Contacts of the strand formed by residues 39 - 44 (chain D) in PDB entry 2OFJ
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 ARG 39 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D ARG* 3.4 4.7 - - - +
36D GLU 2.9 32.6 + - - +
37D GLY 3.4 1.7 - - - +
38D GLU* 1.3 80.6 - - - +
40D GLU* 1.3 95.6 + - - +
42D TRP* 5.8 0.2 - - - -
93D GLU* 3.5 21.8 + - - +
94D LEU* 3.4 33.0 - - + +
96D ASP* 3.5 22.7 + - - +
100D GLN* 5.4 5.3 + - - -
301D ARG* 4.9 6.1 - - - +
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Residues in contact with GLU 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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33D CYS* 4.2 6.2 - - - -
34D LEU 3.1 12.8 - - - +
35D ARG* 3.5 33.9 + - + -
39D ARG* 1.3 129.3 + - - +
41D GLY* 1.3 54.6 + - - +
42D TRP* 3.3 30.6 + - + +
93D GLU 4.2 0.5 - - - +
94D LEU* 3.8 5.8 - - - -
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Residues in contact with GLY 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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33D CYS* 3.5 0.9 - - - -
34D LEU* 2.7 40.6 + - - -
40D GLU* 1.3 74.4 - - - +
42D TRP* 1.3 64.5 + - - -
90D ALA* 3.5 29.1 - - - +
93D GLU* 3.5 13.0 - - - -
94D LEU* 4.0 2.9 - - - +
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Residues in contact with TRP 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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7D TYR* 3.9 35.7 - + - -
31D TYR* 4.2 14.8 - + + -
32D VAL 3.2 17.0 - - - -
33D CYS* 3.7 21.7 - - + -
35D ARG* 4.4 6.3 - - - -
39D ARG* 5.8 0.4 - - - -
40D GLU* 3.3 26.1 + - + -
41D GLY* 1.3 80.6 - - - -
43D GLY* 1.3 56.7 + - - +
89D CYS 3.5 0.7 - - - -
90D ALA* 3.1 20.5 + - - -
93D GLU* 2.9 8.0 + - - +
269D LEU* 3.9 24.5 - - + -
273D GLN* 2.8 21.5 - - - +
300D VAL* 4.3 13.5 - - + -
301D ARG* 3.5 31.2 - - - +
313D VAL* 4.0 29.6 - - + -
316D LEU* 5.4 0.2 - - + -
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Residues in contact with GLY 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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31D TYR* 3.2 8.0 - - - +
32D VAL* 2.9 39.2 + - - +
42D TRP* 1.3 76.3 - - - +
44D GLU* 1.3 60.6 + - - -
45D ILE* 4.0 0.7 - - - -
86D GLY* 3.2 21.3 - - - -
89D CYS* 4.3 0.9 - - - -
269D LEU* 4.0 5.6 - - - +
273D GLN* 4.1 7.0 - - - -
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Residues in contact with GLU 44 (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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9D TRP* 3.5 12.2 - - + -
30D LEU 3.5 11.9 - - - +
31D TYR* 3.5 10.3 - - + -
43D GLY* 1.3 71.6 - - - -
45D ILE* 1.3 66.4 + - - +
46D SER* 2.6 25.8 + - - +
82D SER 3.9 2.1 - - - +
85D PHE* 4.0 13.9 - - + -
86D GLY* 3.2 20.1 + - - -
89D CYS* 5.9 0.2 - - - -
237D THR* 5.1 0.9 + - - +
266D GLU* 3.3 14.6 - - + +
267D SER* 2.5 45.2 + - - -
269D LEU* 4.0 7.6 - - + +
270D GLY* 3.2 21.5 + - - -
273D GLN* 4.1 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