Contacts of the strand formed by residues 29 - 36 (chain D) in PDB entry 2EWY
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 GLY 29 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24D GLY* 3.4 6.6 - - - -
25D ASP* 2.9 28.2 + - - +
26D SER 4.3 2.5 + - - -
27D GLY 3.6 1.4 - - - -
28D ARG* 1.3 81.5 - - - +
30D TYR* 1.3 65.1 + - - -
31D TYR* 4.1 7.4 - - - -
46D LEU* 4.0 11.9 - - - -
131D TRP* 5.0 0.6 - - - -
242D SER 5.7 4.5 - - - -
245D THR* 5.0 1.9 + - - -
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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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22D LEU* 4.2 17.3 - - + -
23D GLN 3.3 7.2 - - - +
24D GLY 3.6 19.7 - - - -
25D ASP* 3.5 21.4 - - - -
26D SER* 3.6 6.6 + - - -
29D GLY* 1.3 76.0 - - - -
31D TYR* 1.3 61.2 + - - +
46D LEU* 3.2 7.6 - - - +
47D VAL* 2.9 31.2 + - + +
168D MET* 5.7 2.5 - - - -
170D MET* 3.2 49.3 - - + +
171D CYS 3.3 11.2 + - - -
184D GLY 3.5 29.6 - - - -
185D GLY* 4.4 4.3 - - - -
242D SER 5.8 2.8 + - - -
347D ALA* 5.2 2.7 - - + -
351D GLU* 2.6 29.3 + - - -
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Residues in contact with TYR 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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21D ASN 4.1 0.5 - - - +
22D LEU* 3.5 7.9 - - - -
23D GLN* 2.7 85.2 + - + +
24D GLY* 3.9 7.2 - - - -
29D GLY 4.1 7.4 - - - -
30D TYR* 1.3 77.6 - - - +
32D LEU* 1.3 58.5 + - - +
33D GLU 4.3 0.5 + - - -
44D GLN* 3.7 33.2 - - + -
45D ILE 2.9 22.7 - - - +
46D LEU* 4.0 0.9 - - - -
47D VAL 4.4 0.2 - - - +
130D LYS* 3.3 49.4 + - + +
131D TRP* 4.0 24.2 - + + -
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Residues in contact with LEU 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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21D ASN* 3.5 42.2 - - + +
22D LEU* 3.7 13.0 - - + +
31D TYR* 1.3 74.6 - - - +
33D GLU* 1.3 67.4 + - - +
34D MET* 3.5 29.2 - - + -
44D GLN* 3.6 2.9 - - - -
45D ILE* 2.6 46.2 + - + +
47D VAL* 4.1 7.6 - - + +
103D ILE* 4.0 27.1 - - + -
105D LYS 5.5 0.2 - - - +
135D LEU* 4.4 4.7 - - + -
187D LEU* 4.0 18.6 - - + -
189D LEU* 4.9 1.1 - - + -
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Residues in contact with GLU 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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21D ASN 4.5 2.8 + - - +
31D TYR 4.3 0.4 + - - -
32D LEU* 1.3 83.6 - - - +
34D MET* 1.3 65.9 + - - +
35D LEU* 4.3 4.2 - - - +
42D LYS* 2.9 41.2 + - + +
43D LEU 3.5 12.1 - - - +
44D GLN* 3.6 19.5 + - - +
103D ILE* 4.4 2.8 - - - +
104D PRO* 3.2 40.7 - - + +
105D LYS* 5.6 5.4 + - - -
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Residues in contact with MET 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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32D LEU* 3.5 27.6 - - + +
33D GLU* 1.3 76.3 - - - +
35D LEU* 1.3 65.7 - - - +
36D ILE* 4.0 3.9 + - + +
41D GLN 3.8 0.3 - - - +
42D LYS* 3.9 0.9 - - - -
43D LEU* 2.9 31.8 + - - +
45D ILE* 3.3 26.2 - - + -
54D PHE* 3.2 34.5 - - + -
101D VAL* 4.0 14.1 - - + -
102D THR 3.6 11.9 - - - +
103D ILE* 4.0 9.0 - - + -
104D PRO* 3.9 0.7 - - - -
135D LEU* 4.0 13.9 - - + -
152D PHE* 3.6 23.6 - - + -
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Residues in contact with LEU 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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33D GLU* 4.3 8.5 - - - +
34D MET* 1.3 73.9 - - - +
36D ILE* 1.3 61.0 + - - +
40D PRO* 4.0 26.7 - - + -
41D GLN 3.4 2.7 - - - -
42D LYS* 3.8 34.8 - - + +
100D LEU 4.0 0.3 - - - +
101D VAL* 3.5 5.2 - - - +
102D THR* 2.9 50.9 + - + +
104D PRO* 3.8 21.3 - - + -
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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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34D MET* 4.4 8.3 - - + +
35D LEU* 1.3 79.9 - - - +
37D GLY* 1.3 67.5 + - - +
39D PRO 3.6 1.2 - - - +
40D PRO* 4.3 0.2 - - - -
41D GLN* 2.8 46.5 + - - +
43D LEU* 3.2 35.0 - - + -
45D ILE* 5.2 0.2 - - + -
54D PHE* 4.1 17.7 - - + -
56D VAL* 4.0 13.9 - - + -
68D PHE* 3.5 30.8 - - + -
99D ASP* 4.6 5.8 - - + -
100D LEU 3.8 6.1 - - - +
101D VAL* 4.7 12.3 - - + -
115D ILE* 4.1 14.6 - - + -
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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