Contacts of the helix formed by residues 95 - 104 (chain A) in PDB entry 2RCY
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 ASN 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A GLY 3.0 3.0 + - - +
94A LEU* 1.3 74.9 - - - +
96A ILE* 1.3 61.6 + - - +
97A GLY* 3.4 8.1 - - - +
98A LYS* 3.1 29.5 + - - +
99A LEU* 2.9 28.7 + - - +
111A TRP* 3.6 23.8 - - + -
156A GLU* 3.2 16.0 + - + +
160A ASP* 5.6 2.0 - - - +
261A GLY* 3.2 29.3 + - - +
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Residues in contact with ILE 96 (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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95A ASN* 1.3 75.2 - - - +
97A GLY* 1.3 53.8 + - - +
99A LEU* 3.2 9.8 + - + +
100A GLU* 2.7 58.7 + - + +
109A ILE* 5.0 8.3 - - + +
111A TRP* 4.4 10.5 - - + +
128A CYS* 3.6 32.8 - - + +
129A SER* 3.6 29.6 - - - +
130A ASN* 3.7 17.0 - - + +
156A GLU* 3.0 23.4 + - + +
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Residues in contact with GLY 97 (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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95A ASN* 3.3 8.9 - - - +
96A ILE* 1.3 79.9 - - - +
98A LYS* 1.3 56.6 + - - +
100A GLU* 3.6 11.7 + - - +
101A GLU* 3.1 27.2 + - - +
156A GLU* 3.8 3.4 + - - -
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Residues in contact with LYS 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 4.4 22.9 - - + +
95A ASN* 3.1 27.4 + - - +
97A GLY* 1.3 72.7 - - - +
99A LEU* 1.3 60.6 + - - +
101A GLU* 3.4 22.0 + - - +
102A MSE 3.2 39.9 + - + +
260A MSE 2.9 27.7 + - - -
261A GLY 3.9 7.1 - - - +
262A SER* 3.0 33.9 + - - -
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Residues in contact with LEU 99 (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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75A LEU* 3.8 25.5 - - + +
87A LEU* 5.5 2.7 - - + -
89A SER* 3.6 36.6 - - - +
94A LEU* 3.6 32.1 - - + +
95A ASN 2.9 21.1 + - - +
96A ILE* 3.6 4.3 - - - +
98A LYS* 1.3 73.4 - - - +
100A GLU* 1.3 58.9 + - - +
101A GLU 3.1 1.6 - - - -
102A MSE 3.0 21.3 + - - +
103A VAL* 3.0 21.7 + - + +
109A ILE* 3.9 28.9 - - + -
111A TRP* 4.2 13.2 - - + -
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Residues in contact with GLU 100 (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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96A ILE* 2.7 35.3 + - + +
97A GLY* 3.9 10.7 - - - +
99A LEU* 1.3 72.3 - - - +
101A GLU* 1.3 57.0 + - - +
102A MSE 3.3 0.2 - - - -
104A GLY* 3.0 28.1 + - - -
105A SER* 3.7 25.4 + - - +
109A ILE* 3.6 23.1 - - + -
130A ASN* 3.3 26.5 + - - +
131A LYS* 4.8 2.4 + - - +
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Residues in contact with GLU 101 (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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76A ASN* 5.9 0.2 + - - -
79A LYS* 5.7 2.1 - - - -
97A GLY 3.1 15.0 + - - +
98A LYS* 3.4 30.6 - - - +
99A LEU 3.1 0.4 - - - -
100A GLU* 1.3 76.7 - - - +
102A MSE 1.3 61.6 + - + +
103A VAL 3.6 0.2 - - - -
104A GLY 4.9 0.3 + - - -
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Residues in contact with MSE 102 (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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68A PRO 4.8 3.4 - - - +
71A ALA 4.2 0.9 - - - +
72A GLY* 3.8 35.4 - - - +
75A LEU* 3.8 33.7 - - + -
76A ASN* 4.1 27.3 + - - +
79A LYS* 4.2 6.6 - - - +
94A LEU* 3.8 37.7 - - + -
98A LYS* 3.2 25.3 + - + +
99A LEU* 3.0 13.7 + - - +
101A GLU* 1.3 81.4 - - + +
103A VAL* 1.3 62.0 + - - +
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Residues in contact with VAL 103 (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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75A LEU* 3.3 49.6 - - + +
79A LYS* 3.3 29.0 + - + +
82A LEU* 3.7 17.9 - - + -
87A LEU* 4.0 13.0 - - + -
99A LEU* 3.2 14.1 - - - +
102A MSE 1.3 74.3 - - - +
104A GLY* 1.3 61.5 + - - +
106A GLU* 3.7 2.1 - - - +
107A ASN* 3.0 27.7 + - + +
109A ILE* 3.6 22.7 - - + -
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Residues in contact with GLY 104 (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 LYS* 4.4 6.0 - - - +
100A GLU 3.0 16.9 + - - -
101A GLU 4.7 0.8 - - - -
103A VAL* 1.3 81.6 - - - +
105A SER* 1.3 65.3 + - - -
106A GLU* 3.2 15.2 + - - -
107A ASN* 3.5 9.0 + - - +
109A ILE* 3.6 16.5 - - - +
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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