Contacts of the strand formed by residues 56 - 68 (chain A) in PDB entry 3RIE
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 56 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A PHE* 4.1 1.2 - - - +
45A SER* 3.6 0.2 - - - -
46A GLU* 2.9 44.3 + - - +
55A ALA* 1.3 72.5 - - - +
57A SER* 1.3 71.4 + - - +
58A LEU* 3.5 35.7 - - + -
82A TYR* 4.6 11.9 - + - -
92A ILE* 3.9 18.8 - - + +
262A PRO* 4.4 13.0 - - + -
263A THR* 3.9 31.6 - - + -
264A TYR 6.1 1.1 - - - +
265A PRO* 5.9 5.8 - - + -
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Residues in contact with SER 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TRP* 3.6 29.7 - - - -
44A PHE 3.1 11.4 - - - -
45A SER* 2.8 22.9 + - - -
55A ALA* 4.4 3.9 + - - +
56A PHE* 1.3 86.7 - - - +
58A LEU* 1.3 70.6 + - - +
92A ILE* 6.3 0.2 - - - -
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TRP* 3.4 6.4 - - - -
44A PHE* 2.8 34.3 + - + +
56A PHE* 3.5 33.4 - - + -
57A SER* 1.3 74.6 - - - +
59A LYS* 1.3 67.7 + - - +
60A ILE* 4.1 0.3 - - - +
77A PHE* 4.4 11.9 - - + -
79A SER* 4.4 8.7 - - - -
81A THR* 5.2 1.8 - - - +
82A TYR* 3.6 29.4 - - + -
85A VAL* 4.0 28.5 - - + -
92A ILE* 4.2 21.3 - - + -
95A THR* 4.5 9.4 - - + -
263A THR* 4.8 0.2 - - + -
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Residues in contact with LYS 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 4.2 28.4 - - + +
42A LYS 3.8 7.9 - - - +
43A TRP* 3.5 50.1 - - + +
58A LEU* 1.3 75.0 - - - +
60A ILE* 1.3 62.1 + - - +
79A SER* 3.2 9.6 - - - -
80A THR* 3.0 52.5 + - + +
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Residues in contact with ILE 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 3.3 24.4 - - - +
42A LYS* 3.0 31.2 + - + +
43A TRP 3.6 8.5 - - - +
44A PHE* 3.5 31.2 - - + +
58A LEU 4.1 0.7 - - - +
59A LYS* 1.3 73.3 - - - +
61A LYS* 1.3 64.2 + - - +
62A LYS* 3.5 28.3 - - - +
63A ILE* 3.9 24.5 - - + +
77A PHE* 4.0 19.1 - - + -
78A GLU 3.9 4.0 - - - +
79A SER* 4.4 1.1 - - - +
80A THR* 4.0 2.9 - - - -
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Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 3.6 26.8 + - - +
59A LYS 3.8 0.4 + - - -
60A ILE* 1.3 75.0 - - - +
62A LYS* 1.3 60.5 + - + +
78A GLU* 2.8 49.4 + - + +
79A SER 3.9 13.0 - - - +
80A THR* 3.8 14.2 - - + +
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Residues in contact with LYS 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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60A ILE* 3.5 7.7 - - - +
61A LYS* 1.3 83.4 - - + +
63A ILE* 1.3 76.8 + - - +
64A LEU* 3.6 18.6 + - + +
77A PHE* 3.5 1.4 - - - +
78A GLU* 2.9 38.8 + - - +
62B LYS* 6.3 2.9 - - - -
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Residues in contact with ILE 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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60A ILE* 3.9 25.2 - - + +
62A LYS* 1.3 89.8 - - - +
64A LEU* 1.3 63.4 + - - +
65A TYR 4.0 3.8 - - - +
66A GLU* 3.8 41.1 - - + +
75A LEU* 3.9 13.5 - - + -
76A VAL 4.0 0.7 - - - +
77A PHE* 3.9 10.1 - - + -
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Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS* 4.0 26.7 - - + +
63A ILE* 1.3 80.9 - - - +
65A TYR* 1.3 61.8 + - - +
76A VAL* 2.8 30.3 + - + +
78A GLU* 4.0 21.1 - - + +
84A LYS* 3.6 38.6 - - + -
159A TYR* 3.8 28.0 + - + -
64B LEU* 6.1 1.0 - - - +
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Residues in contact with TYR 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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63A ILE* 3.8 2.5 - - - +
64A LEU* 1.3 81.2 - - - +
66A GLU* 1.3 73.9 + - - +
67A THR* 3.4 43.2 + - + +
74A VAL* 4.9 3.8 - - + -
75A LEU* 3.6 0.5 - - - -
76A VAL* 2.9 40.9 + - + +
151A THR* 4.8 0.2 - - - +
155A VAL* 3.8 26.7 - - + -
159A TYR* 3.8 30.3 - + + -
157B LYS 4.7 1.4 + - - -
158B ILE* 2.7 50.4 + - + +
159B TYR* 4.1 12.1 - + - -
161B LYS* 4.8 0.2 - - - +
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Residues in contact with GLU 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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63A ILE* 3.8 22.6 - - + +
65A TYR* 1.3 88.6 - - - +
67A THR* 1.3 63.6 + - - +
74A VAL 3.2 10.3 - - - +
75A LEU* 3.6 28.2 - - + +
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Residues in contact with THR 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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65A TYR* 3.4 30.3 - - + +
66A GLU* 1.3 75.6 - - - +
68A LYS* 1.3 61.5 + - - +
69A SER* 4.1 9.9 - - - +
73A ASN* 3.7 2.9 - - - +
74A VAL* 2.9 36.9 + - + +
151A THR* 3.8 23.1 - - + -
161B LYS* 2.9 35.9 - - - +
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Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A THR* 1.3 74.9 + - - +
69A SER* 1.3 71.9 + - - +
72A GLN 3.8 6.5 - - - +
73A ASN* 3.4 26.6 + - - +
161B LYS* 2.9 25.0 + - - +
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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