Contacts of the strand formed by residues 60 - 68 (chain A) in PDB entry 4ED5
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 SER 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A PRO 4.7 2.8 + - - -
29A GLN* 3.6 29.5 + - - +
31A MET 4.8 2.0 - - - -
51A LEU* 3.7 29.0 - - - +
52A ILE 3.7 5.6 - - - -
53A ARG* 4.0 8.3 - - - +
58A GLY 3.8 1.8 + - - -
59A HIS* 1.3 78.0 - - - +
61A LEU* 1.3 57.0 + - - +
62A GLY* 2.8 22.8 + - - -
7D A 3.5 20.8 + - - -
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Residues in contact with LEU 61 (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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52A ILE* 2.7 31.3 + - + +
53A ARG 3.9 2.7 - - - +
54A ASP* 3.7 39.0 - - + +
59A HIS* 4.0 1.8 - - - +
60A SER* 1.3 74.0 - - - +
62A GLY* 1.3 60.4 + - - +
63A TYR* 3.3 21.7 + - + +
7D A 2.5 75.0 + - + +
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Residues in contact with GLY 62 (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 TYR* 3.2 10.6 + - - -
27A LEU* 2.9 46.4 + - - -
28A PRO 5.0 2.0 - - - -
29A GLN* 5.3 2.9 - - - -
52A ILE 4.1 0.2 + - - -
60A SER* 2.8 16.6 + - - -
61A LEU* 1.3 79.3 - - - +
63A TYR* 1.3 58.6 + - - +
7D A 4.3 9.8 + - - +
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Residues in contact with TYR 63 (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 ILE* 4.1 11.0 - - + -
24A VAL 3.1 14.4 - - - +
25A ASN* 3.6 14.4 - - - +
27A LEU* 3.8 8.4 - - - +
51A LEU* 3.8 4.5 - - - +
52A ILE* 2.9 58.1 + - + +
60A SER* 4.6 0.4 + - - -
61A LEU* 3.5 27.3 - - + +
62A GLY* 1.3 79.5 - - - +
64A GLY* 1.3 61.7 + - - +
65A PHE* 3.9 16.4 - + - -
7D A 3.4 20.2 - - + +
8D U 3.8 35.2 - - - -
9D U 3.4 25.3 + - - -
10D U 5.1 0.9 - - - -
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Residues in contact with GLY 64 (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 ILE* 3.5 7.3 - - - +
24A VAL* 2.8 34.3 + - - +
27A LEU* 3.9 2.2 - - - +
36A LEU* 4.2 8.7 - - - -
50A LYS 3.0 14.8 - - - -
51A LEU* 4.2 2.0 - - - -
52A ILE 4.2 1.6 - - - -
63A TYR* 1.3 78.1 - - - +
65A PHE* 1.3 69.2 + - - -
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Residues in contact with PHE 65 (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* 4.2 6.3 - - - +
22A LEU 3.2 15.5 - - - +
23A ILE* 3.8 31.0 - - + -
36A LEU* 4.3 0.5 - - - +
48A SER 4.0 0.4 - - - +
49A ALA* 3.1 4.7 - - - -
50A LYS* 2.8 35.9 + - + +
52A ILE* 3.9 20.6 - - + -
63A TYR* 3.9 8.1 - + - -
64A GLY* 1.3 74.1 - - - -
66A VAL* 1.3 65.6 + - - +
67A ASN 4.2 0.7 - - - +
96A ALA* 4.1 6.5 - - + -
9D U 3.3 39.3 - + - -
10D U 3.4 66.6 - + - +
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Residues in contact with VAL 66 (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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20A THR 3.7 3.1 - - - +
21A ASN* 3.9 1.3 - - - -
22A LEU* 2.8 37.9 + - + +
24A VAL* 4.1 11.4 - - + +
36A LEU* 4.0 17.9 - - + -
40A PHE* 3.8 44.6 - - + -
46A VAL* 4.2 16.8 - - + -
48A SER 3.5 2.2 - - - -
49A ALA* 4.2 5.6 - - + -
65A PHE* 1.3 79.8 - - - +
67A ASN* 1.3 62.5 + - - +
68A TYR* 3.8 26.0 + - + -
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Residues in contact with ASN 67 (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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20A THR* 2.7 35.4 + - - -
21A ASN* 3.3 21.6 + - - +
46A VAL* 3.6 2.6 - - - +
47A GLU* 2.6 72.3 + - - +
48A SER* 2.7 21.9 + - - +
65A PHE 4.2 0.6 - - - -
66A VAL* 1.3 73.8 - - - +
68A TYR* 1.3 57.9 + - - +
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Residues in contact with TYR 68 (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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20A THR* 3.0 29.7 + - - +
22A LEU* 3.6 13.9 - - + -
40A PHE* 2.7 45.8 + + - -
43A ILE* 3.5 7.0 - - + +
44A GLY 3.7 14.8 - - - -
45A GLU 3.5 17.9 - - - -
46A VAL* 3.7 10.3 - - + -
47A GLU* 3.9 2.4 - - - +
66A VAL* 3.8 15.5 - - + -
67A ASN* 1.3 80.2 + - - +
69A VAL* 1.3 64.0 + - - +
70A THR 3.5 20.4 - - - +
73A ASP* 3.8 12.8 - - + -
74A ALA* 3.6 20.9 - - + +
77A ALA* 3.4 29.1 - - + +
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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