Contacts of the helix formed by residues 107 - 123 (chain D) in PDB entry 3ZXR
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 107 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25D PHE* 5.8 0.2 - - - +
26D CYS 4.6 3.3 + - - +
61D PHE* 4.7 1.6 - - - -
93D PHE 4.8 0.9 - - - +
94D PHE* 3.3 15.6 - - - +
95D VAL* 2.7 52.5 + - + +
104D TYR* 3.3 19.8 + - + +
105D SER 3.6 0.2 - - - -
106D ARG* 1.3 76.1 - - - +
108D PRO* 1.4 71.5 - - - +
109D ARG* 3.0 19.3 + - - +
110D ASN* 2.9 28.8 + - + +
111D ILE* 3.2 13.5 + - - +
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Residues in contact with PRO 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D CYS* 3.4 20.9 - - + +
27D ASP 3.3 15.3 - - - +
28D LEU* 4.2 8.5 - - + -
61D PHE* 4.5 2.0 - - + -
106D ARG 3.3 9.8 - - - +
107D ASP* 1.4 88.5 - - - +
109D ARG* 1.3 60.0 + - - +
111D ILE* 3.1 13.6 + - + +
112D ALA 3.2 5.7 + - - -
375D ASN* 3.3 40.2 - - - +
377D TYR* 3.2 24.6 - - + +
378D LEU* 4.0 13.9 - - + -
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Residues in contact with ARG 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D PHE* 5.3 0.2 - - - +
26D CYS* 4.5 13.5 - - + +
32D MET* 5.1 1.8 - - - -
74D ASP* 2.7 29.7 + - - +
77D THR* 3.7 3.4 - - - +
92D ASN* 4.0 14.9 - - - +
93D PHE 3.3 29.8 + - - +
94D PHE* 3.4 44.1 - - + -
107D ASP* 3.0 12.0 + - - +
108D PRO* 1.3 75.4 - - - +
110D ASN* 1.3 61.1 + - - +
112D ALA* 3.5 3.2 + - - +
113D ARG* 3.1 20.4 + - - +
236D LEU* 4.0 9.2 - - + +
240D ASP* 2.9 36.3 + - - -
377D TYR* 3.5 35.8 - - + -
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Residues in contact with ASN 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D PHE* 4.5 0.7 - - - -
103D PRO* 3.5 24.4 + - + +
104D TYR 3.0 26.3 + - - +
105D SER* 4.5 1.0 - - - +
107D ASP* 2.9 22.6 + - + +
109D ARG* 1.3 78.0 - - - +
111D ILE* 1.3 60.3 + - - +
113D ARG* 3.1 35.1 + - - +
114D LYS* 2.8 57.0 + - - +
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Residues in contact with ILE 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D SER 3.4 25.6 - - - +
106D ARG 5.4 0.7 - - - -
107D ASP 3.2 13.7 + - - +
108D PRO* 3.1 6.9 + - + +
110D ASN* 1.3 76.9 - - - +
112D ALA* 1.3 56.4 + - - +
114D LYS* 3.3 17.0 + - - +
115D ALA* 2.8 28.8 + - - +
378D LEU* 3.7 24.0 - - + -
381D SER* 3.9 10.1 - - - +
442D VAL* 3.6 23.9 - - + +
443D PHE* 3.9 30.5 - - + -
444D THR 5.6 0.2 - - - +
447D LEU* 3.5 15.9 - - + -
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Residues in contact with ALA 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D PRO 3.2 8.6 + - - +
109D ARG 3.7 8.5 - - - +
110D ASN 3.2 0.2 - - - -
111D ILE* 1.3 75.5 - - - +
113D ARG* 1.3 64.8 + - - +
115D ALA* 3.2 3.1 + - - +
116D GLU* 3.0 28.6 + - - +
235D LEU* 3.7 20.9 - - + +
236D LEU* 3.7 21.5 - - + -
377D TYR* 4.1 13.2 - - + -
381D SER* 3.4 12.9 + - - +
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Residues in contact with ARG 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D PHE* 3.3 62.8 - - + +
95D VAL 5.3 0.2 + - - -
96D HIS* 3.9 8.1 + - - -
103D PRO* 3.6 23.9 - - - +
107D ASP* 5.0 0.2 + - - -
109D ARG 3.1 11.6 + - - +
110D ASN* 3.1 30.9 + - - +
112D ALA* 1.3 75.2 - - - +
114D LYS* 1.3 63.0 + - + +
116D GLU* 3.3 9.2 + - - +
117D ASN* 3.2 36.3 + - - +
236D LEU* 4.7 12.7 - - + +
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Residues in contact with LYS 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D SER* 4.6 5.7 + - - +
110D ASN* 2.8 45.9 + - - +
111D ILE* 3.6 20.2 - - - +
113D ARG* 1.3 74.4 - - + +
115D ALA* 1.3 57.0 + - - +
117D ASN* 3.3 8.4 + - - +
118D TYR* 2.9 31.2 + - - +
440D GLY 5.6 2.0 - - - +
441D GLY 3.0 21.0 + - - +
442D VAL* 2.8 36.1 + - + +
444D THR* 4.0 14.8 - - - +
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Residues in contact with ALA 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ILE 2.8 17.6 + - - +
112D ALA 3.2 6.0 + - - +
114D LYS* 1.3 76.5 - - - +
116D GLU* 1.3 62.7 + - - +
118D TYR* 3.3 3.5 + - - +
119D LEU* 3.1 23.2 + - - +
235D LEU* 4.2 12.8 - - + -
381D SER* 3.5 23.3 - - - +
384D LEU* 3.9 11.6 - - + +
385D MET* 5.2 2.7 - - - -
442D VAL* 3.9 19.5 - - + +
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Residues in contact with GLU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D ALA 3.0 15.3 + - - +
113D ARG* 3.3 8.1 + - - +
115D ALA* 1.3 74.6 - - - +
117D ASN* 1.3 65.1 + - - +
119D LEU* 3.5 12.0 + - + +
120D ILE* 3.4 28.7 + - + +
126D ASP 5.0 0.7 - - - +
128D ALA* 6.2 2.0 - - + +
234D SER* 3.7 13.7 + - - -
235D LEU* 3.1 28.2 + - + -
236D LEU* 3.0 43.8 + - - +
237D HIS* 5.9 0.5 - - - -
384D LEU* 5.2 1.8 - - + -
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Residues in contact with ASN 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D ARG* 3.2 27.1 + - - +
114D LYS* 3.8 9.0 - - - +
116D GLU* 1.3 77.2 - - - +
118D TYR* 1.3 65.0 + - - +
120D ILE* 3.2 18.5 + - - +
121D SER* 3.0 22.5 + - - -
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Residues in contact with TYR 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D LYS 2.9 17.1 + - - +
115D ALA 3.7 3.4 - - - +
117D ASN* 1.3 72.6 - - - +
119D LEU* 1.3 68.2 + - - +
121D SER* 2.8 30.4 + - - -
122D THR* 3.1 27.7 + - + +
385D MET* 3.6 31.2 - - + -
388D LEU* 4.0 18.6 - - + -
392D LYS* 3.4 20.2 + - - +
439D GLU* 3.5 25.5 + - + +
440D GLY* 3.8 31.2 - - - +
442D VAL* 3.6 13.9 - - + -
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Residues in contact with LEU 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D ALA 3.1 13.3 + - - +
116D GLU* 3.5 13.0 - - + +
118D TYR* 1.3 76.1 - - - +
120D ILE* 1.3 62.6 + - - +
122D THR* 2.6 26.6 + - - +
123D GLY 3.7 0.2 + - - -
125D ALA* 3.3 36.7 - - + +
126D ASP 4.0 2.5 - - - +
127D THR* 3.6 16.6 - - - +
128D ALA* 3.4 41.5 - - + +
281D LEU* 4.3 5.4 - - + -
384D LEU* 4.2 8.5 - - + -
388D LEU* 3.8 34.1 - - + -
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Residues in contact with ILE 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D GLU* 3.4 17.4 + - + +
117D ASN* 3.2 20.3 + - - +
119D LEU* 1.3 77.2 - - - +
121D SER* 1.3 63.1 + - - +
123D GLY* 3.1 15.4 + - - -
125D ALA 3.7 8.3 - - - +
126D ASP* 3.7 34.1 - - + +
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Residues in contact with SER 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D ASN 3.0 13.4 + - - -
118D TYR* 2.8 32.0 + - - -
120D ILE* 1.3 78.7 - - - +
122D THR* 1.3 58.4 + - - +
123D GLY 3.3 0.6 + - - -
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Residues in contact with THR 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D TYR* 3.1 38.1 + - + +
119D LEU* 2.6 22.7 + - - +
121D SER* 1.3 77.4 - - - +
123D GLY* 1.3 57.3 + - - +
124D ILE* 3.1 34.0 + - + +
388D LEU* 4.7 3.6 - - + -
392D LYS* 3.2 32.4 + - - +
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Residues in contact with GLY 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D LEU 3.7 0.4 + - - -
120D ILE 3.1 14.5 + - - -
121D SER 3.3 0.8 - - - -
122D THR* 1.3 77.2 + - - +
124D ILE* 1.3 60.7 + - - +
125D ALA 3.3 4.3 - - - -
283D LYS* 2.7 32.9 + - - +
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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