Contacts of the helix formed by residues 105 - 119 (chain A) in PDB entry 2YRY
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 PRO 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A HIS* 3.3 44.8 - - + +
104A SER* 1.3 87.8 - - - +
106A GLU* 1.3 81.6 + - - +
107A GLU 3.4 0.2 - - - -
108A GLN* 4.0 8.1 - - - +
109A GLU* 3.4 26.0 + - - +
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Residues in contact with GLU 106 (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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104A SER* 3.1 14.8 - - - -
105A PRO* 1.3 97.6 - - - +
107A GLU* 1.3 76.4 + - - +
109A GLU* 3.3 18.5 - - - +
110A ALA* 3.2 24.9 + - - +
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Residues in contact with GLU 107 (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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24A LYS* 6.0 0.2 - - - +
28A LEU* 5.8 1.1 - - + -
102A ALA* 4.4 7.4 - - + -
103A GLU* 5.5 2.0 - - + +
104A SER* 2.5 30.2 + - - +
106A GLU* 1.3 87.9 - - - +
108A GLN* 1.3 59.8 + - - +
110A ALA* 3.3 5.5 + - - +
111A TRP* 2.8 49.8 + - + +
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Residues in contact with GLN 108 (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 ALA* 3.7 20.2 - - - +
76A VAL* 5.2 0.4 - - - +
86A HIS* 3.5 32.1 + - + +
87A THR 2.6 32.3 + - - +
88A PHE* 3.6 23.1 - - + -
102A ALA* 3.7 11.3 - - + +
104A SER 3.5 5.7 + - - +
105A PRO* 4.0 11.4 - - - +
106A GLU 3.4 0.2 - - - -
107A GLU* 1.3 77.8 - - - +
109A GLU* 1.3 67.5 + - - +
111A TRP* 3.1 4.9 + - - +
112A ILE* 3.0 33.7 + - + +
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Residues in contact with GLU 109 (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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105A PRO 3.4 11.4 + - - +
106A GLU* 3.3 28.6 - - - +
108A GLN* 1.3 81.7 - - - +
110A ALA* 1.3 79.6 + - + +
112A ILE* 3.1 13.7 + - - +
113A GLN* 3.1 31.4 + - + +
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Residues in contact with ALA 110 (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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24A LYS* 3.5 24.8 + - - +
106A GLU 3.2 16.7 + - - +
107A GLU* 3.5 6.3 - - - +
108A GLN 3.2 0.2 - - - -
109A GLU* 1.3 85.4 - - + +
111A TRP* 1.3 63.4 + - - +
113A GLN* 3.1 30.5 + - - +
114A ALA* 3.5 4.0 + - - +
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Residues in contact with TRP 111 (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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24A LYS* 3.3 58.7 - - + +
25A ALA* 3.7 3.6 - - - -
26A GLY* 3.3 41.3 - - - -
27A TRP 5.3 0.4 + - - -
28A LEU* 3.5 34.4 - - + +
44A PHE* 4.1 13.2 - - + -
45A VAL 5.5 0.2 - - - -
46A LEU* 4.6 10.8 - - + -
51A LEU* 5.9 0.9 - - + -
88A PHE* 4.1 16.4 - + + -
107A GLU* 2.8 40.0 + - + +
108A GLN 3.1 7.6 + - - +
110A ALA* 1.3 73.3 - - - +
112A ILE* 1.3 52.6 + - - +
114A ALA* 3.1 4.3 + - + +
115A MET* 2.7 69.0 + - + +
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Residues in contact with ILE 112 (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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73A VAL* 3.9 30.1 - - + +
74A ALA* 5.4 1.1 - - - -
75A ALA* 4.1 28.0 - - + +
88A PHE* 4.2 11.0 - - + -
108A GLN* 3.0 34.7 + - + +
109A GLU* 3.1 11.6 + - - +
111A TRP* 1.3 75.6 - - - +
113A GLN* 1.3 60.1 + - + +
115A MET* 4.5 0.2 - - - -
116A GLY* 2.6 40.4 + - - +
117A GLU* 3.6 0.5 + - - +
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Residues in contact with GLN 113 (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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109A GLU* 3.1 24.8 + - + +
110A ALA* 3.1 18.0 - - - +
111A TRP 3.1 0.4 - - - -
112A ILE* 1.3 78.3 - - + +
114A ALA* 1.3 56.9 + - - +
117A GLU* 3.1 32.6 - - - +
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Residues in contact with ALA 114 (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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23A THR* 4.6 7.6 - - + -
24A LYS* 4.1 24.7 - - + -
46A LEU* 4.0 19.1 - - + -
110A ALA 3.5 1.3 + - - +
111A TRP 3.1 6.3 + - - +
113A GLN* 1.3 77.6 - - - +
115A MET* 1.3 56.8 + - + +
117A GLU* 4.0 1.0 - - - +
118A ALA* 2.8 39.6 + - - +
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Residues in contact with MET 115 (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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28A LEU* 4.1 9.0 - - + -
44A PHE* 4.7 1.3 - - + -
46A LEU* 4.5 8.7 - - + -
51A LEU* 3.3 33.4 - - + -
68A LEU* 3.7 23.8 - - + +
73A VAL* 4.0 16.6 - - + +
88A PHE* 3.8 27.8 - - + -
100A PHE* 4.9 7.6 - - + -
111A TRP* 2.7 56.2 + - + +
112A ILE* 4.5 1.8 - - - -
114A ALA* 1.3 71.6 - - - +
116A GLY* 1.3 67.1 + - - +
118A ALA* 3.6 4.9 - - - +
119A ALA* 2.8 26.5 + - - +
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Residues in contact with GLY 116 (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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72A ARG* 6.0 0.2 - - - -
73A VAL* 3.8 25.5 + - - +
112A ILE* 2.6 27.7 + - - -
115A MET* 1.3 75.1 - - - +
117A GLU* 1.3 61.7 + - - +
119A ALA* 3.3 12.6 - - - +
120A ARG* 3.4 16.2 + - - +
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Residues in contact with GLU 117 (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 ARG* 5.7 0.5 + - - -
112A ILE 3.6 0.6 + - - -
113A GLN* 3.1 24.7 + - - +
114A ALA* 4.0 1.6 - - - +
115A MET 3.2 0.2 - - - -
116A GLY* 1.3 70.5 - - - +
118A ALA* 1.3 55.1 - - - +
119A ALA 2.8 14.6 + - - -
120A ARG* 2.8 52.4 + - - +
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Residues in contact with ALA 118 (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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23A THR* 5.8 2.7 - - + -
46A LEU* 4.4 15.5 - - + -
49A ARG* 3.0 56.0 - - + +
68A LEU* 4.9 2.7 - - + -
69A LEU* 3.8 2.9 - - - -
114A ALA 2.8 25.4 + - - +
115A MET* 3.8 4.5 - - - +
117A GLU* 1.3 73.3 - - - +
119A ALA* 1.3 61.4 + - - +
120A ARG 3.8 2.1 - - - +
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Residues in contact with ALA 119 (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 LEU* 2.9 30.0 - - + +
69A LEU* 2.7 24.8 - - - +
71A PHE 3.1 22.0 - - - +
72A ARG* 5.0 0.2 - - - -
73A VAL* 4.6 6.5 - - + +
115A MET 2.8 17.9 + - - +
116A GLY* 3.3 9.6 - - - +
117A GLU 2.8 1.4 + - - -
118A ALA* 1.3 75.1 - - - +
120A ARG* 1.3 69.7 + - - +
121A VAL* 3.4 0.9 + - - +
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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