Contacts of the strand formed by residues 61 - 68 (chain A) in PDB entry 6J7Z
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 ILE 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A LEU* 4.3 22.9 - - + -
49A GLU 3.5 6.5 - - - +
50A MET* 3.6 31.4 - - + -
60A ILE* 1.3 77.4 - - - +
62A GLU* 1.3 73.3 + - - +
63A MET* 4.0 3.5 + - + +
81A LEU 3.8 0.5 - - - +
82A ILE* 3.4 7.0 - - - -
83A ILE* 2.9 43.5 + - + +
84A LYS 4.5 12.1 - - - +
150A PHE* 3.7 33.9 - - + -
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Residues in contact with GLU 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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47A ASP 3.8 0.7 - - - +
48A LEU* 3.2 4.9 - - - -
49A GLU* 2.9 40.9 + - + +
60A ILE 4.3 0.4 - - - -
61A ILE* 1.3 75.2 - - - +
63A MET* 1.3 62.8 + - - +
80A ASN* 3.2 15.9 - - - +
81A LEU 3.4 4.7 - - - +
82A ILE* 3.6 22.3 - - + +
194A HIS 4.2 4.0 - - - +
195A ARG* 3.0 56.9 + - - +
196A ALA* 3.3 21.7 + - + +
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Residues in contact with MET 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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46A VAL* 4.7 9.9 - - + -
47A ASP 3.4 3.4 - - - -
48A LEU* 3.6 31.0 - - + -
61A ILE* 4.9 2.0 - - + -
62A GLU* 1.3 75.8 - - - +
64A ALA* 1.3 64.0 + - - +
80A ASN* 3.4 4.5 - - - +
81A LEU 2.9 32.6 + - - -
83A ILE* 4.3 12.3 - - + -
124A PHE* 3.4 50.7 - - + -
150A PHE* 6.2 0.2 - - - -
151A LEU* 3.8 23.8 - - + -
155A MET* 3.9 21.8 - - - +
158A PHE* 4.3 14.4 - - + -
196A ALA* 4.5 0.4 - - - -
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Residues in contact with ALA 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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46A VAL* 3.3 5.2 - - - +
47A ASP 2.9 31.3 + - - +
63A MET* 1.3 76.6 - - - +
65A CYS* 1.3 61.7 + - - +
79A PRO 3.7 5.6 - - - +
80A ASN* 3.8 18.2 - - + +
124A PHE* 4.4 1.3 - - - -
196A ALA* 3.6 19.9 - - + +
197A LEU* 3.8 19.7 - - + +
200A ILE* 3.7 9.2 - - + -
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Residues in contact with CYS 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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44A VAL* 3.7 30.1 - - - -
45A TRP 3.2 8.1 - - - +
46A VAL* 3.9 9.2 - - + -
64A ALA* 1.3 77.8 - - - +
66A LEU* 1.3 63.6 + - - +
77A GLU* 4.2 0.5 - - - +
78A GLY* 2.8 31.8 + - - +
79A PRO 3.6 5.0 + - - +
124A PHE* 3.7 25.6 - - + -
127A PHE* 4.0 22.4 - - - -
128A VAL* 4.4 4.7 - - - -
158A PHE* 4.8 2.0 - - - -
197A LEU* 5.1 4.0 - - - +
200A ILE* 3.9 2.2 - - - +
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Residues in contact with LEU 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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44A VAL* 3.7 0.5 - - - -
45A TRP* 2.9 38.0 + - + +
65A CYS* 1.3 76.8 - - - +
67A ILE* 1.3 76.5 + - - +
68A THR* 3.7 26.2 - - + -
74A ILE* 4.0 22.9 - - + -
76A ALA 3.3 15.0 - - - +
77A GLU* 4.0 13.7 - - + -
78A GLY 4.1 2.2 - - - +
127A PHE* 4.3 0.9 - - - -
197A LEU* 4.1 20.2 - - + -
200A ILE* 3.6 24.0 - - + -
201A SER* 5.5 3.4 - - - +
204A ILE* 3.7 12.6 - - + -
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Residues in contact with ILE 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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42A ARG* 4.1 23.3 - - + -
43A MET 3.4 6.3 - - - +
44A VAL* 3.8 31.2 - - + -
66A LEU* 1.3 83.7 - - - +
68A THR* 1.3 74.8 + - - +
74A ILE* 3.5 4.9 - - - -
75A LEU* 2.8 29.3 + - + -
76A ALA 2.9 15.4 + - - +
127A PHE* 3.5 27.6 - - + -
128A VAL* 4.5 3.4 - - + -
131A GLN* 3.6 33.9 - - + +
132A THR* 4.2 3.1 - - + -
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Residues in contact with THR 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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42A ARG* 3.3 8.7 - - - +
43A MET* 2.9 36.5 + - - +
45A TRP* 2.7 39.1 + - + +
66A LEU* 3.7 11.4 - - + -
67A ILE* 1.3 79.1 - - - +
69A ASP* 1.3 69.3 + - - +
72A LEU* 3.9 17.4 - - - +
73A ASN 3.2 12.3 - - - +
74A ILE* 4.1 4.3 - - + -
75A LEU* 4.0 5.8 - - - +
204A ILE* 3.8 12.6 - - + -
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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