Contacts of the strand formed by residues 39 - 47 (chain A) in PDB entry 4EWE
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 PHE 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A ILE* 3.9 18.8 - - + +
35A ASN* 3.6 4.0 - - - +
36A LEU* 2.8 50.4 + - + +
37A ASP* 4.0 0.5 + - - -
38A PRO* 1.3 94.2 - - + +
40A LEU* 1.3 60.6 + - - +
116A LEU* 3.8 21.3 - - + -
117A TRP 3.5 3.8 - - - +
118A VAL* 4.0 17.9 - - + -
169A THR* 4.0 14.8 - - + -
191A THR* 4.2 10.5 - - + -
193A PHE* 3.9 14.8 - + - -
241A ILE* 3.5 25.8 - - + -
242A ALA* 3.5 9.0 - - - -
243A GLY* 3.5 34.3 - - - -
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Residues in contact with LEU 40 (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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28A ILE* 3.7 6.3 - - - +
29A GLY* 4.1 4.5 - - - -
34A LYS 3.5 18.7 - - - +
35A ASN* 4.2 7.4 - - + +
38A PRO 5.5 0.2 - - - -
39A PHE* 1.3 76.8 - - - +
41A LEU* 1.3 62.5 + - + +
61A PHE* 3.8 39.9 - - + -
117A TRP* 2.9 19.4 + - + +
119A ASN* 3.8 28.3 - - + +
250A VAL* 3.6 32.5 - - + -
252A GLN* 4.6 13.4 - - - +
257A VAL* 3.7 23.8 - - + -
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Residues in contact with LEU 41 (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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26A ARG* 3.6 36.1 - - - +
28A ILE* 3.3 16.6 - - - +
29A GLY* 5.3 2.0 - - - -
39A PHE 3.7 0.2 - - - -
40A LEU* 1.3 80.0 - - - +
42A PHE* 1.3 64.6 + - - +
43A ASP* 3.7 21.3 - - + +
115A GLN 3.8 11.4 - - - +
116A LEU* 3.4 8.4 - - - +
117A TRP* 2.9 79.4 + - + +
252A GLN* 5.6 2.2 - - - +
1005A EDO 4.3 3.6 - - - +
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Residues in contact with PHE 42 (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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25A ARG 4.0 0.5 - - - +
26A ARG* 3.6 0.2 - - - -
27A SER* 3.0 45.7 + - - +
28A ILE* 3.0 25.4 + - + +
41A LEU* 1.3 73.7 - - - +
43A ASP* 1.3 68.7 + - - +
44A GLU 5.0 0.2 - - - -
114A LEU* 3.9 40.8 - - + -
115A GLN 3.4 12.8 - - - -
116A LEU* 3.7 22.2 - - + -
171A TYR* 4.2 4.5 - - - -
193A PHE* 4.3 5.4 - + - -
195A TYR* 3.5 38.6 - + + -
239A VAL* 4.1 11.4 - - + -
241A ILE* 3.6 19.5 - - + -
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Residues in contact with ASP 43 (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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24A VAL* 3.4 19.4 - - + +
25A ARG 3.4 2.2 - - - -
26A ARG* 2.8 60.6 + - - +
41A LEU* 3.8 5.4 - - + +
42A PHE* 1.3 77.9 - - - +
44A GLU* 1.3 59.2 + - - +
45A PHE* 4.0 2.0 + - + +
113A GLY 4.0 0.2 - - - +
114A LEU* 3.4 5.4 - - - +
115A GLN* 2.8 39.3 + - + +
1005A EDO 2.6 32.7 + - - +
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Residues in contact with GLU 44 (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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24A VAL* 3.5 3.0 - - - -
25A ARG* 2.8 41.3 + - + +
42A PHE* 5.0 1.2 - - - -
43A ASP* 1.3 71.4 - - - +
45A PHE* 1.3 59.0 + - - +
112A HIS* 2.6 36.4 + - - +
113A GLY 3.5 3.4 - - - +
114A LEU* 4.0 17.7 - - + -
195A TYR* 2.6 43.7 + - + +
197A ILE* 4.4 8.9 - - - +
215A HIS* 3.1 27.6 + - - -
1002A EDO 3.2 18.0 + - - +
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Residues in contact with PHE 45 (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 ALA* 3.9 15.0 - - + -
23A ARG 3.3 19.1 - - - -
24A VAL* 4.1 9.6 - - + -
43A ASP* 4.0 2.9 - - + +
44A GLU* 1.3 72.8 - - - +
46A LYS* 1.4 64.6 + - - +
47A GLY* 3.5 41.1 - - - -
51A GLY 6.0 0.2 - - - -
52A GLY* 5.2 0.2 - - - -
53A PHE* 3.7 34.8 - + + -
67A LEU* 6.1 0.4 - - + -
73A MET* 4.0 19.3 - - + -
105A PRO* 3.8 20.9 - - + -
111A ALA* 4.2 6.3 - - + -
112A HIS* 3.2 8.0 - - - -
113A GLY* 2.8 48.2 + - - +
114A LEU 6.2 0.2 - - - -
115A GLN* 6.2 2.5 - - + +
1002A EDO 3.8 2.9 - - - -
1005A EDO 5.7 1.1 - - - +
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Residues in contact with LYS 46 (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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23A ARG* 4.0 4.0 + - - +
45A PHE* 1.4 81.9 - - - +
47A GLY* 1.3 60.6 + - - +
110A PRO* 4.1 27.4 - - + -
111A ALA 3.1 10.3 - - - +
112A HIS* 4.2 25.2 + - + +
1002A EDO 2.9 32.7 + - - +
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Residues in contact with GLY 47 (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 ALA* 6.1 1.6 - - - -
45A PHE* 3.5 20.0 - - - -
46A LYS* 1.3 77.4 - - - +
48A GLY* 1.3 58.3 + - - -
105A PRO* 3.4 12.0 - - - +
110A PRO* 3.6 9.6 - - - -
111A ALA* 2.8 28.3 + - - +
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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