Contacts of the helix formed by residues 101 - 110 (chain A) in PDB entry 3ZUU
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 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ASN* 2.8 28.8 - - - +
99A GLY 4.8 0.9 - - - +
100A GLY* 1.3 72.9 - - - -
102A LEU* 1.3 65.2 + - - +
103A PHE* 4.0 21.6 - - - +
104A GLU* 3.0 37.2 + - + +
105A ARG* 3.4 6.6 + - - +
145A ASN* 3.0 34.7 + - - +
146A THR 3.7 4.9 - - - +
147A LEU* 3.9 8.1 - - + -
148A LEU* 4.6 2.8 - - - +
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Residues in contact with LEU 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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100A GLY 3.7 2.8 + - - -
101A GLU* 1.3 70.7 - - - +
103A PHE* 1.3 57.3 + - - +
105A ARG* 3.3 2.3 + - - +
106A ILE* 3.0 32.4 + - + +
112A PHE* 4.1 24.5 - - + -
120A PHE* 4.3 16.2 - - + -
146A THR* 3.1 38.6 + - - +
147A LEU* 4.1 1.2 - - - +
148A LEU* 4.1 31.1 - - + +
156A LEU* 4.0 9.9 - - + -
206A THR* 4.0 24.2 - - + -
210A MET* 4.4 12.1 - - + -
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Residues in contact with PHE 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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101A GLU* 3.1 20.1 - - + +
102A LEU* 1.3 76.4 - - - +
104A GLU* 1.3 72.7 + - - +
106A ILE* 3.3 12.7 + - + +
107A CYS* 2.9 52.1 + - - -
144A GLU 6.0 1.6 - - - +
145A ASN* 5.2 3.3 + - - +
146A THR 4.7 0.6 + - - -
182A TYR* 5.8 0.7 - - - -
209A VAL* 4.2 21.1 - - + -
213A GLY 5.5 4.3 - - - -
214A ALA* 6.1 0.7 - - - -
215A TYR* 3.5 42.2 - + - +
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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 GLY* 6.0 0.7 - - - -
101A GLU* 3.0 32.6 + - + +
103A PHE* 1.3 92.1 - - - +
105A ARG* 1.3 58.4 + - - +
107A CYS* 3.4 10.6 + - - +
108A ASN* 2.9 46.9 + - - +
104B GLU* 5.5 14.2 - - + +
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Residues in contact with ARG 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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101A GLU 3.4 2.9 + - - +
102A LEU* 3.3 9.4 + - - +
104A GLU* 1.3 77.0 - - - +
106A ILE* 1.3 64.8 + - - +
108A ASN* 3.5 11.1 + - + +
109A ALA* 2.9 23.1 + - + +
112A PHE* 3.8 12.3 - - + -
116A GLU* 3.3 28.3 + - - -
120A PHE* 3.8 14.6 - - - -
148A LEU* 3.5 30.2 - - + +
152A PRO 5.6 0.2 + - - -
154A PRO* 3.7 31.0 - - - +
150B GLY 5.5 5.9 + - - -
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Residues in contact with ILE 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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102A LEU* 3.0 22.8 + - + +
103A PHE* 3.5 17.7 - - + +
105A ARG* 1.3 74.8 - - - +
107A CYS* 1.3 64.9 + - - +
109A ALA* 2.9 12.8 + - - +
110A GLY 2.9 14.1 + - - +
111A ARG* 4.6 2.2 - - - -
112A PHE* 3.7 23.5 - - + -
209A VAL* 3.5 34.8 - - + +
210A MET* 3.5 42.0 - - + +
213A GLY* 4.0 16.8 - - - +
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Residues in contact with CYS 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 PHE* 2.9 54.7 + - - +
104A GLU* 3.7 15.0 - - - +
106A ILE* 1.3 74.3 - - - +
108A ASN* 1.3 64.1 + - - +
110A GLY* 3.2 13.5 + - - +
213A GLY 5.6 5.8 - - - -
27B ILE* 5.2 6.1 - - - +
37B LEU* 5.1 1.6 - - - +
96B TYR* 4.1 4.5 + - - -
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Residues in contact with ASN 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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104A GLU* 2.9 32.8 + - - +
105A ARG* 3.5 10.2 - - + +
107A CYS* 1.3 79.2 - - - +
109A ALA* 1.3 57.7 + - - +
96B TYR* 2.6 36.2 + - - -
98B SER* 3.4 21.4 - - - +
99B GLY 3.8 5.9 + - - -
100B GLY* 3.5 32.9 - - - +
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Residues in contact with ALA 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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105A ARG* 2.9 17.6 + - + +
106A ILE 2.9 6.2 + - - +
108A ASN* 1.3 74.9 - - - +
110A GLY* 1.3 57.5 + - - +
111A ARG 3.1 25.6 + - - +
112A PHE* 3.6 17.3 - - + -
116A GLU* 5.7 0.7 - - - +
24B VAL* 3.7 10.9 - - - +
37B LEU* 4.2 3.2 - - - +
46B LEU* 3.9 19.3 - - + +
98B SER* 4.5 4.5 + - - +
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Residues in contact with GLY 110 (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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106A ILE* 2.9 11.2 + - - +
107A CYS* 3.2 13.2 + - - -
108A ASN 3.4 0.6 + - - -
109A ALA* 1.3 73.0 - - - +
111A ARG* 1.3 62.6 + - - +
213A GLY* 3.3 19.8 - - - +
24B VAL* 4.1 0.9 - - - -
25B LYS* 3.8 32.8 + - - +
27B ILE* 5.4 1.3 - - - -
37B LEU* 4.0 10.0 - - - +
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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