Contacts of the strand formed by residues 161 - 165 (chain D) in PDB entry 1NZX
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 161 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63D VAL* 4.6 6.1 - - + +
66D ALA* 4.0 17.7 - - + -
67D ARG* 3.3 47.8 - - + +
160D GLY* 1.3 68.3 - - - -
162D CYS* 1.3 61.5 + - - +
188D VAL* 3.4 18.4 - - + +
190D VAL* 4.3 14.1 - - + -
237D ASP* 3.8 13.2 - - - +
238D VAL* 3.5 15.6 - - + +
239D ASP* 2.7 38.8 + - - +
240D LYS 3.3 6.1 + - - -
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Residues in contact with CYS 162 (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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159D VAL* 4.7 2.9 - - - -
160D GLY 3.6 14.8 - - - -
161D VAL* 1.3 75.0 - - - +
163D GLY* 1.3 59.7 + - - +
164D GLN* 3.7 9.7 + - + +
187D ASN* 3.7 17.7 - - - -
188D VAL 2.8 14.5 + - - +
189D VAL* 3.4 7.6 - - + +
190D VAL 3.0 24.6 + - - -
238D VAL* 4.5 0.4 - - - -
240D LYS* 3.2 22.7 - - + +
485D TYR* 3.7 37.7 - - + -
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Residues in contact with GLY 163 (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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162D CYS* 1.3 71.5 - - - +
164D GLN* 1.3 60.3 + - - +
165D ILE 4.2 0.4 - - - -
190D VAL* 3.4 12.8 - - - -
232D ILE* 3.6 26.5 - - - -
238D VAL* 3.7 6.7 - - - +
240D LYS 2.7 13.4 + - - -
241D VAL* 3.1 8.6 - - - +
242D ALA 2.9 24.9 + - - -
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Residues in contact with GLN 164 (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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162D CYS* 3.9 11.2 - - + +
163D GLY* 1.3 78.6 - - - +
165D ILE* 1.3 56.9 + - - +
166D ILE* 4.1 0.7 - - - -
178D LYS* 3.1 41.8 + - + +
179D LEU* 3.6 6.1 - - - +
182D ALA* 3.6 6.1 - - - +
189D VAL* 3.2 26.7 - - + +
190D VAL 3.1 7.5 + - - -
191D MET* 3.2 21.2 - - + +
192D LYS 2.7 31.8 + - - -
232D ILE* 4.8 0.4 - - - +
242D ALA* 3.4 7.0 - - + +
485D TYR* 2.9 38.6 + - - +
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Residues in contact with ILE 165 (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* 1.3 77.7 - - - +
166D ILE* 1.3 62.1 + - - +
178D LYS* 4.5 0.5 - - - -
192D LYS* 3.6 19.7 - - + +
229D GLY* 3.5 29.8 - - - +
232D ILE* 4.7 10.8 - - + -
233D ALA* 5.0 0.9 - - + -
241D VAL* 4.6 10.5 - - + -
242D ALA 3.0 9.7 + - - +
243D PHE* 3.6 12.4 - - + -
244D THR* 3.1 24.8 + - - +
253D ILE* 3.8 23.8 - - + -
4502D NAD 3.3 46.0 - - - +
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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
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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