Contacts of the helix formed by residues 100 - 108 (chain B) in PDB entry 5UFL
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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93B LEU* 5.3 0.7 - - - +
94B GLN* 5.2 12.1 + - - +
99B LEU* 1.3 77.5 - - - +
101B SER* 1.3 56.6 + - - +
103B LEU* 4.2 5.6 - - - +
104B ALA* 3.0 30.7 + - - +
124B LEU* 4.6 10.0 - - + +
127B LEU* 3.3 37.1 + - - +
128B THR* 3.6 31.3 - - + +
131B VAL* 4.8 8.1 - - - +
133B ILE* 5.2 7.3 - - + +
134B PHE* 4.3 17.3 - - + -
140B ILE* 4.5 6.9 - - + +
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Residues in contact with SER 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 LEU 3.2 3.3 - - - +
100B ASN* 1.3 79.7 - - - +
102B VAL* 1.3 65.5 + - - +
104B ALA* 3.6 12.5 - - - +
105B GLY* 3.6 5.0 + - - -
134B PHE* 4.1 15.3 - - - -
138B ALA* 3.2 42.7 + - - +
139B ASN* 4.1 6.8 - - - +
140B ILE* 5.0 0.4 - - - -
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Residues in contact with VAL 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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60B VAL* 3.8 18.6 - - + -
63B LEU* 3.9 11.3 - - + +
64B GLU* 3.2 41.5 - - + +
96B THR 5.1 5.8 - - - +
99B LEU* 3.3 32.1 - - + +
101B SER* 1.3 79.3 - - - +
103B LEU* 1.3 67.8 + - - +
104B ALA 3.3 0.4 - - - -
105B GLY* 3.2 12.3 + - - -
106B VAL* 3.5 13.9 + - - +
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Residues in contact with LEU 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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63B LEU* 4.5 17.0 - - + -
77B ILE* 4.5 19.3 - - + -
80B LEU* 4.9 5.2 - - + -
99B LEU* 2.8 48.7 + - + +
100B ASN* 4.2 3.4 - - - +
102B VAL* 1.3 71.2 - - - +
104B ALA* 1.3 63.4 + - - +
106B VAL* 3.3 22.1 + - + +
107B VAL* 3.9 3.1 + - - +
120B CYS* 3.8 30.0 - - - +
123B LEU* 4.5 11.4 - - + -
124B LEU* 3.8 26.0 - - + +
127B LEU* 3.9 19.1 - - + -
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Residues in contact with ALA 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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100B ASN 3.0 20.5 + - - +
101B SER 3.6 6.5 - - - +
102B VAL 3.3 0.2 - - - -
103B LEU* 1.3 77.3 - - - +
105B GLY* 1.3 57.6 + - - +
107B VAL* 3.2 26.9 - - - +
108B CYS* 3.3 11.3 - - - -
124B LEU* 4.4 7.1 - - - +
139B ASN* 3.5 24.5 - - - +
140B ILE* 4.3 11.2 - - + -
143B LEU* 4.4 14.7 - - + +
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Residues in contact with GLY 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 SER 3.6 3.7 + - - -
102B VAL* 3.2 10.9 + - - -
104B ALA* 1.3 77.8 - - - +
106B VAL* 1.3 62.4 + - - +
107B VAL 3.5 0.2 - - - -
108B CYS* 3.6 17.1 + - - +
139B ASN* 3.4 18.3 - - - +
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Residues in contact with VAL 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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63B LEU* 3.9 33.0 - - + +
73B ILE* 5.3 12.3 - - + -
102B VAL 3.6 14.1 - - - +
103B LEU* 3.5 17.3 - - + +
104B ALA 3.3 1.0 - - - -
105B GLY* 1.3 76.4 - - - +
107B VAL* 1.3 66.3 + - + +
108B CYS 3.3 4.7 + - - -
116B VAL* 5.1 18.6 - - + +
117B PHE* 4.9 2.6 - - - -
120B CYS* 4.0 17.3 - - + -
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Residues in contact with VAL 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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103B LEU 3.9 2.2 + - - +
104B ALA* 3.2 19.9 + - - +
106B VAL* 1.3 76.2 - - + +
108B CYS* 1.3 65.9 + - - +
117B PHE* 3.4 37.6 - - + -
120B CYS* 3.6 31.6 - - + -
121B ILE* 4.2 18.4 - - + -
124B LEU* 5.4 1.6 - - + -
143B LEU* 3.8 26.2 - - + -
146B PHE* 4.2 26.3 - - + -
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Residues in contact with CYS 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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104B ALA 3.3 19.1 - - - -
105B GLY* 3.8 15.3 - - - +
106B VAL 3.2 5.6 - - - -
107B VAL* 1.3 85.4 - - - +
139B ASN* 3.8 9.4 - - - +
142B GLU* 3.6 45.3 - - - +
143B LEU* 4.7 1.6 - - - -
146B PHE* 5.8 5.4 - - - -
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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