Contacts of the strand formed by residues 39 - 43 (chain C) in PDB entry 3ORH
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 39 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B LEU 4.4 5.0 + - - -
38B GLY* 5.2 0.4 - - - -
9C ILE* 3.0 38.4 + - + +
10C PHE* 3.7 25.4 - - + -
14C GLU* 2.6 33.3 + - - -
16C CYS* 4.0 11.0 - - - -
20C TRP* 4.6 7.0 - - + -
35C ARG* 3.2 20.4 - - - -
36C ILE 2.9 17.9 + - - +
37C LEU* 3.7 11.3 + - + +
38C GLY* 1.3 77.9 - - - +
40C PRO* 1.4 64.6 - - - +
41C VAL* 3.0 10.7 + - + +
137C TYR* 3.7 22.0 - - + +
221C ARG* 5.7 0.4 - - - +
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Residues in contact with PRO 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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9C ILE* 4.3 21.3 - - + -
34C LEU 4.2 4.0 - - - +
35C ARG* 4.2 21.7 - - + +
38C GLY 4.2 4.5 - - - +
39C LYS* 1.4 77.1 - - - +
41C VAL* 1.3 63.7 + - - +
42C MET 3.6 2.7 - - - +
43C GLU* 3.8 22.0 - - - +
137C TYR* 3.7 22.7 + - - +
221C ARG* 4.5 17.3 - - + +
222C TYR* 3.8 30.7 - - + -
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Residues in contact with VAL 41 (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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20C TRP* 3.7 30.1 - - + -
34C LEU* 3.1 20.9 + - + +
36C ILE* 3.9 13.2 - - + +
39C LYS 3.0 19.9 + - - +
40C PRO* 1.3 74.7 - - - +
42C MET* 1.3 61.5 + - - +
46C GLU* 5.0 2.6 - - - +
136C THR 5.4 0.5 - - - +
137C TYR* 3.8 27.6 - - + -
222C TYR* 5.3 1.3 + - - -
4002C SAH 3.7 46.9 - - + -
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Residues in contact with MET 42 (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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33C HIS* 3.4 0.3 - - - +
34C LEU* 2.8 36.9 + - + +
40C PRO 3.6 0.4 - - - -
41C VAL* 1.3 81.5 + - - +
43C GLU* 1.3 86.3 + - - +
46C GLU* 3.3 25.4 - - + +
50C MET* 3.5 33.4 - - + +
71C MET* 3.8 27.8 - - + +
73C ILE* 3.8 11.9 - - + -
135C ASP* 5.0 0.9 - - - +
222C TYR* 4.8 0.2 - - - -
4002C SAH 3.6 43.7 - - + +
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Residues in contact with GLU 43 (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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32C THR 3.3 4.9 - - - -
33C HIS* 3.3 29.7 + - + +
35C ARG* 5.7 1.4 + - - -
40C PRO* 3.8 14.2 - - + +
42C MET* 1.3 91.7 - - - +
44C ARG* 1.3 64.7 + - - +
45C TRP* 3.0 35.2 + - + -
46C GLU* 3.2 20.6 + - - +
71C MET* 4.3 3.4 - - - -
217C PRO* 5.5 0.3 - - - +
220C CYS* 4.3 9.8 - - - +
221C ARG* 5.7 1.2 + - - +
222C TYR* 3.4 32.5 + - + +
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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