Contacts of the strand formed by residues 119 - 125 (chain B) in PDB entry 1ORR
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 119 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75B ASP* 2.9 14.3 + - - +
76B SER* 3.2 22.5 + - - +
77B CYS 2.7 32.4 + - - +
117B ASN 3.8 3.0 + - - +
118B CYS* 1.3 72.8 - - - +
120B ILE* 1.3 56.6 + - - +
121B ILE* 6.1 0.4 - - + -
186B ASN* 3.3 33.1 + - - +
253B LEU* 3.9 16.1 + - + +
256B VAL* 3.4 29.1 - - + +
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Residues in contact with ILE 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B CYS* 3.3 17.5 - - + +
79B HIS* 4.1 16.6 - - + -
107B LEU* 4.3 9.6 - - + -
108B LEU* 4.4 13.5 - - + -
111B VAL* 4.0 32.5 - - + -
118B CYS* 3.9 10.3 - - - +
119B ASN* 1.3 80.6 - - - +
121B ILE* 1.3 66.9 + - - +
176B MET* 4.0 23.1 - - + +
185B LEU* 4.7 2.2 - - + -
186B ASN 2.8 13.1 + - - +
187B THR* 3.3 23.3 - - + -
188B VAL* 2.9 26.9 + - - +
256B VAL* 5.5 0.4 - - - +
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Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B CYS 3.0 7.7 + - - +
78B PHE* 3.6 34.0 - - + +
79B HIS 2.9 24.8 + - - +
80B LEU* 4.8 0.3 - - - +
119B ASN* 6.1 0.4 - - + -
120B ILE* 1.3 79.0 - - - +
122B TYR* 1.3 62.5 + - - +
123B SER 4.1 0.2 + - - -
188B VAL* 3.4 19.5 - - + +
190B PHE* 3.6 20.6 - - + -
249B TYR* 3.2 47.0 - - + +
252B ALA* 4.1 17.5 - - + -
253B LEU* 4.2 14.1 - - + +
256B VAL* 6.3 1.3 - - + -
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Residues in contact with TYR 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B HIS* 3.4 42.6 - + - -
81B ALA 5.4 3.1 - - - -
100B ASN* 4.2 4.9 + - - +
104B THR* 3.6 7.4 + - - -
120B ILE 4.1 0.4 - - - -
121B ILE* 1.3 77.6 - - - +
123B SER* 1.3 63.7 + - - +
124B SER* 3.4 27.8 + - - -
169B LYS* 3.3 36.0 + - - +
172B ALA* 3.2 31.2 - - + +
173B ASP* 3.8 11.7 - - - -
176B MET* 3.8 36.6 - - + -
188B VAL 2.9 11.5 + - - +
189B VAL* 3.7 4.8 - - + -
190B PHE* 2.9 29.3 + - - +
1300B NAD 5.4 0.2 - - - -
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 4.9 0.9 - - - -
79B HIS 3.5 7.4 + - - -
80B LEU* 3.5 14.2 - - - +
121B ILE 4.1 0.6 + - - -
122B TYR* 1.3 78.0 - - - +
124B SER* 1.3 60.6 + - - +
169B LYS* 2.9 23.9 + - - -
192B HIS* 3.7 14.6 - - - -
249B TYR* 3.4 18.8 + - - -
1300B NAD 3.2 37.3 + - - -
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Residues in contact with SER 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B TYR* 3.4 15.8 + - - -
123B SER* 1.3 76.1 - - - +
125B THR* 1.3 69.7 + - - +
128B VAL* 3.9 8.7 - - - +
169B LYS* 4.1 8.5 + - - +
173B ASP* 2.8 33.4 + - - +
189B VAL* 3.6 13.9 - - - -
190B PHE 2.7 19.9 + - - +
191B ARG* 4.0 1.4 - - - +
192B HIS* 3.3 9.9 + - - +
1300B NAD 3.2 17.1 - - - -
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Residues in contact with THR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B SER* 1.3 84.7 + - - +
126B ASN* 1.3 73.7 + - - +
127B LYS* 3.0 27.4 + - + +
128B VAL* 3.3 28.8 + - + +
165B TYR* 3.5 27.7 + - + +
166B GLY* 5.0 0.4 - - - -
169B LYS* 3.5 31.2 - - + -
191B ARG* 3.9 5.5 - - - +
192B HIS 3.6 11.5 + - - +
1300B NAD 4.5 2.5 - - - -
1301B CDP 5.1 1.0 + - - -
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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