Contacts of the strand formed by residues 77 - 84 (chain A) in PDB entry 4O6M
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 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A VAL* 3.1 3.0 - - - -
74A SER* 2.7 36.8 + - - +
75A ASP* 3.0 18.8 + - + -
76A GLY* 1.3 77.5 - - - +
78A THR* 1.3 63.1 + - - +
79A VAL* 3.3 1.9 + - - +
117A LYS* 3.7 38.6 - - + -
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Residues in contact with THR 78 (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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55A GLU* 5.2 4.0 - - - +
71A ILE* 3.6 29.5 - - + +
72A LEU 3.4 5.8 - - - +
73A VAL* 4.0 5.5 - - - +
76A GLY 3.7 3.8 + - - -
77A PHE* 1.3 70.9 - - - +
79A VAL* 1.3 62.4 + - - +
80A GLY* 4.0 10.5 - - - +
81A TYR* 4.2 26.2 - - + +
117A LYS* 3.4 19.6 + - - -
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Residues in contact with VAL 79 (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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53A ILE* 3.9 22.1 - - + +
54A LEU 4.7 2.6 + - - -
55A GLU* 4.9 6.4 + - - +
57A VAL* 3.9 33.4 - - + +
59A ILE* 5.3 3.1 - - + -
72A LEU* 2.5 20.4 + - + +
73A VAL 3.8 4.0 - - - -
74A SER* 3.5 38.4 - - - +
77A PHE 3.7 2.2 - - - +
78A THR* 1.3 76.1 - - - +
80A GLY* 1.3 56.6 + - - +
113A ILE* 3.9 19.5 - - + -
115A ALA* 4.3 8.3 - - + -
117A LYS* 5.0 9.9 - - + +
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Residues in contact with GLY 80 (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 3.2 13.0 - - - -
53A ILE* 4.4 7.2 - - - -
54A LEU 5.4 0.2 - - - -
71A ILE* 3.8 6.9 - - - +
72A LEU* 2.8 37.4 + - - +
78A THR* 3.6 3.0 - - - -
79A VAL* 1.3 81.9 - - - +
81A TYR* 1.3 70.1 + - - -
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Residues in contact with TYR 81 (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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50A TYR 3.6 1.7 - - - +
51A LEU* 3.3 6.2 - - - +
52A ILE* 2.7 55.5 + - + +
54A LEU* 3.6 32.8 - - + +
70A LYS 4.2 2.9 - - - -
71A ILE* 4.3 19.5 - - + +
78A THR* 4.2 22.2 - - + +
80A GLY* 1.3 77.9 - - - -
82A PHE* 1.3 60.2 + - - +
83A PHE* 3.6 37.7 - + + -
99A ILE* 4.2 20.1 - - + +
103A LEU* 4.1 19.2 - - + +
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Residues in contact with PHE 82 (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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2A ARG* 3.2 26.9 - - - -
34A PHE* 3.9 11.2 - + - -
49A ASP* 3.6 34.1 - - + -
50A TYR 3.4 14.1 - - - -
51A LEU* 4.3 9.9 - - + -
66A LEU* 3.6 38.8 - - + -
68A GLY* 3.0 38.6 - - - -
69A ARG* 3.2 8.5 - - - +
70A LYS* 2.9 42.2 + - + +
72A LEU* 4.7 6.7 - - + +
80A GLY 4.2 0.6 + - - -
81A TYR* 1.3 71.4 - - - +
83A PHE* 1.3 64.6 + - - +
108A LEU* 4.8 0.2 - - - +
412A SO4 5.1 1.1 - - - -
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Residues in contact with PHE 83 (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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49A ASP* 3.9 5.5 - - - +
50A TYR* 2.8 36.5 + - + +
52A ILE* 4.2 10.8 - - + -
69A ARG* 4.5 2.9 - - - -
81A TYR* 3.6 35.2 - + + -
82A PHE* 1.3 83.2 - - - +
84A GLY* 1.3 64.9 + - - +
87A PHE* 3.5 41.7 - + + -
99A ILE* 4.2 17.7 - - + -
102A TYR* 3.2 38.4 - + + -
103A LEU* 4.0 13.9 - - + -
108A LEU* 3.6 20.9 - - + -
412A SO4 5.3 0.4 - - - -
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Residues in contact with GLY 84 (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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48A GLU 3.9 3.8 - - - -
49A ASP* 4.5 1.1 - - - -
50A TYR* 3.6 4.8 - - - -
69A ARG* 3.9 15.5 - - - +
83A PHE* 1.3 77.3 - - - +
85A GLY* 1.3 66.2 + - - -
86A ASP* 3.1 10.3 - - - -
87A PHE* 3.1 18.5 + - - +
102A TYR* 3.1 12.5 + - - -
412A SO4 4.1 15.5 - - - -
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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