Contacts of the strand formed by residues 92 - 97 (chain C) in PDB entry 1RZR
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 ASN 92 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61C THR* 2.9 10.1 + - - +
62C THR* 2.8 25.8 - - - -
63C VAL 3.0 4.3 + - - -
83C GLU* 5.6 1.8 - - - -
90C LYS 4.4 0.7 + - - +
91C TYR* 1.3 76.2 - - - +
93C ILE* 1.3 63.0 + - - +
846C SO4 3.3 9.7 + - - -
94G ILE* 3.7 23.8 - - + +
95G LEU 5.6 0.6 + - - -
96G SER* 5.2 5.3 - - - -
111G ASN* 2.7 43.3 + - - -
112G MSE 3.9 4.4 - - - +
115G LYS* 2.5 36.0 + - - +
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Residues in contact with ILE 93 (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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63C VAL* 3.2 11.7 - - + +
65C VAL* 3.8 23.6 - - + -
79C ALA* 5.5 3.4 - - + +
82C ILE* 4.6 6.5 - - + -
83C GLU* 4.0 28.0 + - + +
86C ALA* 3.5 28.5 - - + -
91C TYR 4.7 0.2 - - - +
92C ASN* 1.3 81.2 - - - +
94C ILE* 1.3 66.3 + - - +
95C LEU* 4.1 12.3 + - + +
302C MSE 4.5 12.3 - - + -
70G ILE* 6.1 0.9 - - + -
94G ILE* 3.6 23.7 - - - +
95G LEU* 3.6 26.4 + - + +
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Residues in contact with ILE 94 (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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62C THR* 3.6 18.8 - - + +
63C VAL 2.8 10.9 + - - +
64C GLY* 3.5 0.5 - - - -
65C VAL* 2.6 34.7 + - - +
93C ILE* 1.3 79.2 - - - +
95C LEU* 1.3 64.1 + - - +
96C SER* 5.8 1.1 - - - -
112C MSE 3.2 34.8 - - + +
115C LYS* 4.6 29.2 - - + +
117C VAL* 5.1 2.0 - - + -
62G THR* 5.4 1.8 - - - +
92G ASN* 4.4 28.5 - - + +
93G ILE 4.2 6.7 - - - +
94G ILE* 4.2 19.7 - - + -
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Residues in contact with LEU 95 (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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65C VAL* 3.4 26.2 - - + -
67C ILE* 3.5 27.8 - - + -
70C ILE* 3.6 33.4 - - + -
79C ALA* 4.9 7.4 - - + -
93C ILE* 4.0 10.6 + - + -
94C ILE* 1.3 78.6 - - - +
96C SER* 1.3 65.7 + - - +
97C ASN* 4.7 3.4 - - - +
70G ILE* 6.1 0.4 - - + -
79G ALA 6.0 1.1 - - - +
83G GLU* 3.4 10.7 - - - +
92G ASN* 5.7 1.2 + - - -
93G ILE* 3.7 30.8 + - + +
95G LEU* 4.1 31.4 - - + -
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Residues in contact with SER 96 (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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65C VAL 3.1 9.5 + - - -
66C ILE* 3.6 7.9 - - - +
67C ILE* 3.4 25.1 + - - +
94C ILE* 5.2 2.5 - - - -
95C LEU* 1.3 79.5 - - - +
97C ASN* 1.3 66.3 + - - +
98C SER 3.9 0.2 + - - -
108C LEU* 2.7 43.0 - - - +
112C MSE 5.3 7.0 - - - -
947C SO4 4.5 3.3 + - - -
83G GLU* 3.5 10.2 + - - -
87G THR* 5.0 1.4 + - - -
92G ASN* 5.3 5.5 + - - -
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Residues in contact with ASN 97 (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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67C ILE* 3.5 6.7 - - - +
68C PRO 3.7 6.3 - - - +
69C ASP* 3.3 5.1 - - - -
70C ILE* 2.9 51.2 + - - +
95C LEU* 4.7 3.0 - - - +
96C SER* 1.3 79.6 + - - +
98C SER* 1.3 61.5 + - - +
99C ASP* 4.1 4.1 - - - +
104C LYS* 4.4 6.2 - - - +
108C LEU* 4.0 7.5 - - - +
80G ARG* 3.0 31.2 + - - +
83G GLU* 3.2 33.8 + - + +
87G THR* 5.6 0.2 + - - -
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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
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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