Contacts of the strand formed by residues 72 - 79 (chain L) in PDB entry 5OA3
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 72 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8562 C 5.3 4.3 + - - -
42L LEU* 5.0 18.4 - - + -
44L PHE* 4.5 15.5 - - + -
68L ILE* 5.7 3.4 - - + -
70L GLY 3.5 17.3 - - - +
71L ARG* 1.3 74.9 - - - +
73L LEU* 1.3 67.7 + - - +
127L THR* 4.1 19.1 - - + -
128L VAL 3.1 17.3 - - - +
129L GLY* 4.2 8.3 - - - -
130L GLU 5.1 0.2 - - - +
143L LEU* 4.8 7.6 - - + -
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Residues in contact with LEU 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3532 C 4.1 24.5 - - - +
8562 C 6.0 2.2 - - - +
71L ARG* 4.1 17.0 + - + +
72L ILE* 1.3 87.3 - - - +
74L SER* 1.3 61.5 + - - +
90L ARG* 3.9 36.6 - - - +
109L MET* 4.2 8.7 - - + -
127L THR* 3.8 4.5 - - - +
128L VAL* 2.8 43.2 + - + +
140L PHE* 3.6 32.5 - - + -
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Residues in contact with SER 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73L LEU* 1.3 78.0 - - - +
75L GLY* 1.3 62.1 + - - +
88L ILE* 4.7 2.7 - - - -
90L ARG* 3.6 23.1 + - - +
125L ILE* 4.1 14.3 - - - +
126L VAL 3.5 9.6 - - - -
127L THR* 4.2 12.8 - - - -
128L VAL* 5.0 0.7 - - - -
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Residues in contact with GLY 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74L SER* 1.3 78.6 + - - +
76L VAL* 1.3 60.8 + - - -
88L ILE* 3.8 17.7 - - - +
89L ARG 4.1 7.6 - - - -
90L ARG* 4.4 2.5 - - - -
125L ILE* 3.5 8.7 - - - +
126L VAL* 2.9 37.2 + - - +
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Residues in contact with VAL 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75L GLY* 1.3 74.1 - - - -
77L VAL* 1.3 79.1 + - - +
78L THR* 3.5 4.5 - - + +
88L ILE* 3.4 3.1 - - - +
89L ARG* 3.2 50.4 + - + +
91L ASP* 5.0 4.0 - - - +
123L GLY* 4.0 18.6 - - - -
124L ASP 3.5 7.4 - - - +
125L ILE* 4.2 13.7 - - + -
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Residues in contact with VAL 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75L GLY 4.2 0.4 - - - -
76L VAL* 1.3 80.6 - - - +
78L THR* 1.3 66.2 - - - +
79L LYS 4.4 0.9 - - - +
80L MET* 4.0 29.8 - - + -
86L ILE* 3.7 25.1 - - + -
87L VAL 4.5 2.2 - - - +
88L ILE* 3.9 6.5 - - + -
120L VAL* 4.1 9.0 - - + -
122L ILE* 4.2 11.4 - - - +
123L GLY* 3.0 21.7 + - - -
124L ASP* 3.2 27.7 + - - +
126L VAL* 3.6 22.9 - - + -
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Residues in contact with THR 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76L VAL* 3.5 11.9 - - + +
77L VAL* 1.3 79.4 - - - +
79L LYS* 1.3 88.8 + - - +
87L VAL* 2.9 23.0 + - - +
88L ILE* 4.1 0.9 - - - -
89L ARG* 3.6 35.2 - - + +
108L ASN* 4.6 3.0 + - - +
122L ILE* 3.2 29.8 - - - +
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Residues in contact with LYS 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3952 G 3.1 37.7 + - - +
3962 U 3.6 32.3 + - - -
77L VAL* 4.9 0.2 - - - -
78L THR* 1.3 93.7 + - - +
80L MET* 1.3 60.1 + - - +
81L LYS* 3.2 28.0 + - - +
82L MET* 5.1 0.7 - - - +
86L ILE* 3.8 0.9 - - - -
87L VAL* 2.9 39.5 + - + +
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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