Contacts of the strand formed by residues 188 - 192 (chain D) in PDB entry 1ZUM
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 VAL 188 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D ALA* 3.4 31.9 - - + +
69D ALA* 4.0 7.6 - - + -
70D PHE* 3.8 16.4 - - + -
76D TRP* 3.8 25.4 - - + -
160D GLY 3.0 13.0 + - - +
161D VAL* 3.7 19.1 - - + -
162D CYS* 2.9 27.2 + - - +
187D ASN* 1.3 74.0 - - - +
189D VAL* 1.3 65.1 + - - +
216D GLY 4.0 4.3 - - - +
217D VAL* 3.3 21.8 - - - +
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Residues in contact with VAL 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D ALA* 4.9 0.4 - - - -
162D CYS* 3.5 4.9 - - + +
164D GLN* 3.2 37.5 - - - +
179D LEU* 4.0 21.3 - - + -
182D ALA* 4.0 18.4 - - + -
183D LEU* 4.7 6.1 - - + -
188D VAL* 1.3 80.7 - - - +
190D VAL* 1.3 67.8 + - - +
191D MET* 3.7 22.0 - - + +
217D VAL 2.7 15.0 + - - +
218D VAL* 3.7 6.0 - - + -
219D ASN* 2.8 35.9 + - - +
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Residues in contact with VAL 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D VAL* 4.8 1.1 - - + +
62D ALA* 3.8 45.1 - - + +
63D VAL* 3.9 19.1 - - + -
66D ALA* 3.9 9.0 - - + -
161D VAL* 4.0 11.0 - - + -
162D CYS 3.0 7.8 + - - +
163D GLY* 3.3 8.1 - - - -
164D GLN 2.9 21.7 + - - +
189D VAL* 1.3 78.9 - - - +
191D MET* 1.3 59.2 + - - +
219D ASN* 3.4 4.3 - - - +
221D VAL* 4.7 7.0 - - + -
232D ILE* 3.8 28.7 - - + +
238D VAL* 5.7 0.7 - - + -
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Residues in contact with MET 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D GLN* 3.2 37.0 - - + +
166D ILE* 3.7 22.9 - - + -
175D GLN* 3.7 38.8 - - + +
178D LYS* 3.7 20.4 - - + -
179D LEU* 4.2 8.7 - - + -
189D VAL* 3.8 10.3 - - + -
190D VAL* 1.3 73.2 - - - +
192D LYS* 1.3 67.2 + - - +
193D VAL* 4.3 7.0 - - + -
218D VAL* 5.6 0.4 - - + -
219D ASN 2.7 14.7 + - - +
220D ILE* 3.3 13.8 - - + +
221D VAL* 2.7 32.9 + - - +
232D ILE* 4.4 2.7 - - - -
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Residues in contact with LYS 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D GLN 2.7 11.7 + - - +
165D ILE* 4.1 20.5 - - + +
166D ILE* 3.0 28.3 + - - +
191D MET* 1.3 73.2 - - - +
193D VAL* 1.3 89.3 + - - +
194D ALA* 4.9 3.1 - - - +
195D GLU 5.1 0.4 - - - +
221D VAL 3.6 15.3 - - - +
223D GLY 3.4 24.5 - - - +
224D PHE 3.1 28.6 + - - -
225D GLY* 3.1 13.9 - - - +
228D ALA* 4.1 4.9 - - + -
229D GLY* 3.5 19.8 - - - +
232D ILE* 3.7 17.7 - - + +
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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