Contacts of the strand formed by residues 40 - 47 (chain E) 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 LEU 40 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A CYS 4.3 1.6 - - - +
164A GLY* 4.6 0.3 - - - -
165A VAL* 3.8 24.3 + - + +
169A ARG* 6.0 1.0 - - - -
31E ILE* 3.7 24.7 - - + -
32E TRP* 3.4 12.1 - - - +
33E ILE* 4.3 5.2 - - + -
38E GLU 3.9 2.8 + - - +
39E GLY* 1.3 76.6 - - - -
41E ARG* 1.3 68.7 + - - +
98E LEU* 5.2 2.0 - - + -
219E TRP* 3.9 42.8 - - + +
222E ARG* 4.2 6.5 - - + -
223E PHE* 3.8 42.6 - - + +
226E HIS* 4.4 11.9 - - + -
238E PHE* 6.1 0.4 - - + -
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Residues in contact with ARG 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLY 3.2 28.1 + - - -
160A PRO* 3.6 19.7 + - - +
162A TYR* 2.7 39.0 + - - +
163A CYS* 3.1 11.0 - - + +
164A GLY* 4.5 2.5 - - - -
31E ILE* 3.2 8.0 - - - +
32E TRP* 2.9 61.5 + - + +
34E ASP* 3.0 43.5 + - + +
36E THR* 5.7 2.8 - - - +
40E LEU* 1.3 79.7 + - - +
42E CYS* 1.3 63.0 + - - +
66E SER 3.7 9.1 + - - -
67E THR* 4.0 24.5 + - + +
223E PHE* 5.1 1.3 - - - -
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Residues in contact with CYS 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A CYS* 3.0 34.0 + - - +
164A GLY 4.6 7.0 - - - -
165A VAL* 4.8 3.6 - - - -
173A ARG* 4.4 14.4 - - - -
194A ASN* 5.1 1.0 - - - +
195A ALA 5.3 1.2 + - - -
29E MET* 3.8 37.0 - - + -
30E TYR 3.1 13.5 - - - +
31E ILE* 4.2 1.8 - - + -
32E TRP* 3.7 6.5 - - - -
41E ARG* 1.3 77.1 - - - +
43E LYS* 1.3 62.1 + - - +
223E PHE* 3.9 20.9 - - + -
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Residues in contact with LYS 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A TYR* 5.0 3.9 + - - +
163A CYS* 4.1 12.1 - - - -
193A THR 3.5 10.8 - - - +
194A ASN* 3.8 17.0 - - + +
319A ARG* 6.1 0.6 - - - +
501A ADP 4.8 13.9 + - - -
1403A CL 3.8 9.6 - - - -
28E ALA 3.9 0.2 - - - +
29E MET* 3.4 3.0 - - - -
30E TYR* 2.9 30.1 + - - +
32E TRP* 4.0 11.7 - - + -
42E CYS* 1.3 76.6 - - - +
44E THR* 1.3 63.8 + - - +
60E TRP* 3.6 42.3 - - + +
61E ASN* 2.8 31.8 + - - +
62E PHE* 4.1 17.4 - - - +
79E LEU* 4.7 2.2 - - - -
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Residues in contact with THR 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A TYR* 3.5 25.6 - - + +
192A GLY* 2.9 9.5 - - - -
193A THR* 2.9 43.5 + - - +
205A GLN* 4.4 0.3 - - - +
1403A CL 3.1 8.2 - - - +
27E GLN* 3.9 11.0 - - + -
28E ALA 3.4 9.2 - - - +
29E MET* 3.4 5.9 - - - +
43E LYS* 1.3 78.7 + - - +
45E ARG* 1.4 57.2 + - - +
60E TRP* 3.7 8.7 - - - -
90E ARG* 3.1 39.7 + - - +
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Residues in contact with ARG 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A TYR* 3.6 6.5 - - - -
191A ALA 3.3 9.9 - - - +
192A GLY* 4.0 0.2 - - - -
27E GLN* 3.7 1.7 - - - -
28E ALA* 3.0 40.1 + - + +
30E TYR* 3.7 17.4 + - + -
44E THR* 1.4 71.9 - - - +
46E THR* 1.3 63.6 + - - +
47E LEU* 3.9 19.2 + - + +
58E PRO* 3.4 23.8 - - - +
59E GLU 3.3 17.2 + - - -
60E TRP* 3.3 60.3 - - + +
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Residues in contact with THR 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A TYR* 2.9 24.3 + - + -
184A LEU* 4.3 6.7 - - + -
190A ILE 2.7 29.6 + - - +
191A ALA* 2.9 13.4 + - - +
25E LYS* 3.6 36.6 - - + -
26E VAL 3.3 8.5 - - - +
45E ARG* 1.3 77.8 + - - +
47E LEU* 1.3 71.1 + - - +
48E ASP* 5.6 0.3 - - - +
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Residues in contact with LEU 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E LYS* 3.4 7.7 - - - +
26E VAL* 2.7 38.5 + - + +
28E ALA* 4.0 18.8 - - + -
45E ARG* 4.1 21.1 - - + +
46E THR* 1.3 81.3 - - - +
48E ASP* 1.3 65.3 + - - +
49E SER 3.3 9.6 + - - +
51E PRO* 3.9 33.4 - - + -
57E LEU* 3.9 15.0 - - + -
58E PRO* 4.1 24.0 - - + -
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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