Contacts of the helix formed by residues 100 - 111 (chain B) in PDB entry 1W5A
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 100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B ALA* 3.0 15.2 + - - +
98B GLY 3.2 2.7 - - - +
99B GLY* 1.3 76.5 - - - +
101B PRO* 1.3 66.7 - - - +
102B LYS* 2.9 30.0 + - - +
103B ILE* 3.0 33.6 + - + +
104B GLY 3.4 7.6 + - - -
134B GLY* 3.4 6.7 - - - -
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Residues in contact with PRO 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLY 3.0 11.2 - - - +
100B ASN* 1.3 85.5 - - - +
102B LYS* 1.3 63.5 + - + +
104B GLY 3.3 0.9 + - - -
105B GLU* 3.0 20.9 + - - +
133B GLY 3.7 15.9 - - - +
134B GLY 3.4 11.0 - - - +
137B THR* 4.3 8.3 - - + -
138B GLY* 3.3 10.9 - - - +
172B ASN* 3.8 33.7 - - + +
179B ARG* 3.9 23.1 - - - +
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Residues in contact with LYS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ASN* 2.9 15.0 + - - +
101B PRO* 1.3 77.0 - - + +
103B ILE* 1.3 62.4 + - + +
105B GLU* 3.2 11.0 + - - +
106B GLU* 2.9 39.1 + - + +
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Residues in contact with ILE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B THR* 5.3 0.7 - - + -
91B LEU* 3.5 26.7 - - + +
92B THR* 3.4 26.2 - - + +
97B ALA* 3.7 21.1 - - + +
100B ASN* 3.0 36.0 + - + +
102B LYS* 1.3 77.1 - - + +
104B GLY* 1.3 58.8 + - - +
105B GLU 3.3 0.2 + - - -
106B GLU* 3.3 2.5 + - + -
107B ALA* 2.8 34.4 + - + +
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Residues in contact with GLY 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B THR* 5.1 0.7 - - - -
87B ILE* 4.0 0.3 - - - +
97B ALA* 4.1 3.5 - - - +
100B ASN 3.4 4.8 + - - -
101B PRO 3.3 3.2 + - - -
102B LYS 3.3 0.4 - - - -
103B ILE* 1.3 80.2 - - - +
105B GLU* 1.3 56.8 + - - +
107B ALA* 3.6 6.3 + - - +
108B ALA* 3.0 29.3 + - - +
134B GLY 3.3 18.6 + - - -
135B THR* 4.0 15.7 - - - -
138B GLY 3.8 6.3 - - - -
139B SER* 3.6 5.9 + - - -
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Residues in contact with GLU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B PRO 3.0 13.2 + - - +
102B LYS* 3.5 14.5 - - - +
103B ILE 3.2 0.2 - - - -
104B GLY* 1.3 73.6 - - - +
106B GLU* 1.3 62.0 + - - +
108B ALA* 3.2 3.5 + - - +
109B LYS* 2.7 69.7 + - - +
138B GLY* 3.5 14.5 - - - +
142B VAL* 4.0 13.0 - - + +
179B ARG* 4.0 28.4 + - - -
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Residues in contact with GLU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LEU* 3.3 24.7 - - + -
102B LYS* 2.9 24.4 + - + +
103B ILE* 4.8 2.2 - - + -
105B GLU* 1.3 77.6 - - + +
107B ALA* 1.3 55.3 + - - +
109B LYS* 3.1 25.6 + - - +
110B GLU* 2.7 36.3 + - - +
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B THR* 3.7 13.9 - - + -
87B ILE* 3.5 27.1 - - + +
88B GLY* 3.6 27.3 + - - +
91B LEU* 3.5 6.4 - - + +
103B ILE* 2.8 19.7 + - + +
104B GLY 3.7 1.6 - - - +
106B GLU* 1.3 76.7 - - - +
108B ALA* 1.3 62.9 + - - +
110B GLU* 3.2 7.0 + - - +
111B SER* 3.2 15.6 + - - -
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ILE* 3.3 8.9 - - + +
104B GLY 3.0 18.7 + - - +
105B GLU 3.2 4.2 + - - +
107B ALA* 1.3 76.0 - - - +
109B LYS* 1.3 63.6 + - - +
111B SER 3.0 4.9 + - - -
112B ALA* 2.9 21.1 + - - +
115B ILE* 3.6 14.8 - - + +
139B SER* 3.6 23.1 - - - +
142B VAL* 3.6 23.9 - - + +
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Residues in contact with LYS 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B GLU* 2.7 52.6 + - - +
106B GLU* 3.5 24.6 + - - +
108B ALA* 1.3 75.2 - - - +
110B GLU* 1.3 61.7 + - - +
112B ALA* 3.1 24.2 + - - +
142B VAL* 4.3 17.0 - - + -
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Residues in contact with GLU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B GLY* 3.7 19.5 + - - -
89B LYS* 3.5 21.8 + - - +
90B LYS* 3.8 37.0 + - + +
91B LEU* 3.8 18.5 + - - +
106B GLU 2.7 16.2 + - - +
107B ALA 3.4 9.0 - - - +
109B LYS* 1.3 75.6 - - - +
111B SER* 1.3 59.2 + - - +
112B ALA 3.7 0.7 + - - -
113B GLU* 5.1 1.9 + - - +
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Residues in contact with SER 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ILE* 4.6 2.0 - - - -
86B LEU 4.3 2.4 + - - -
87B ILE* 3.3 45.9 - - - +
88B GLY 3.8 2.8 + - - -
89B LYS* 5.8 1.6 - - - +
107B ALA 3.2 3.6 + - - -
108B ALA 3.0 6.6 + - - -
110B GLU* 1.3 79.9 + - - +
112B ALA* 1.3 65.2 + - - +
113B GLU* 3.2 3.6 - - - -
114B GLU* 3.0 28.1 + - - +
115B ILE* 3.0 14.1 + - - +
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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