Contacts of the strand formed by residues 61 - 66 (chain A) in PDB entry 4M7D
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE* 4.1 17.7 - - + -
16A ILE 4.2 2.2 - - - -
17A LEU* 4.6 0.7 - - + +
18A VAL* 3.8 2.5 - - - +
34A THR* 3.3 32.8 - - + +
36A LEU* 3.7 21.5 - - + -
56A LEU* 4.0 13.7 - - + -
57A ARG 3.6 18.6 - - - +
58A GLY* 3.1 14.0 + - - +
59A SER 4.5 0.9 - - - +
60A GLU* 1.3 79.4 - - - +
62A ALA* 1.3 64.4 + - - +
63A LEU* 3.7 13.0 - - - +
64A VAL* 3.8 19.7 - - + -
61B PHE* 5.5 1.6 - - + -
63B ARG* 3.7 17.1 + - + +
66B THR* 3.4 15.2 - - - +
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Residues in contact with ALA 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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16A ILE* 2.9 15.2 + - + +
17A LEU 3.9 14.8 - - - +
18A VAL* 4.1 7.2 - - - +
60A GLU 3.9 0.4 + - - -
61A ILE* 1.3 78.6 - - - +
63A LEU* 1.3 64.2 + - + +
19B LEU* 4.5 8.9 - - + +
21B ASN* 4.4 10.8 - - - +
62B ILE* 3.6 5.0 - - - +
63B ARG* 3.0 24.5 + - - +
66B THR* 3.6 27.6 + - + +
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Residues in contact with LEU 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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14A VAL 3.9 0.2 - - - +
15A ILE* 3.3 5.0 - - - +
16A ILE* 2.8 63.3 + - + +
61A ILE* 3.7 1.9 - - - +
62A ALA* 1.3 84.4 - - + +
64A VAL* 1.3 71.2 + - - +
65A GLY* 4.3 0.4 - - - -
19B LEU* 3.7 21.8 - - + -
23B ILE* 4.4 2.7 - - + -
25B ILE* 3.6 25.8 - - + -
54B LEU* 5.6 2.2 - - + -
60B ILE* 3.5 35.9 - - + -
61B PHE 3.2 16.6 - - - +
62B ILE* 4.1 6.3 - - + -
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Residues in contact with VAL 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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5A LEU* 4.1 10.1 - - + -
8A TYR* 3.6 24.5 - - + -
13A VAL* 3.9 18.6 - - + -
14A VAL 3.3 5.4 - - - +
15A ILE* 4.5 7.2 - - + -
27A LEU* 5.1 4.5 - - + -
34A THR* 5.5 0.2 - - + -
36A LEU* 4.3 18.6 - - + -
61A ILE* 3.8 20.0 - - + -
63A LEU* 1.3 84.6 - - - +
65A GLY* 1.3 60.0 + - - +
60B ILE* 3.3 1.0 - - - -
61B PHE* 2.6 59.0 + - + +
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Residues in contact with GLY 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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8A TYR* 4.3 1.1 - - - -
13A VAL* 3.1 12.0 - - - -
14A VAL* 2.7 40.6 + - - +
63A LEU* 4.3 1.2 - - - +
64A VAL* 1.3 76.1 - - - +
66A LEU* 1.3 60.4 + - - -
67A ILE 3.3 1.6 + - - -
54B LEU* 6.1 0.2 - - - -
57B VAL* 3.6 15.5 - - - -
59B ASN 3.4 8.3 - - - -
60B ILE* 4.0 5.8 - - - -
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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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7A ASP* 4.2 2.9 - - + +
8A TYR* 3.5 45.2 - - + +
11A LYS* 3.9 36.1 - - + +
12A ARG 4.1 4.0 - - - +
13A VAL* 4.4 1.6 - - + -
65A GLY* 1.3 69.2 - - - -
67A ILE* 1.3 66.9 + - - +
56B SER* 5.1 0.5 + - - +
57B VAL* 3.4 16.4 - - - +
58B ARG 4.4 2.8 + - - -
59B ASN* 2.8 29.4 + - + +
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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