Contacts of the strand formed by residues 119 - 125 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75D ASP* 2.9 22.0 + - - +
76D SER* 3.4 9.0 + - - +
77D CYS 2.8 26.9 + - - -
117D ASN 3.6 3.8 + - - +
118D CYS* 1.3 72.9 - - - +
120D ILE* 1.4 62.3 + - - +
121D ILE* 6.3 0.2 - - + -
186D ASN* 3.2 31.5 + - - +
253D LEU* 3.7 23.1 - - + +
256D VAL* 3.5 29.0 - - + +
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Residues in contact with ILE 120 (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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77D CYS* 3.3 15.7 - - + +
79D HIS* 4.3 10.5 - - + -
107D LEU* 4.4 10.3 - - + -
108D LEU* 4.3 14.4 - - + -
111D VAL* 4.0 34.1 - - + -
118D CYS* 3.8 10.5 - - - +
119D ASN* 1.4 80.3 - - - +
121D ILE* 1.3 73.8 + - - +
176D MET* 4.0 23.5 - - + +
185D LEU* 4.9 1.1 - - + -
186D ASN 2.7 14.1 + - - +
187D THR* 3.2 20.5 - - + -
188D VAL* 2.8 27.9 + - - +
256D VAL* 5.4 0.6 - - - +
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Residues in contact with ILE 121 (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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77D CYS 2.9 8.5 + - - +
78D PHE* 3.6 37.3 - - + +
79D HIS* 2.8 29.5 + - - +
80D LEU* 5.2 0.3 - - - +
120D ILE* 1.3 79.1 - - - +
122D TYR* 1.3 59.5 - - - +
188D VAL* 3.4 20.0 - - + +
190D PHE* 3.6 24.5 - - + -
249D TYR* 3.6 41.8 - - + +
252D ALA* 4.2 11.7 - - + -
253D LEU* 4.0 20.4 - - + +
256D VAL* 6.3 1.8 - - + -
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Residues in contact with TYR 122 (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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79D HIS* 3.5 40.6 - + - -
81D ALA 5.7 2.0 - - - -
100D ASN* 4.4 4.7 + - - +
104D THR* 3.8 6.1 + - - -
120D ILE 4.1 0.2 - - - -
121D ILE* 1.3 75.3 - - - +
123D SER* 1.3 73.1 + - - +
124D SER* 3.4 26.7 + - - -
169D LYS* 3.4 29.5 + - - +
172D ALA* 3.4 30.7 - - + +
173D ASP* 3.9 10.3 - - - -
176D MET* 3.7 37.0 - - + -
188D VAL 2.8 13.8 + - - +
189D VAL* 3.7 5.3 - - + -
190D PHE* 2.9 29.3 + - - +
1500D NAD 5.4 0.7 - - - -
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Residues in contact with SER 123 (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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13D LEU* 4.7 0.4 - - - -
79D HIS 3.4 13.2 + - - -
80D LEU* 3.6 7.0 - - - +
121D ILE 4.2 0.8 + - - -
122D TYR* 1.3 77.1 - - - +
124D SER* 1.3 56.7 + - - +
169D LYS* 2.7 33.4 + - - -
192D HIS* 3.7 15.0 - - - -
249D TYR* 3.4 19.7 + - - -
1500D NAD 3.2 36.0 + - - -
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Residues in contact with SER 124 (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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122D TYR* 3.4 15.1 + - - -
123D SER* 1.3 77.8 - - - +
125D THR* 1.3 68.7 + - - +
128D VAL* 3.7 10.0 - - - +
169D LYS* 4.0 7.5 + - - +
173D ASP* 2.8 33.7 + - - +
189D VAL* 3.6 13.0 - - - -
190D PHE 2.7 20.4 + - - +
191D ARG* 4.0 1.3 - - - +
192D HIS* 3.4 10.1 + - - +
1500D NAD 3.2 17.5 - - - -
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Residues in contact with THR 125 (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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124D SER* 1.3 85.4 + - - +
126D ASN* 1.3 79.8 + - - +
127D LYS* 3.0 27.2 + - + +
128D VAL* 3.3 28.6 + - + +
165D TYR* 3.7 27.1 + - + +
166D GLY* 5.1 0.9 - - - -
169D LYS* 3.6 30.7 - - + -
191D ARG* 3.8 5.3 - - - +
192D HIS 3.6 11.7 - - - +
1500D NAD 4.5 2.7 - - - -
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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
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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