (chain C) in PDB entry 4ZZ7
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 CYS 168 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ALA* 3.2 41.5 - - + +
52C ALA* 3.8 13.5 - - - -
53C PHE* 3.5 26.6 - - + -
56C TRP* 4.5 2.9 - - - -
140C GLY 3.0 9.1 + - - +
141C VAL* 3.4 2.6 - - + -
142C VAL* 2.7 33.8 + - - +
167C ASN* 1.3 80.9 - - - +
169C PHE* 1.3 56.5 + - - +
197C VAL* 3.4 20.2 - - - +
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Residues in contact with PHE 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ALA* 4.4 0.2 - - - +
142C VAL* 3.4 26.0 - - + -
143C ALA 4.8 0.2 - - - -
144C GLY* 3.6 30.7 - - - -
158C MET* 3.6 27.6 - - + -
159C PHE* 3.7 26.2 - + + -
162C ALA* 3.6 28.7 - - + -
163C ILE* 4.3 6.3 - - + -
168C CYS* 1.3 74.8 - - - +
170C VAL* 1.3 78.1 + - - +
171C LEU* 3.8 21.1 - - + -
197C VAL 2.8 14.8 + - - +
198C MET* 3.8 15.3 - - - -
199C ASN* 2.8 34.2 + - - -
221C SER* 5.6 0.2 - - - -
471C TYR* 4.6 2.0 - - - -
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Residues in contact with VAL 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C VAL* 5.1 0.7 - - + +
45C ALA* 3.9 45.1 - - + +
46C ILE* 4.2 6.1 - - + -
49C ALA* 4.1 2.0 - - + -
141C VAL* 4.1 21.3 - - + -
142C VAL 3.0 8.6 + - - +
143C ALA* 3.4 4.4 - - - +
144C GLY 3.0 22.7 + - - +
169C PHE* 1.3 80.9 - - - +
171C LEU* 1.3 61.0 + - - +
199C ASN* 3.6 6.1 - - + +
201C VAL* 4.3 16.8 - - + -
211C LEU* 3.7 27.4 - - + +
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Residues in contact with LEU 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C GLY* 3.4 17.3 - - - +
146C THR* 3.8 30.1 - - + +
155C PRO* 4.0 18.4 - - + -
158C MET* 5.0 0.4 - - - -
159C PHE* 4.5 2.2 - - + -
169C PHE* 3.8 13.2 - - + -
170C VAL* 1.3 72.7 - - - +
172C LYS* 1.3 59.7 + - - +
173C PRO* 3.6 7.6 - - + +
181C THR* 3.7 29.6 - - + -
185C ALA* 5.9 0.4 - - + -
198C MET* 3.8 24.5 - - + -
199C ASN 2.8 16.0 + - - +
200C VAL* 3.5 7.9 - - + -
201C VAL* 2.7 35.6 + - - +
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Residues in contact with LYS 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C GLY 2.8 14.1 + - - +
145C ILE* 3.4 6.8 - - + -
146C THR 3.4 18.2 + - - -
170C VAL 4.1 0.2 + - - -
171C LEU* 1.3 74.3 - - - +
173C PRO* 1.3 87.6 + - - +
175C GLU* 3.5 1.8 + - - -
201C VAL* 3.2 15.5 - - + +
203C GLY 3.1 30.0 + - - +
204C ASP* 4.3 0.6 - - - +
207C ALA* 3.8 21.5 - - + -
208C VAL* 3.6 23.1 - - + -
211C LEU* 3.9 19.5 - - + -
501C NAD 2.7 44.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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