Contacts of the strand formed by residues 26 - 33 (chain D) in PDB entry 2OJW
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 VAL 26 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D GLN* 4.0 0.2 - - - +
24D GLU 3.7 8.3 - - - +
25D LYS* 1.3 80.3 - - - +
27D GLN* 1.3 72.9 - - - +
46D THR* 3.3 4.9 - - - -
47D LEU* 2.6 43.3 + - + +
49D SER 3.5 31.9 - - - +
50D GLU* 3.5 8.3 - - + +
51D PRO* 4.4 14.1 - - + -
93D PRO* 3.1 44.6 - - + +
94D ASN* 3.8 2.9 - - - -
95D LYS* 4.8 2.2 - - + -
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Residues in contact with GLN 27 (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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18D MET* 5.8 0.2 - - - +
22D GLN* 4.2 3.3 + - - +
26D VAL* 1.3 76.3 - - - +
28D ALA* 1.3 58.8 + - - +
29D MET 4.2 0.4 - - - -
44D THR* 3.9 9.2 - - + -
45D ARG 3.6 4.0 - - - -
46D THR* 5.3 0.9 - - - +
90D ARG* 3.6 37.0 + - - +
94D ASN* 2.9 33.7 + - + +
95D LYS 3.1 24.6 + - - +
177E GLU* 5.0 1.6 + - - -
180E TYR* 3.3 58.8 - - + +
181E ARG* 4.5 10.8 + - - +
184E LEU* 4.2 14.2 - - + +
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Residues in contact with ALA 28 (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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26D VAL 4.1 0.2 + - - -
27D GLN* 1.3 73.8 - - - +
29D MET* 1.3 61.7 + - - +
30D TYR* 3.6 26.5 - - + -
44D THR* 3.4 3.7 - - - +
45D ARG* 2.9 36.2 + - + +
47D LEU* 3.9 26.2 - - + -
57D LEU* 4.4 7.6 - - + -
95D LYS* 3.6 8.7 - - + -
97D VAL* 4.5 6.1 - - + -
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Residues in contact with MET 29 (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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27D GLN 4.2 0.8 - - - -
28D ALA* 1.3 69.9 - - - +
30D TYR* 1.3 62.0 + - - +
31D ILE* 3.8 4.1 + - + +
42D CYS* 3.9 23.6 - - + -
43D LYS 3.4 9.9 - - - +
44D THR* 3.6 19.9 - - - +
87D ASP* 4.6 1.6 - - - +
89D PHE* 5.7 2.2 - - - -
90D ARG* 3.8 22.4 - - - +
95D LYS 3.0 12.6 + - - +
96D LEU* 3.6 15.8 - - + -
97D VAL* 2.9 24.5 + - - +
223D PHE* 3.6 32.1 - - - -
227D ARG* 5.3 7.6 - - - +
1404D CL 3.8 14.6 - - + -
173E ARG* 4.4 9.4 - - - +
177E GLU* 4.9 1.6 - - - +
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Residues in contact with TYR 30 (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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28D ALA* 3.6 26.5 - - + -
29D MET* 1.3 73.6 - - - +
31D ILE* 1.3 59.5 + - - +
32D TRP* 3.7 4.2 - - + -
42D CYS* 3.2 24.8 - - - +
43D LYS 2.9 14.1 + - - +
45D ARG* 3.3 28.5 + - - -
57D LEU* 4.0 7.0 - - + +
58D PRO* 2.6 41.8 + - - +
60D TRP* 3.6 40.2 - + + -
79D LEU* 4.3 12.3 - - + -
81D PRO* 4.3 13.9 - - + -
97D VAL* 3.4 14.1 - - + -
99D CYS* 3.6 21.3 - - - -
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Residues in contact with ILE 31 (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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29D MET* 4.0 7.0 - - + +
30D TYR* 1.3 79.0 - - - +
32D TRP* 1.3 62.8 + - - +
40D LEU* 3.9 24.0 - - + -
41D ARG 3.4 9.6 - - - +
42D CYS* 4.3 2.2 - - + -
96D LEU* 3.9 31.6 - - + -
97D VAL 2.7 16.5 + - - +
98D LEU* 3.5 14.2 - - + +
99D CYS* 2.8 33.2 + - - +
220D VAL* 5.0 9.2 - - + -
223D PHE* 3.7 51.4 - - + -
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Residues in contact with TRP 32 (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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30D TYR 3.7 20.4 - - - -
31D ILE* 1.3 76.0 - - - +
33D ILE* 1.3 78.0 + - - +
40D LEU* 3.5 9.3 - - - +
41D ARG* 3.0 62.0 + - + +
42D CYS* 3.8 7.0 - - - -
43D LYS* 4.0 12.3 - - + -
62D PHE* 3.5 49.3 - + + -
67D THR* 4.4 1.2 - - + +
69D GLN* 4.2 3.4 + - - -
79D LEU* 3.8 33.2 - - + -
98D LEU* 5.0 2.9 - - - -
99D CYS 4.2 8.1 - - - +
101D VAL* 3.7 23.8 - - + -
162E TYR* 4.7 2.9 - + - -
163E CYS* 4.0 28.5 - - + -
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Residues in contact with ILE 33 (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 TRP* 1.3 85.4 - - - +
34D ASP* 1.3 74.0 + - - +
37D GLY* 3.6 29.6 - - - +
39D GLY 3.6 5.6 - - - +
40D LEU* 4.0 15.3 - - + -
69D GLN* 3.4 12.3 + - - -
98D LEU* 5.4 6.7 - - + -
99D CYS 5.1 2.5 + - - +
101D VAL* 4.0 8.2 - - + +
111D THR* 3.8 20.4 + - - +
219D TRP* 3.4 46.9 - - + +
347D ASP* 4.7 5.6 - - - +
349D PHE* 4.8 8.1 - - + -
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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