Contacts of the strand formed by residues 59 - 66 (chain D) in PDB entry 1EFX
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 59 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27D GLN* 5.5 0.7 - - - +
29D TRP* 3.6 41.7 - - + -
30D SER 4.3 5.2 - - - +
31D ASP* 5.5 1.1 - - - +
54D GLU 3.0 13.5 - - - +
55D HIS* 4.5 0.9 - - - -
56D HIS 3.1 22.9 + - - +
57D ASP* 3.1 9.4 - - + +
58D GLY* 1.3 88.6 - - - +
60D SER* 1.3 75.9 + - - +
61D LYS* 3.7 16.1 - - + +
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Residues in contact with SER 60 (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 TRP* 3.1 2.8 - - - -
30D SER 3.0 29.8 + - - -
31D ASP* 4.3 1.9 + - - +
32D VAL 3.1 28.8 + - - -
33D ARG* 3.2 13.3 + - - +
34D PHE 4.2 2.2 - - - -
37D PHE* 3.3 10.9 - - - -
54D GLU 3.4 5.4 - - - -
55D HIS* 2.9 30.0 + - - +
59D VAL* 1.3 72.7 - - - +
61D LYS* 1.3 60.2 + - - +
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Residues in contact with LYS 61 (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* 3.6 22.3 + - + +
28D CYS 3.1 11.4 - - - +
29D TRP* 3.6 12.6 - - + -
37D PHE* 3.8 1.6 - - - -
53D GLY* 3.2 4.2 - - - -
54D GLU* 2.6 45.1 + - + +
56D HIS* 2.9 40.4 + - - -
57D ASP* 4.6 8.2 + - - +
59D VAL* 3.7 11.7 - - + +
60D SER* 1.3 75.4 - - - +
62D ALA* 1.3 64.2 + - - +
63D ASN* 4.3 13.6 + - - +
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Residues in contact with ALA 62 (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 LEU 4.0 0.2 - - - +
27D GLN* 3.5 1.2 - - - -
28D CYS 2.9 27.2 + - - +
37D PHE* 3.5 33.4 - - + -
51D LEU* 4.0 15.7 - - + -
52D ILE 4.0 12.3 - - - +
54D GLU* 4.8 6.1 - - - -
61D LYS* 1.3 80.8 - - - +
63D ASN* 1.3 64.7 + - - +
64D PHE* 3.7 5.4 + - + -
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Residues in contact with ASN 63 (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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13D HIS* 6.0 0.2 + - - -
25D ILE* 3.8 21.0 - - + +
26D LEU 3.9 2.0 - - - -
27D GLN* 2.9 40.9 + - - +
51D LEU* 3.6 13.4 - - - +
54D GLU* 5.7 3.5 - - - +
61D LYS* 4.3 18.2 + - - +
62D ALA* 1.3 73.4 - - - +
64D PHE* 1.3 63.3 + - - +
65D SER* 3.6 4.2 + - - -
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Residues in contact with PHE 64 (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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10D LEU* 5.8 0.4 - - + -
25D ILE* 3.4 5.7 - - - -
26D LEU* 2.8 46.6 + - + +
28D CYS* 4.1 14.6 - - + -
37D PHE* 3.5 36.8 - - + -
38D LEU 4.7 0.4 - - - -
39D LEU* 3.6 48.2 - - + -
49D LEU* 3.4 30.3 - - + -
50D HIS 3.9 3.6 - - - -
51D LEU* 3.3 34.3 - - + -
62D ALA 4.0 7.2 - - - -
63D ASN* 1.3 70.7 - - - +
65D SER* 1.3 61.8 + - - +
66D ILE* 3.6 5.0 + - + -
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Residues in contact with SER 65 (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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23D THR* 4.0 16.5 - - - +
24D VAL 3.9 4.0 - - - -
25D ILE* 4.7 9.3 - - - +
49D LEU* 5.2 6.3 - - - +
63D ASN 3.6 5.0 + - - -
64D PHE* 1.3 71.9 - - - +
66D ILE* 1.3 63.2 + - - +
67D GLY* 3.1 9.7 + - - -
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Residues in contact with ILE 66 (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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23D THR* 3.4 15.6 - - - +
24D VAL* 2.9 33.1 + - + +
26D LEU* 3.8 27.6 - - + -
39D LEU* 4.2 12.8 - - + -
41D ARG* 5.9 0.2 - - - +
49D LEU* 4.6 13.9 - - + -
64D PHE* 3.6 3.8 + - + +
65D SER* 1.3 73.5 - - - +
67D GLY* 1.3 70.4 + - - +
69D MET* 4.4 8.6 - - + +
73D LEU* 3.7 29.8 - - + -
77D TYR* 3.7 37.0 - - + +
99D ILE* 5.6 0.9 - - + -
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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