Contacts of the strand formed by residues 39 - 43 (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 LYS 39 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ALA* 5.2 2.2 - - + +
22A ALA* 3.9 38.1 + - - +
23A ALA* 5.1 2.5 - - - +
24A PRO* 5.6 3.8 - - - -
20D TRP* 4.4 15.7 - - + -
35D ARG* 3.3 17.3 - - - -
36D ILE 2.9 18.1 + - - +
37D LEU* 3.1 13.2 + - + +
38D GLY* 1.4 79.3 - - - +
40D PRO* 1.4 68.5 - - + +
41D VAL* 3.1 8.3 + - + +
137D TYR* 3.8 30.9 - - + +
138D PRO 5.4 4.4 + - - -
139D LEU* 5.7 4.9 + - - +
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Residues in contact with PRO 40 (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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34D LEU 4.2 3.8 - - - +
35D ARG* 4.6 6.7 - - + -
38D GLY 3.8 3.1 - - - +
39D LYS* 1.4 82.3 - - + +
41D VAL* 1.3 63.9 + - - +
42D MET 3.6 3.6 - - - +
43D GLU* 3.8 22.9 - - + +
137D TYR* 3.8 20.0 - - - +
221D ARG* 6.0 5.2 - - + -
222D TYR* 3.9 34.6 - - + +
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Residues in contact with VAL 41 (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* 3.6 27.4 - - + -
34D LEU* 3.2 28.8 + - + +
36D ILE* 4.4 7.0 - - + +
39D LYS 3.1 11.1 + - - +
40D PRO* 1.3 73.8 - - - +
42D MET* 1.4 62.3 + - - +
46D GLU* 5.0 2.5 - - - +
137D TYR* 3.4 42.9 - - + -
222D TYR* 5.8 0.2 - - - -
4003D SAH 3.6 39.1 - - + +
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Residues in contact with MET 42 (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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33D HIS* 3.5 0.3 - - - +
34D LEU* 2.9 38.1 + - + +
40D PRO 3.6 0.6 - - - -
41D VAL* 1.4 81.2 - - + +
43D GLU* 1.3 88.4 + - - +
46D GLU* 3.4 24.0 - - + +
50D MET* 3.4 33.0 - - + +
71D MET* 3.8 23.8 - - + +
73D ILE* 3.8 12.6 - - + -
135D ASP* 4.9 0.9 - - - +
222D TYR* 5.2 0.4 - - - -
4003D SAH 3.7 48.0 - - + +
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Residues in contact with GLU 43 (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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32D THR 3.3 7.9 - - - +
33D HIS* 3.2 35.9 + - + +
34D LEU 5.7 0.2 - - - +
40D PRO* 3.8 20.6 - - + +
42D MET* 1.3 89.4 - - - +
44D ARG* 1.3 64.3 + - - +
45D TRP* 2.9 36.0 + - + +
46D GLU* 3.2 24.1 + - - +
71D MET* 4.3 3.4 - - - -
217D PRO* 4.9 1.6 - - - +
219D ASP* 5.6 1.4 - - - +
220D CYS* 4.2 8.9 - - - +
222D TYR* 3.4 21.8 + - + +
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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