Contacts of the strand formed by residues 33 - 36 (chain D) 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 HIS 33 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215B VAL* 6.4 2.2 - - + -
26D ALA 4.3 0.4 - - - -
27D TYR* 3.5 8.5 - - - +
28D ASP* 2.8 31.7 + - - +
31D ASP* 3.7 0.7 - - - +
32D THR* 1.3 110.4 + - - +
34D LEU* 1.3 60.7 + - - +
35D ARG* 3.5 40.8 - - + +
42D MET 3.5 5.2 - - - +
43D GLU* 3.2 38.7 + - + -
45D TRP* 5.9 0.9 - + - -
71D MET* 4.1 5.0 - - - +
219D ASP* 5.5 8.0 + - - -
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Residues in contact with LEU 34 (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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25D ALA* 4.1 7.4 - - + -
26D ALA 3.5 6.5 - - - +
27D TYR* 3.8 29.4 - - + +
33D HIS* 1.3 72.5 - - - +
35D ARG* 1.3 79.8 + - - +
36D ILE* 4.0 13.5 - - + -
39D LYS 3.9 0.2 - - - +
40D PRO* 4.0 1.2 - - - +
41D VAL* 3.2 48.4 + - + -
42D MET* 2.9 16.3 + - + +
70D GLY* 3.8 33.4 - - - +
71D MET* 4.0 15.0 - - + -
95D VAL* 4.2 9.0 - - + -
4003D SAH 4.6 0.2 - - - +
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Residues in contact with ARG 35 (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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15A ASN 5.6 5.6 - - - -
24D PRO 4.0 0.9 - - - +
26D ALA* 2.8 52.7 + - + +
28D ASP* 3.4 35.0 + - - +
33D HIS* 3.5 38.5 + - + +
34D LEU* 1.3 75.6 - - - +
36D ILE* 1.3 64.6 + - - +
38D GLY* 3.7 25.1 - - - +
39D LYS 3.3 14.8 - - - +
40D PRO* 4.6 5.6 - - + -
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Residues in contact with ILE 36 (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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20D TRP* 3.7 37.2 - - + -
23D ALA* 3.8 24.0 - - + -
24D PRO 4.1 5.2 - - - +
25D ALA* 4.2 8.5 - - - -
34D LEU* 4.0 19.5 + - + -
35D ARG* 1.3 77.8 - - - +
37D LEU* 1.3 65.3 + - + +
38D GLY 2.9 2.5 - - - -
39D LYS* 2.9 30.8 + - - +
41D VAL* 4.4 6.6 - - + +
92D ASN* 3.9 14.8 - - - +
95D VAL* 3.9 21.5 - - + -
4003D SAH 3.7 23.1 - - - +
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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