Contacts of the helix formed by residues 99 - 113 (chain A) in PDB entry 2W27
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 GLY 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A LEU* 2.7 28.8 + - - -
97A ASP* 2.9 5.0 + - - -
98A HIS* 1.3 71.8 - - - +
100A GLU* 1.3 64.0 + - - +
101A SER 3.4 2.2 - - - -
102A PHE* 3.5 2.2 + - - -
103A LEU* 3.1 13.3 + - - +
138A MET* 4.0 9.2 - - - -
142A TYR* 2.6 31.8 + - - -
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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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97A ASP* 3.0 24.4 + - - +
98A HIS* 3.1 4.3 + - + +
99A GLY* 1.3 77.8 - - - +
101A SER* 1.3 64.8 + - - +
103A LEU* 3.4 5.8 + - - +
104A GLU* 3.2 39.7 + - + +
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Residues in contact with SER 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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97A ASP* 2.8 25.5 + - - -
100A GLU* 1.3 71.6 - - - +
102A PHE* 1.3 72.8 + - - +
104A GLU* 3.1 13.3 + - - +
105A LEU* 3.1 18.0 + - - +
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Residues in contact with PHE 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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69A ILE* 3.9 19.1 - - + -
87A MET* 3.9 24.0 - - + -
89A GLN* 3.4 35.4 - - + -
94A LEU* 3.6 18.8 - - + -
97A ASP* 5.0 0.2 + - - -
99A GLY* 3.5 2.5 + - - +
100A GLU 3.4 0.4 - - - -
101A SER* 1.3 82.8 + - - +
103A LEU* 1.3 58.6 + - - +
105A LEU* 2.9 34.5 + - + +
106A LEU* 3.0 28.6 + - + +
121A LEU* 3.6 26.0 - - + -
142A TYR* 3.5 26.2 - + - +
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Residues in contact with LEU 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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99A GLY 3.1 16.7 + - - +
100A GLU* 3.7 5.4 - - - +
102A PHE* 1.3 77.3 - - - +
104A GLU* 1.3 53.1 + - + +
106A LEU* 3.1 12.0 + - + +
107A LYS* 2.7 56.0 + - + +
116A LEU* 5.2 2.5 - - + -
141A TYR* 3.8 21.3 - - + -
142A TYR* 3.5 16.5 + - + +
145A TYR* 3.6 35.7 - - + -
147A ILE* 3.6 31.4 - - + -
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Residues in contact with GLU 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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100A GLU* 3.2 28.5 + - + +
101A SER* 3.1 13.7 + - - +
103A LEU* 1.3 75.7 - - + +
105A LEU* 1.3 57.0 - - - +
107A LYS* 3.3 14.1 + - + +
108A GLU* 2.9 29.3 + - - +
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Residues in contact with LEU 105 (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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66A ASN* 3.6 22.4 - - - +
69A ILE* 3.9 34.8 - - + -
70A ARG* 3.1 39.0 - - + +
73A LEU* 5.6 0.4 - - + -
101A SER 3.1 9.5 + - - +
102A PHE* 2.9 24.5 + - + +
104A GLU* 1.3 74.5 - - - +
106A LEU* 1.3 67.0 + - + +
108A GLU* 3.4 8.1 - - - +
109A TYR* 3.3 31.6 - - + -
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Residues in contact with LEU 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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69A ILE* 5.9 0.2 - - + -
73A LEU* 4.5 7.9 - - + -
87A MET* 3.9 12.8 - - + -
102A PHE* 3.0 42.7 + - + +
103A LEU* 3.1 11.9 + - + +
105A LEU* 1.3 79.5 - - + +
107A LYS* 1.3 62.2 + - - +
109A TYR* 2.9 17.1 + - - +
110A GLU 3.2 8.8 + - - -
116A LEU* 4.0 17.3 - - + +
119A PHE* 3.8 42.2 - - + -
121A LEU* 4.6 6.7 - - + -
142A TYR* 4.9 0.9 - - + -
147A ILE* 3.8 28.0 - - + -
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Residues in contact with LYS 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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103A LEU* 2.7 39.8 + - + +
104A GLU* 3.3 16.1 + - + +
106A LEU* 1.3 71.3 - - - +
108A GLU* 1.3 63.6 + - - +
110A GLU* 3.2 29.1 + - - +
111A ALA* 3.4 6.2 + - - +
116A LEU* 4.5 10.3 - - + +
141A TYR* 5.4 0.2 + - - -
145A TYR* 2.9 47.0 + - - -
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Residues in contact with GLU 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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70A ARG* 2.9 43.8 + - - -
104A GLU 2.9 13.1 + - - +
105A LEU* 3.4 9.7 - - - +
106A LEU 3.1 0.2 + - - -
107A LYS* 1.3 77.2 - - - +
109A TYR* 1.3 74.4 + - + +
111A ALA* 3.3 22.9 - - - +
112A LYS* 3.3 32.8 + - - +
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Residues in contact with TYR 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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70A ARG* 3.6 25.0 + - - +
73A LEU* 3.4 50.5 - - + -
74A ASP* 2.9 27.3 + - - -
77A LEU* 4.3 19.1 - - + -
105A LEU* 3.3 30.5 - - + +
106A LEU 2.9 9.1 + - - +
108A GLU* 1.3 100.8 + - + +
110A GLU* 1.3 60.9 + - - +
112A LYS* 3.5 18.5 + - + +
113A GLY 2.8 22.0 + - - -
114A ILE* 2.8 22.3 + - + +
119A PHE* 4.8 2.0 - - + -
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Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A LEU 3.2 7.0 + - - +
107A LYS* 3.2 19.5 + - - +
109A TYR* 1.3 77.2 - - - +
111A ALA* 1.3 64.2 + - - +
113A GLY* 3.0 14.7 + - - -
114A ILE 3.7 13.2 + - - +
115A GLU* 4.4 15.2 + - + +
116A LEU* 3.7 36.9 + - + +
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A LYS 3.4 4.9 + - - +
108A GLU* 3.3 14.3 + - - +
109A TYR 3.3 0.2 - - - -
110A GLU* 1.3 81.7 + - - +
112A LYS* 1.3 62.7 + - + +
113A GLY* 3.4 1.2 + - - -
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Residues in contact with LYS 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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70A ARG* 5.2 2.0 - - - +
74A ASP* 5.8 0.4 + - - -
77A LEU* 3.1 35.7 - - + +
108A GLU* 3.3 43.5 + - + +
109A TYR* 3.3 26.0 + - + +
110A GLU 3.2 0.8 - - - -
111A ALA* 1.3 76.8 - - + +
113A GLY* 1.3 55.6 + - - +
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Residues in contact with GLY 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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77A LEU* 4.1 3.2 - - - +
81A SER* 6.1 0.3 - - - -
109A TYR 2.8 7.3 + - - -
110A GLU 3.0 9.5 + - - -
111A ALA 4.3 1.1 - - - -
112A LYS* 1.3 80.9 - - - +
114A ILE* 1.3 61.2 + - - +
115A GLU* 3.7 5.3 + - - +
118A ARG* 4.1 7.4 + - - -
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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