Contacts of the helix formed by residues 99 - 109 (chain B) in PDB entry 6UZA
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 GLU 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B ARG* 5.3 3.5 + - - -
95B LEU* 3.8 22.1 - - + +
96B SER* 3.5 28.4 + - - -
97B ILE 3.4 0.2 - - - -
98B GLU* 1.3 82.3 - - - +
100B GLU* 1.3 60.7 + - - +
101B ARG 3.2 1.3 - - - -
102B PHE* 3.3 6.1 + - - +
103B LEU* 2.9 32.7 + - - +
123B SER 5.1 3.5 - - - +
124B LEU* 4.3 11.2 - - + -
125B ASN* 4.0 19.4 + - - +
128B CYS* 3.7 27.9 - - - +
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Residues in contact with GLU 100 (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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95B LEU* 4.5 18.9 - - + +
96B SER 3.2 17.2 + - - +
97B ILE* 4.9 4.5 - - + +
99B GLU* 1.3 75.2 - - - +
101B ARG* 1.3 57.7 + - - +
103B LEU* 3.8 5.1 - - - +
104B ASP* 2.9 39.5 + - - +
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Residues in contact with ARG 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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97B ILE* 3.4 23.8 + - + +
98B GLU* 4.7 5.9 - - - +
99B GLU 3.2 0.4 - - - -
100B GLU* 1.3 79.1 - - + +
102B PHE* 1.3 56.6 + - - +
104B ASP* 3.4 5.7 + - - +
105B ALA* 2.9 30.5 + - - +
113B VAL* 3.9 18.1 - - + +
116B LYS* 3.1 27.5 - - - +
117B MET* 3.4 34.6 - - + +
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Residues in contact with PHE 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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98B GLU 4.2 4.5 - - - +
99B GLU* 3.3 8.9 + - - +
101B ARG* 1.3 78.9 - - - +
103B LEU* 1.3 60.5 + - + +
105B ALA* 3.8 1.9 - - - +
106B ALA* 2.9 28.7 + - + +
114B VAL* 4.1 28.5 - - + -
117B MET* 3.7 35.4 - - + +
118B LEU* 3.8 30.1 - - + -
124B LEU* 4.3 14.8 - - + -
125B ASN 4.8 0.2 - - - -
126B VAL* 4.3 21.1 - - + -
128B CYS* 4.4 16.6 - - - -
136B ALA* 3.7 24.5 - - + -
152B LEU* 3.9 14.8 - - + -
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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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95B LEU* 3.9 24.2 - - + -
99B GLU 2.9 16.8 + - - +
100B GLU* 4.0 4.0 - - - +
102B PHE* 1.3 75.7 - - + +
104B ASP* 1.3 62.7 + - - +
106B ALA* 3.8 2.6 - - - +
107B GLU* 2.9 32.8 + - - +
128B CYS* 3.8 28.9 - - - +
129B VAL 3.8 28.5 - - - +
130B ASP* 3.9 11.2 - - + +
134B GLN 4.4 0.9 - - - +
135B ASN 4.3 1.3 - - - -
136B ALA* 4.2 22.4 - - + +
139B LEU* 4.0 18.8 - - + +
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Residues in contact with ASP 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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175A ARG* 5.6 3.9 + - - +
100B GLU* 2.9 25.6 + - - +
101B ARG* 3.9 5.6 - - - +
103B LEU* 1.3 79.4 - - - +
105B ALA* 1.3 57.8 + - - +
107B GLU* 4.6 3.4 - - - +
108B TYR* 2.9 53.8 + - + +
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Residues in contact with ALA 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 ARG 2.9 18.4 + - - +
102B PHE* 3.8 4.0 - - + +
104B ASP* 1.3 76.7 - - - +
106B ALA* 1.3 61.9 + - - +
109B GLY 3.3 3.1 + - - -
110B ASN* 2.9 42.2 + - + +
113B VAL* 3.8 22.2 - - + -
114B VAL* 3.8 20.2 - - + -
148B ILE* 3.6 5.4 - - - +
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Residues in contact with ALA 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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102B PHE* 2.9 19.2 + - + +
103B LEU* 3.9 4.3 - - - +
105B ALA* 1.3 77.8 - - - +
107B GLU* 1.3 63.2 + - - +
114B VAL* 4.1 6.9 - - + +
136B ALA* 3.7 37.7 - - + +
139B LEU* 4.8 3.4 - - + -
140B ALA* 3.9 11.1 - - - +
145B HIS* 3.6 15.4 - - - -
148B ILE* 3.9 19.0 - - + +
152B LEU* 5.1 0.2 - - + -
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Residues in contact with GLU 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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233A GLU* 5.5 4.6 - - - +
103B LEU 2.9 17.7 + - - +
104B ASP* 4.1 6.2 - - - +
106B ALA* 1.3 78.1 - - - +
108B TYR* 1.3 90.8 + - + +
130B ASP* 5.6 1.0 - - - +
139B LEU* 4.2 29.5 - - + +
143B ASN* 3.4 29.6 + - - +
145B HIS* 3.0 18.5 + - - -
889B GLN* 3.4 4.4 - - - +
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Residues in contact with TYR 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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174A VAL* 5.1 8.3 - - - +
175A ARG* 3.7 62.2 - - + +
233A GLU* 5.2 4.9 + - - -
104B ASP* 2.9 42.4 + - + +
107B GLU* 1.3 109.6 + - + +
109B GLY* 1.3 59.4 + - - +
110B ASN* 3.6 1.8 - - + -
145B HIS* 3.8 4.0 - - - -
889B GLN* 3.7 24.0 - - - -
892B SER* 3.0 26.7 + - - +
893B SER 4.5 0.2 + - - -
896B TYR* 3.6 10.2 - - + +
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Residues in contact with GLY 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 ALA 3.3 4.4 + - - -
107B GLU 3.4 3.0 - - - -
108B TYR* 1.3 80.9 - - - +
110B ASN* 1.3 58.8 + - - +
111B ILE* 2.9 20.2 + - - +
145B HIS* 3.5 22.8 + - - -
148B ILE* 3.7 13.2 - - - -
893B SER* 3.7 17.8 - - - -
896B TYR* 4.0 5.9 - - - +
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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