Contacts of the strand formed by residues 35 - 40 (chain C) in PDB entry 1OPT
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 LYS 35 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C HIS* 5.5 2.9 - - + -
28C TRP 3.7 6.7 - - - +
29C LYS* 4.3 8.7 - - + -
33C GLN 3.4 1.6 + - - +
34C ILE* 1.3 69.4 - - - +
36C ILE* 1.3 60.8 + - - +
37C LEU 5.8 1.1 - - - +
47C GLY* 3.3 26.7 - - - -
48C PRO* 3.9 9.9 - - + +
49C SER* 3.3 14.2 + - - -
280G ASN* 3.1 36.4 + - + +
281G ALA* 4.3 8.7 - - + +
455G THR* 2.9 31.5 + - - +
456G ARG 2.7 33.5 + - - +
457G ASP* 4.5 3.9 + - - +
458G GLY 4.1 9.0 - - - +
469G ARG* 5.9 0.4 - - - +
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Residues in contact with ILE 36 (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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28C TRP* 2.8 17.5 + - + +
29C LYS* 3.7 17.0 - - - -
30C ASN* 4.2 16.4 - - + +
34C ILE* 3.4 22.7 - - + +
35C LYS* 1.3 71.0 - - - +
37C LEU* 1.3 65.8 + - + +
46C LYS* 3.6 5.7 - - - +
47C GLY 3.0 22.3 + - - -
49C SER* 3.0 38.3 - - - +
51C LEU* 4.9 9.0 - - + -
52C ASN* 5.7 1.6 - - - -
55C ALA* 4.2 21.3 - - + +
69C LEU* 4.5 16.8 - - + -
82C TYR* 4.2 18.8 - - + -
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Residues in contact with LEU 37 (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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26C PHE* 5.1 4.0 - - + -
27C HIS* 3.1 5.9 - - - +
28C TRP* 2.6 39.1 + - + +
35C LYS* 5.6 1.3 - - - +
36C ILE* 1.3 82.4 + - - +
38C GLY* 1.3 57.2 + - - +
44C LEU* 3.7 11.0 - - + -
45C THR* 3.7 11.0 - - - +
46C LYS* 4.1 15.9 - - + +
55C ALA* 3.5 40.6 - - + +
56C ASP* 3.4 31.9 - - - +
57C SER* 3.6 16.8 - - - -
68C PRO 4.6 2.0 - - - +
69C LEU* 3.7 17.0 - - + -
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Residues in contact with GLY 38 (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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26C PHE* 3.2 22.7 - - - -
27C HIS* 3.5 8.5 - - - -
37C LEU* 1.3 80.1 - - - +
39C ASN* 1.3 61.1 + - - -
44C LEU* 3.6 7.8 - - - +
45C THR* 2.9 37.5 + - - +
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Residues in contact with ASN 39 (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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23C SER* 4.5 3.0 + - - -
24C ILE 3.0 20.2 + - - -
25C GLN* 2.9 35.0 + - - +
26C PHE* 2.7 57.6 + - + +
38C GLY* 1.3 75.1 - - - -
40C GLN* 1.3 67.6 + - - +
41C GLY 3.1 20.0 + - - -
43C PHE 3.4 10.5 - - - +
45C THR* 4.5 0.7 - - - -
62C TRP* 3.7 20.3 - - + -
67C PHE* 5.1 0.2 - - - -
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Residues in contact with GLN 40 (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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25C GLN* 3.2 24.0 + - - +
39C ASN* 1.3 76.0 - - - +
41C GLY* 1.3 63.2 + - - +
42C SER 3.3 0.5 + - - -
43C PHE* 2.8 22.1 + - - +
45C THR* 3.7 22.4 - - + +
281G ALA 4.6 9.7 - - - +
283G THR* 3.2 25.0 + - - -
371G ILE* 4.5 1.3 - - + -
471G GLY* 6.2 0.7 - - - -
472G GLY* 3.1 27.9 + - - +
473G GLY* 3.3 15.1 - - - -
474G ASP* 3.4 25.3 - - - +
477G ASP* 4.2 3.6 + - - -
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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