Contacts of the strand formed by residues 27 - 32 (chain C) 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 ASP 27 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C ALA 3.4 14.9 + - - +
3C LYS* 3.5 18.2 - - + +
4C LEU 2.7 31.9 + - - -
25C GLY 3.6 6.7 + - - +
26C ILE* 1.3 75.0 - - - +
28C LEU* 1.3 55.9 + - - +
29C ILE* 5.2 1.6 - - + -
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Residues in contact with LEU 28 (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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4C LEU* 3.4 16.4 - - + +
6C ILE* 3.6 32.1 - - + -
18C ALA* 3.7 24.9 - - + +
21C ALA* 4.3 14.1 - - + -
22C LEU* 4.0 20.2 - - + -
26C ILE 3.2 8.4 + - - +
27C ASP* 1.3 74.4 - - - +
29C ILE* 1.3 70.2 + - - +
30C VAL* 3.9 13.0 - - + -
51C ASN 5.5 1.2 + - - -
52C PHE* 3.3 29.3 - - + +
53C GLU* 3.0 23.7 + - - +
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Residues in contact with ILE 29 (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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3C LYS* 4.2 27.1 - - + -
4C LEU 2.8 17.8 + - - +
5C LEU* 3.3 19.3 - - + +
6C ILE* 2.8 32.4 + - - -
27C ASP* 4.9 1.8 - - + +
28C LEU* 1.3 83.8 - - - +
30C VAL* 1.3 61.3 + - - +
53C GLU* 3.4 17.9 - - + +
55C VAL* 4.0 22.2 - - + -
68C LEU* 4.3 8.5 - - + -
72C TYR* 4.0 36.1 - - + +
74C PRO* 4.9 3.8 - - + -
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Residues in contact with VAL 30 (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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6C ILE* 3.6 4.0 - - + +
9C GLY* 3.6 33.7 - - - +
10C CYS* 3.9 18.6 - - - -
18C ALA* 4.6 10.1 - - + -
28C LEU* 3.9 17.9 - - + -
29C ILE* 1.3 78.4 - - - +
31C PHE* 1.3 59.6 + - - +
46C LEU* 4.8 2.2 - - + -
52C PHE* 3.6 33.0 - - + -
53C GLU 2.8 7.9 + - - +
54C PHE* 3.6 9.7 - - + -
55C VAL* 2.7 34.0 + - - +
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Residues in contact with PHE 31 (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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5C LEU* 4.1 10.1 - - + -
6C ILE 3.0 9.0 + - - +
7C THR* 3.4 8.1 - - - -
8C GLY 2.7 27.7 + - - -
9C GLY 3.7 0.2 + - - -
29C ILE 4.1 0.2 - - - -
30C VAL* 1.3 74.0 - - - +
32C ASP* 1.3 61.6 + - - +
55C VAL* 3.3 20.9 - - + -
56C HIS 4.4 1.6 - - - -
57C GLY* 3.4 36.8 - - - -
58C ASP 3.6 10.1 - - - -
59C ILE* 3.7 40.4 - - + -
64C ASP* 4.3 14.8 - - + -
65C VAL* 4.3 10.3 - - + -
68C LEU* 3.6 39.9 - - + -
1400C NAD 4.4 3.4 - + - -
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Residues in contact with ASP 32 (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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8C GLY* 3.2 11.1 - - - -
9C GLY 4.4 0.2 - - - +
10C CYS* 3.1 42.2 + - - +
30C VAL* 4.6 0.4 - - + -
31C PHE* 1.3 75.1 - - - +
33C ASN* 1.3 58.9 + - - +
34C LEU* 2.7 28.8 + - - +
54C PHE* 3.7 11.3 - - + -
55C VAL 3.3 5.1 + - - -
56C HIS* 3.2 10.4 - - - -
57C GLY 3.1 20.5 + - - -
1400C NAD 2.7 49.0 + - - -
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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