Contacts of the helix formed by residues 103 - 115 (chain B) in PDB entry 2UZ3
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 ASP 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B ASP* 1.3 78.0 - - - +
104B ARG* 1.3 62.7 + - + +
105B ILE 3.0 2.3 + - - -
106B CYS* 3.1 23.1 + - - +
107B GLU* 4.3 1.7 + - - +
134B GLY 5.2 1.0 - - - -
135B PRO* 3.8 23.1 - - - +
138B LYS* 4.2 23.5 + - - +
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Residues in contact with ARG 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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73B SER* 3.4 31.8 + - - -
74B ALA* 3.7 7.9 - - + -
75B PRO* 3.4 20.3 - - - +
102B ASP* 2.6 44.0 + - - +
103B ASP* 1.3 78.3 - - + +
105B ILE* 1.3 62.2 + - - +
106B CYS 3.2 0.6 + - - -
107B GLU* 3.4 3.8 + - - +
108B VAL* 3.2 20.4 + - - +
203D LEU* 3.9 17.9 - - + +
204D ASN* 3.2 33.1 - - - +
205D SER 5.9 0.2 - - - +
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Residues in contact with ILE 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ALA* 3.5 19.9 - - + +
77B ILE* 4.1 13.9 - - + -
95B ILE* 4.1 24.7 - - + -
98B VAL* 4.2 19.7 - - + +
101B PHE* 3.9 23.6 - - + -
102B ASP 3.1 17.5 + - - +
103B ASP 3.0 0.8 + - - -
104B ARG* 1.3 78.6 - - - +
106B CYS* 1.3 60.0 + - - +
108B VAL* 3.4 6.0 + - + +
109B ALA* 2.9 28.8 + - + +
121B ILE* 6.0 0.7 - - + -
135B PRO* 3.8 22.0 - - + -
139B LEU* 4.2 18.2 - - + -
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Residues in contact with CYS 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ILE* 5.3 0.2 - - - +
103B ASP* 3.1 16.7 + - - +
105B ILE* 1.3 80.8 - - - +
107B GLU* 1.3 60.5 + - - +
109B ALA* 3.3 2.5 + - - +
110B ASN* 2.9 34.7 + - - +
135B PRO* 4.2 9.6 - - - -
138B LYS* 3.6 31.4 - - - -
139B LEU* 3.7 27.6 - - - -
142B TYR* 3.6 21.2 - - + +
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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
----------------------------------------------------------
103B ASP 4.3 0.6 + - - +
104B ARG* 3.4 10.0 + - - +
105B ILE 3.4 0.2 - - - -
106B CYS* 1.3 78.4 - - - +
108B VAL* 1.3 56.7 + - - +
110B ASN* 3.7 7.8 - - - +
111B ILE* 2.8 43.6 + - + +
200D ARG* 4.6 9.0 - - - +
201D PRO 4.3 3.4 - - - +
202D TYR* 3.6 13.8 - - - +
203D LEU* 2.9 31.9 + - - +
204D ASN* 3.3 19.5 + - - +
207D SER* 2.7 27.9 + - - +
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Residues in contact with VAL 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ALA* 3.7 25.8 - - + +
75B PRO 4.2 0.4 - - - -
77B ILE* 4.2 10.1 - - + -
78B LEU* 4.2 31.2 - - + +
95B ILE* 5.3 1.6 - - + -
104B ARG 3.2 7.9 + - - +
105B ILE* 3.6 18.4 - - + +
106B CYS 3.3 0.2 - - - -
107B GLU* 1.3 77.5 - - - +
109B ALA* 1.3 58.4 + - - +
111B ILE* 3.4 5.5 + - - +
112B LEU* 3.0 39.8 + - + +
204D ASN* 3.4 28.0 - - - +
207D SER* 5.5 0.2 - - - +
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ILE* 3.6 24.7 - - + +
95B ILE* 5.3 4.9 - - + -
105B ILE* 2.9 18.9 + - + +
106B CYS* 3.8 4.9 - - - +
108B VAL* 1.3 74.2 - - - +
110B ASN* 1.3 67.2 + - - +
112B LEU* 3.4 9.9 + - - +
113B ALA* 3.0 18.2 + - - +
119B VAL* 3.7 9.2 - - + +
121B ILE* 3.9 22.9 - - + -
139B LEU* 4.9 3.8 - - + -
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Residues in contact with ASN 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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14B ILE* 3.6 0.9 - - - +
106B CYS 2.9 23.9 + - - +
107B GLU* 3.7 6.9 - - - +
109B ALA* 1.3 74.6 - - - +
111B ILE* 1.3 56.7 + - - +
113B ALA* 3.1 3.8 + - - +
114B GLU* 2.8 47.3 + - - +
142B TYR* 3.3 47.6 - - - +
192D ARG* 2.3 36.8 + - - +
200D ARG* 4.7 5.4 - - - +
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Residues in contact with ILE 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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78B LEU* 4.5 8.5 - - + -
107B GLU* 2.8 29.5 + - + +
108B VAL* 3.8 3.8 - - - +
110B ASN* 1.3 75.8 - - - +
112B LEU* 1.3 63.3 + - - +
114B GLU* 3.2 11.0 + - - +
115B ASN* 3.1 36.9 + - - +
200D ARG* 4.0 15.3 - - - +
202D TYR* 4.4 6.7 - - + -
207D SER* 3.0 43.1 - - - +
210D PHE* 3.6 31.9 - - + -
211D ILE* 4.3 11.4 - - + -
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Residues in contact with LEU 112 (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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77B ILE* 4.3 10.1 - - + -
78B LEU* 3.7 21.5 - - + -
81B ILE* 3.8 8.7 - - + -
93B ILE* 3.7 44.0 - - + -
95B ILE* 5.1 2.7 - - + -
108B VAL* 3.0 33.8 + - + +
109B ALA* 3.7 9.0 - - - +
111B ILE* 1.3 76.9 - - - +
113B ALA* 1.3 58.5 + - - +
115B ASN* 3.3 6.4 + - - -
117B PHE* 3.0 48.1 + - + +
119B VAL* 4.3 10.1 - - + -
210D PHE* 3.9 9.0 - - + -
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Residues in contact with ALA 113 (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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11B ILE 3.7 3.6 - - - +
12B GLY* 3.3 22.5 - - - +
13B TRP* 3.8 21.1 - - - +
14B ILE* 3.9 19.1 - - + -
109B ALA 3.0 14.0 + - - +
110B ASN 3.6 7.0 - - - +
112B LEU* 1.3 72.8 - - - +
114B GLU* 1.3 65.3 + - - +
115B ASN 3.1 0.9 + - - -
116B GLY 3.3 2.9 + - - -
117B PHE 3.4 10.5 - - - +
119B VAL* 4.2 1.5 - - + +
192D ARG* 4.1 14.8 - - - +
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Residues in contact with GLU 114 (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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11B ILE 5.0 2.5 - - - +
110B ASN* 2.8 31.7 + - - +
111B ILE* 3.2 15.9 + - - +
113B ALA* 1.3 75.8 - - - +
115B ASN* 1.3 63.8 + - - +
116B GLY 3.4 2.9 + - - -
192D ARG* 4.7 21.3 + - + +
193D HIS* 5.7 2.6 + - - -
200D ARG* 3.0 43.6 + - - -
211D ILE* 5.3 3.5 - - - +
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Residues in contact with ASN 115 (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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111B ILE* 3.1 38.4 + - - +
112B LEU 3.3 3.6 + - - +
113B ALA 3.1 0.4 - - - -
114B GLU* 1.3 84.1 + - - +
116B GLY* 1.3 57.0 + - - +
117B PHE* 3.4 14.0 + - + -
210D PHE* 4.1 12.8 - - + -
211D ILE* 4.4 21.0 - - - +
214D PHE* 3.9 39.3 - - + +
215D LYS 5.2 0.3 + - - -
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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