Contacts of the strand formed by residues 168 - 172 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ALA* 3.3 40.2 - - + +
52D ALA* 3.8 6.3 - - - -
53D PHE* 3.6 25.3 - - + -
56D TRP* 4.4 3.1 - - - -
140D GLY 3.0 9.5 + - - +
141D VAL* 4.3 3.1 - - + -
142D VAL* 2.8 35.3 + - - +
167D ASN* 1.3 79.3 - - - +
169D PHE* 1.3 57.4 + - - +
197D VAL* 3.2 31.0 - - - +
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Residues in contact with PHE 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D ALA* 4.5 0.6 - - - +
142D VAL* 3.4 21.5 - - + -
143D ALA 4.6 0.2 - - - -
144D GLY* 3.6 29.8 - - - -
158D MET* 3.6 25.6 - - + -
159D PHE* 3.6 36.6 - - + -
162D ALA* 3.6 24.7 - - + -
163D ILE* 4.3 6.1 - - + -
168D CYS* 1.3 74.6 - - - +
170D VAL* 1.3 84.9 + - - +
171D LEU* 3.7 18.2 - - + -
197D VAL 2.7 11.4 + - - +
198D MET* 3.7 18.3 - - - -
199D ASN* 3.0 33.9 + - - -
471D TYR* 4.5 1.1 - - - -
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Residues in contact with VAL 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D VAL* 5.2 0.4 - - + -
45D ALA* 3.9 39.3 - - + +
46D ILE* 4.2 9.9 - - + -
49D ALA* 4.2 2.7 - - + -
141D VAL* 4.1 21.8 - - + -
142D VAL 2.9 10.0 + - - +
143D ALA* 3.5 4.3 - - + +
144D GLY 3.0 23.6 + - - +
169D PHE* 1.3 81.7 - - - +
171D LEU* 1.3 60.9 + - - +
199D ASN* 3.5 6.5 - - + +
201D VAL* 4.3 17.3 - - + -
211D LEU* 3.8 26.6 - - + +
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Residues in contact with LEU 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D GLY* 3.5 10.5 - - - +
146D THR* 3.9 28.0 - - + +
155D PRO* 4.0 17.3 - - + -
158D MET* 5.1 0.4 - - - -
159D PHE* 4.3 2.7 - - + -
169D PHE* 3.7 15.2 - - + -
170D VAL* 1.3 73.3 - - - +
172D LYS* 1.3 65.5 + - - +
173D PRO* 3.6 7.8 - - + +
181D THR* 3.3 33.0 - - + +
198D MET* 3.8 24.7 - - + -
199D ASN 2.8 15.9 + - - +
200D VAL* 3.4 7.7 - - + -
201D VAL* 2.7 34.1 + - - +
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Residues in contact with LYS 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D GLY 2.7 15.2 + - - +
145D ILE* 3.4 7.6 - - + +
146D THR* 3.3 19.3 + - - -
171D LEU* 1.3 75.7 - - - +
173D PRO* 1.3 90.6 + - - +
175D GLU* 3.3 1.4 + - - -
201D VAL* 3.4 14.8 - - + +
203D GLY 3.0 32.6 + - - +
204D ASP* 4.4 3.7 - - - +
207D ALA* 4.3 15.5 - - + -
208D VAL* 3.6 23.5 - - + +
211D LEU* 3.9 21.8 - - + -
501D NAD 2.5 37.0 + - - +
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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
------------------------------------------------------------
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