Contacts of the strand formed by residues 29 - 36 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A GLY* 3.4 6.1 - - - -
25A ASP* 2.9 30.3 + - - +
26A SER 4.3 2.3 + - - -
27A GLY 3.6 1.4 - - - -
28A ARG* 1.3 82.5 - - - +
30A TYR* 1.3 63.1 + - - -
31A TYR* 4.1 7.1 - - - -
46A LEU* 4.0 12.6 - - - -
131A TRP* 5.0 0.4 - - - -
242A SER 5.7 4.3 - - - -
245A THR* 5.0 3.2 + - - -
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Residues in contact with TYR 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LEU* 4.2 17.3 - - + -
23A GLN 3.3 7.2 - - - +
24A GLY 3.6 17.9 - - - -
25A ASP* 3.5 20.6 - - - -
26A SER* 3.6 7.1 + - - -
29A GLY* 1.3 77.7 - - - -
31A TYR* 1.3 62.0 + - - +
46A LEU* 3.2 7.7 - - - +
47A VAL* 2.9 31.9 + - + +
168A MET* 5.7 2.2 - - - -
170A MET* 3.2 48.2 - - + +
171A CYS 3.3 11.6 + - - -
184A GLY 3.5 30.5 - - - -
185A GLY* 4.4 4.3 - - - -
242A SER 5.8 2.8 + - - -
347A ALA* 5.2 1.8 - - + -
351A GLU* 2.6 29.9 + - - -
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Residues in contact with TYR 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ASN 4.1 0.7 - - - +
22A LEU* 3.5 8.0 - - - -
23A GLN* 2.7 83.4 + - + +
24A GLY* 3.9 7.4 - - - -
29A GLY 4.1 7.0 - - - -
30A TYR* 1.3 76.4 - - - +
32A LEU* 1.3 58.1 + - - +
33A GLU 4.3 0.2 + - - -
44A GLN* 3.7 34.5 - - + -
45A ILE 2.9 22.2 - - - +
46A LEU* 4.0 0.9 - - - -
130A LYS* 3.3 49.9 + - + +
131A TRP* 4.0 25.4 - + + -
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ASN* 3.5 42.4 - - + +
22A LEU* 3.7 13.4 - - + +
31A TYR* 1.3 74.5 - - - +
33A GLU* 1.3 67.0 + - - +
34A MET* 3.5 28.7 + - + -
44A GLN* 3.6 2.8 - - - -
45A ILE* 2.6 46.0 + - + +
47A VAL* 4.1 7.4 - - + +
103A ILE* 4.0 28.0 - - + -
105A LYS 5.5 0.2 - - - +
135A LEU* 4.4 4.5 - - + -
187A LEU* 4.0 17.9 - - + -
189A LEU* 4.9 0.9 - - + -
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Residues in contact with GLU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ASN 4.5 3.2 + - - +
31A TYR 4.3 0.8 + - - -
32A LEU* 1.3 83.7 - - - +
34A MET* 1.3 64.6 + - - +
35A LEU* 4.3 4.7 - - - +
42A LYS* 2.9 41.8 + - + +
43A LEU 3.5 11.9 - - - +
44A GLN* 3.6 18.8 + - - +
103A ILE* 4.4 2.8 - - - +
104A PRO* 3.2 39.5 - - + +
105A LYS* 6.0 5.7 - - - -
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Residues in contact with MET 34 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A LEU* 3.5 28.5 - - + +
33A GLU* 1.3 75.1 - - - +
35A LEU* 1.3 65.0 - - - +
36A ILE* 4.6 3.8 - - + -
41A GLN 3.8 0.3 - - - +
42A LYS* 3.9 0.5 - - - -
43A LEU* 2.9 32.9 + - - +
45A ILE* 3.3 26.7 - - + -
54A PHE* 3.2 32.8 - - + -
101A VAL* 4.0 15.0 - - + -
102A THR 3.6 11.2 - - - +
103A ILE* 4.0 8.7 - - + -
104A PRO* 3.9 0.9 - - - -
135A LEU* 4.0 13.7 - - + -
152A PHE* 3.6 23.6 - - + -
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A GLU* 4.3 8.5 - - - +
34A MET* 1.3 74.1 - - - +
36A ILE* 1.3 62.9 + - - +
37A GLY 5.4 0.2 - - - -
40A PRO* 4.0 26.2 - - + -
41A GLN 3.4 1.3 - - - -
42A LYS* 3.8 34.5 - - + +
100A LEU 4.0 0.2 - - - +
101A VAL* 3.5 5.2 - - - +
102A THR* 2.8 50.1 + - + +
104A PRO* 3.8 22.2 - - + -
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Residues in contact with ILE 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A MET* 4.4 8.3 - - + +
35A LEU* 1.3 79.2 - - - +
37A GLY* 1.3 67.3 + - - +
39A PRO 3.6 1.2 - - - +
41A GLN* 2.8 47.4 + - - +
43A LEU* 3.2 35.4 - - + -
54A PHE* 4.1 17.0 - - + -
56A VAL* 4.0 14.4 - - + -
68A PHE* 3.5 30.6 - - + -
99A ASP* 4.6 5.4 - - + -
100A LEU 3.8 7.4 - - - +
101A VAL* 4.7 11.4 - - + -
115A ILE* 4.1 15.3 - - + -
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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