Contacts of the strand formed by residues 138 - 142 (chain C) in PDB entry 1ZYR
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 SER 138 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ILE* 4.1 19.7 - - - +
22C GLN* 4.7 4.0 + - - -
136C ILE* 3.6 3.6 + - - -
137C VAL* 1.3 76.6 - - - +
139C GLN* 1.3 60.1 + - - +
333C ILE* 4.1 16.4 - - - -
334C ARG 4.2 7.2 - - - -
335C THR* 5.3 5.8 - - - +
336C VAL* 5.6 2.6 + - - +
339C LEU* 5.0 1.6 - - - -
407C LYS 4.3 8.5 + - - -
408C ARG 5.0 1.2 - - - -
409C ARG 3.1 21.2 + - - -
410C ILE* 3.9 10.0 - - - +
411C SER* 2.8 25.8 + - - +
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Residues in contact with GLN 139 (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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137C VAL 3.7 0.2 + - - -
138C SER* 1.3 76.3 - - - +
140C ILE* 1.3 66.9 + - - +
333C ILE* 2.8 10.2 - - - -
334C ARG* 2.4 63.9 + - + +
391C LEU* 3.1 24.4 - - + +
410C ILE* 4.1 0.9 - - - -
411C SER 3.1 16.2 - - - +
412C ALA 3.7 7.0 - - - +
413C LEU 3.5 1.7 - - - +
414C GLY* 3.0 13.5 - - - -
415C PRO* 2.8 45.9 - - - +
418C LEU* 3.9 14.1 - - - +
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Residues in contact with ILE 140 (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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139C GLN* 1.3 85.5 + - - +
141C HIS* 1.3 68.6 + - - +
331C ARG* 3.0 40.6 - - + +
332C ARG 2.8 32.1 - - - +
333C ILE* 3.5 14.6 - - + -
410C ILE* 3.2 28.9 - - + -
411C SER 3.5 9.6 + - - +
412C ALA* 4.2 12.1 - - + +
418C LEU* 4.3 2.8 - - - +
419C THR* 4.4 6.0 - - - +
438C ILE* 4.8 7.4 - - + -
450C GLY 6.0 0.9 - - - +
451C LEU 5.4 1.3 - - - +
453C THR* 4.4 15.3 - - + -
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Residues in contact with HIS 141 (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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140C ILE* 1.3 76.5 - - - +
142C ARG* 1.3 69.7 + - - +
143C SER 3.3 0.3 + - - -
144C PRO* 4.6 7.9 - - + -
165C LEU* 4.2 8.7 - - + +
331C ARG* 3.2 13.8 - - - +
332C ARG* 2.6 93.8 + - + +
334C ARG* 3.2 45.2 + - + +
338C GLU* 3.8 1.8 + - - -
418C LEU* 3.4 31.6 - - + -
419C THR* 5.7 2.7 - - - -
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Residues in contact with ARG 142 (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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141C HIS* 1.3 76.7 + - - +
143C SER* 1.3 67.5 + - - +
144C PRO* 3.1 5.9 - - - +
147C TYR* 2.9 53.6 - - - +
149C THR* 5.6 1.2 + - - -
161C SER* 4.2 9.1 + - - -
163C ILE* 2.8 28.6 - - + +
165C LEU* 6.1 0.2 - - - +
171C TRP* 4.6 17.7 - - + -
325C ILE* 3.3 56.1 + - - +
330C ASN 4.0 5.5 + - - -
331C ARG* 5.0 2.2 - - + +
418C LEU* 4.6 7.5 - - + +
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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