Contacts of the helix formed by residues 78 - 89 (chain A) in PDB entry 1RFA
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 LEU 78 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A SER* 1.3 70.1 - - - +
79A HIS* 1.3 53.9 + - - +
81A CYS* 3.0 3.5 + - - -
82A LEU* 2.7 54.1 + - + +
98A VAL* 3.5 35.0 - - + -
112A LEU* 4.6 2.0 - - + -
113A ASP 2.9 26.7 - - - +
114A TRP* 3.5 10.8 - - + +
116A THR* 2.9 57.3 + - + +
118A ALA* 3.9 16.2 - - + +
121A LEU* 4.5 2.2 - - + -
126A LEU* 4.0 10.3 - - + -
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Residues in contact with HIS 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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77A SER* 3.0 1.1 + - - -
78A LEU* 1.3 71.8 - - - +
80A ASP* 1.3 61.8 + - - +
82A LEU* 3.6 1.0 - - - +
83A MET* 2.6 44.4 + - + +
93A PRO* 3.3 38.2 - - + +
94A GLU* 3.8 14.2 - - + +
114A TRP* 2.8 76.4 + + + +
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Residues in contact with ASP 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLY 4.9 2.0 - - - +
76A MET 3.2 19.4 - - - +
77A SER* 2.9 7.1 + - - -
79A HIS* 1.3 83.4 - - - +
81A CYS* 1.3 52.4 + - - +
83A MET* 3.8 23.5 - - - +
84A LYS* 2.7 38.8 + - - +
115A ASN* 5.7 0.5 - - - +
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Residues in contact with CYS 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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70A VAL* 5.0 10.2 - - - +
71A ASN 4.3 12.1 - - - +
72A VAL* 4.2 22.7 - - - -
73A ARG 5.0 0.7 - - - -
76A MET* 3.4 26.2 + - + -
77A SER 2.5 26.6 + - - +
78A LEU* 3.5 4.3 - - - +
80A ASP* 1.3 76.3 - - - +
82A LEU* 1.3 67.5 + - + +
84A LYS* 3.3 28.2 - - - +
85A ALA* 4.1 2.1 + - - +
118A ALA* 4.5 6.3 - - + -
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Residues in contact with LEU 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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60A VAL* 4.0 26.7 - - + -
70A VAL* 5.4 3.6 - - + -
78A LEU* 2.7 31.6 + - + +
79A HIS 3.8 1.8 - - - +
81A CYS* 1.3 86.7 - - + +
83A MET* 1.3 55.3 - - - +
84A LYS 2.8 6.1 - - - -
85A ALA* 2.7 8.0 + - + +
86A LEU* 2.6 50.0 + - + +
98A VAL* 3.8 16.6 - - + -
114A TRP* 3.8 12.6 - - + -
118A ALA* 5.8 2.5 - - + -
126A LEU* 5.4 3.8 - - + -
128A VAL* 3.8 29.6 - - + -
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Residues in contact with MET 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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79A HIS* 2.6 23.6 + - + +
80A ASP* 3.8 24.2 - - - +
82A LEU* 1.3 75.8 - - - +
84A LYS* 1.3 57.8 + - - +
86A LEU* 4.5 6.5 - - - -
87A LYS* 2.9 34.0 + - + +
93A PRO* 4.0 15.7 - - + -
94A GLU* 3.9 23.3 - - + +
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Residues in contact with LYS 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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70A VAL* 5.4 5.6 - - + -
71A ASN 5.9 3.8 - - - +
73A ARG* 5.9 8.3 - - - +
75A GLY 3.8 18.8 + - - -
76A MET* 4.8 1.4 - - - +
80A ASP* 2.7 36.5 + - - +
81A CYS* 3.3 24.2 - - - +
83A MET* 1.3 76.8 - - - +
85A ALA* 1.3 67.2 + - - +
87A LYS* 3.0 13.4 - - - +
88A VAL* 3.0 20.5 - - + +
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Residues in contact with ALA 85 (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 VAL* 4.3 18.6 - - + -
68A THR* 5.1 5.8 - - + -
70A VAL* 4.0 25.4 - - + -
82A LEU* 2.7 22.0 + - + +
84A LYS* 1.3 75.9 - - - +
86A LEU* 1.3 63.9 + - + +
88A VAL* 2.9 22.5 + - - +
89A ARG* 2.8 23.4 - - + +
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Residues in contact with LEU 86 (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 VAL* 5.2 3.8 - - + -
62A LEU* 4.0 18.6 - - + -
82A LEU* 2.6 38.6 + - + +
83A MET* 4.9 0.4 - - - -
85A ALA* 1.3 76.2 - - + +
87A LYS* 1.3 57.6 + - - +
88A VAL 3.1 0.2 - - - -
89A ARG* 3.8 6.5 - - - -
90A GLY 2.5 31.7 + - - -
91A LEU* 2.6 42.7 + - + +
92A GLN 5.0 2.5 - - - +
93A PRO* 3.3 41.1 - - + -
114A TRP* 4.6 0.7 - - + -
128A VAL* 4.5 21.8 - - + -
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Residues in contact with LYS 87 (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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83A MET* 2.9 33.3 + - + +
84A LYS* 3.0 8.0 - - - +
86A LEU* 1.3 82.0 - - - +
88A VAL* 1.3 63.8 + - + +
89A ARG 3.2 0.3 + - - -
90A GLY* 3.4 9.5 + - - -
91A LEU 4.5 4.0 - - - -
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Residues in contact with VAL 88 (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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84A LYS* 3.0 20.2 - - + +
85A ALA* 3.0 12.8 - - - +
87A LYS* 1.3 81.7 - - + +
89A ARG* 1.3 69.3 + - + +
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Residues in contact with ARG 89 (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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62A LEU* 3.4 33.6 - - + +
66A GLN* 3.5 25.8 - - - +
67A ARG 2.7 37.5 + - - +
68A THR* 3.6 23.1 + - - +
85A ALA* 2.8 23.6 - - - +
86A LEU* 3.0 9.1 + - - +
88A VAL* 1.3 88.9 - - + +
90A GLY* 1.3 60.1 + - - +
91A LEU* 4.4 15.3 - - + +
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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