Contacts of the helix formed by residues 93 - 111 (chain D) in PDB entry 1Z1G
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 LYS 93 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D ILE* 1.3 77.0 - - - +
94D GLN* 1.3 73.8 + - - +
95D LYS* 2.8 5.4 + - - +
96D THR* 2.9 20.5 + - - +
97D LEU 3.3 4.0 + - - -
234D SER* 4.6 13.0 + - - +
20I A 3.1 25.9 + - - +
21I A 3.4 39.1 + - - +
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Residues in contact with GLN 94 (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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92D ILE 3.6 11.3 + - - -
93D LYS* 1.3 78.2 - - - +
95D LYS* 1.3 60.4 + - - +
97D LEU* 3.3 38.8 - - - +
98D ILE* 3.4 13.6 + - - +
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Residues in contact with LYS 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D LYS* 2.8 6.9 + - - +
94D GLN* 1.3 70.5 - - - +
96D THR* 1.3 64.7 + - - +
97D LEU 3.1 1.3 - - - -
98D ILE* 3.0 7.1 + - + +
99D ASN* 2.9 35.4 + - - +
20I A 5.4 1.1 - - + -
21I A 3.9 45.6 + - + +
22I G 2.7 49.3 + - - -
23I T 5.0 6.3 + - - +
7L A 5.8 0.4 - - - +
8L C 5.7 0.2 - - - +
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Residues in contact with THR 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D ILE* 3.9 16.2 - - + -
93D LYS* 2.9 10.7 + - - +
95D LYS* 1.3 75.4 - - - +
97D LEU* 1.3 66.8 + - - +
99D ASN* 2.9 15.0 + - - +
100D TYR* 2.9 49.8 + - + +
19I A 4.6 7.9 - - - +
20I A 3.4 56.9 + - + +
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Residues in contact with LEU 97 (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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84D GLU 5.5 0.2 - - - +
87D LEU* 3.9 32.5 - - + -
88D ALA* 4.3 18.6 - - + +
92D ILE* 3.5 22.9 - - + +
93D LYS 3.3 0.8 + - - -
94D GLN* 3.3 38.6 - - - +
96D THR* 1.3 77.9 - - - +
98D ILE* 1.3 59.8 + - + +
100D TYR* 2.9 16.3 - - + +
101D MSE 2.8 45.6 + - + +
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Residues in contact with ILE 98 (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 GLN 3.4 10.4 + - - +
95D LYS* 3.0 9.6 + - + +
97D LEU* 1.3 76.7 - - + +
99D ASN* 1.3 70.6 + - - +
101D MSE 4.0 17.5 - - + -
102D SER* 2.9 23.6 + - - +
5L C 6.5 0.4 - - + -
6L A 5.2 15.0 - - + +
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Residues in contact with ASN 99 (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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95D LYS* 2.9 33.2 + - - +
96D THR* 3.0 11.4 - - - +
98D ILE* 1.3 79.3 - - - +
100D TYR* 1.3 70.4 - - + +
102D SER* 3.0 8.4 + - - -
103D LYS* 2.8 40.3 + - - +
142D LEU* 6.1 0.4 - - + -
20I A 5.0 6.6 - - - +
21I A 2.6 48.4 - - - +
22I G 4.3 1.4 + - - -
8L C 3.6 15.0 - - - +
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Residues in contact with TYR 100 (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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83D TYR* 5.0 4.3 - + - -
87D LEU* 4.8 22.7 - - + -
90D ARG* 5.9 3.6 - - - -
92D ILE* 6.4 0.4 - - + -
96D THR* 3.1 37.5 - - + -
97D LEU* 2.9 20.6 + - + +
99D ASN* 1.3 84.2 - - + +
101D MSE 1.3 56.0 + - + +
103D LYS* 2.8 38.0 + - + +
104D ILE* 2.9 14.8 + - + +
142D LEU* 6.3 2.9 - - + -
146D THR* 4.3 22.7 - - + +
149D ASP* 5.5 3.1 - - + -
18I C 3.8 15.1 + - - +
19I A 3.0 36.0 + + - -
20I A 5.2 3.4 - - - -
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Residues in contact with MSE 101 (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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84D GLU* 3.7 44.9 - - + +
87D LEU* 5.0 3.8 - - + -
97D LEU* 2.8 43.3 + - + +
98D ILE* 3.1 19.2 + - + +
100D TYR* 1.3 72.4 - - + +
102D SER* 1.3 61.7 + - - +
104D ILE* 3.0 16.3 - - + +
105D LYS* 3.0 31.2 + - + +
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Residues in contact with SER 102 (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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98D ILE* 2.9 14.5 + - - +
99D ASN* 3.1 13.7 + - - -
101D MSE 1.3 73.7 - - - +
103D LYS* 1.3 80.4 + - - +
105D LYS* 3.4 8.8 + - - +
106D ALA* 2.9 21.5 + - - +
6L A 5.6 0.7 - - - -
7L A 3.7 36.0 + - - +
8L C 4.8 8.4 - - - -
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Residues in contact with LYS 103 (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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99D ASN* 2.8 52.4 + - - +
100D TYR* 2.8 25.7 + - + +
102D SER* 1.3 80.3 + - - +
104D ILE* 1.3 69.8 + - - +
106D ALA* 2.6 22.0 + - - +
107D ILE* 2.9 13.2 + - + +
142D LEU* 3.9 33.6 - - + +
143D ILE* 4.8 14.5 - - + +
146D THR* 4.0 26.2 - - + +
8L C 4.9 4.8 - - - +
9L T 4.2 13.6 + - - +
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Residues in contact with ILE 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D LEU* 2.9 27.8 - - + -
83D TYR* 4.5 14.4 - - + -
84D GLU* 3.4 26.0 - - + +
87D LEU* 4.2 14.6 - - + -
100D TYR* 3.4 7.9 - - + +
101D MSE 3.0 47.3 - - - +
103D LYS* 1.3 72.4 - - + +
105D LYS* 1.3 59.4 + - + +
107D ILE* 2.5 50.3 + - + +
108D ARG* 3.0 9.5 + - - +
146D THR* 5.5 2.7 - - + -
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Residues in contact with LYS 105 (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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101D MSE 3.0 15.5 + - + +
102D SER* 3.4 10.1 - - - +
104D ILE* 1.3 80.0 - - + +
106D ALA* 1.3 68.1 + - - +
108D ARG* 2.8 35.7 + - - +
109D ARG* 3.1 20.0 + - + +
6L A 4.1 33.9 + - - +
7L A 4.5 21.8 + - - +
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Residues in contact with ALA 106 (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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102D SER* 2.9 12.7 + - - +
103D LYS* 2.6 21.8 + - - +
105D LYS* 1.3 72.9 - - - +
107D ILE* 1.3 58.4 - - + +
109D ARG* 3.1 10.5 + - - +
110D GLY* 3.0 16.6 + - - -
127D MSE 5.2 3.4 - - - +
131D TYR* 3.9 23.9 + - + +
143D ILE* 4.3 20.0 - - + -
7L A 5.3 2.8 + - - +
8L C 5.4 4.9 - - - +
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Residues in contact with ILE 107 (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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76D LEU* 4.5 18.6 - - + -
80D LEU* 4.2 19.5 - - + -
83D TYR* 6.5 0.7 - - + -
103D LYS* 3.3 7.9 - - + +
104D ILE* 2.5 44.6 + - + +
106D ALA* 1.3 67.8 - - - +
108D ARG* 1.3 66.8 + - - +
110D GLY 2.7 12.9 + - - +
111D LEU* 2.8 21.5 + - + +
127D MSE 4.8 10.5 - - - -
143D ILE* 4.5 16.4 - - + +
146D THR* 5.5 2.9 - - + -
147D LEU* 4.0 40.4 - - + +
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Residues in contact with ARG 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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76D LEU* 6.2 0.2 - - - -
77D HIS* 2.9 58.2 + - + +
80D LEU* 3.8 18.8 - - + +
81D ASP* 3.1 28.1 + - - +
84D GLU* 3.0 31.9 + - - -
104D ILE* 3.0 8.4 + - - +
105D LYS* 2.8 33.0 + - - +
107D ILE* 1.3 78.0 - - - +
109D ARG* 1.3 61.1 + - + +
111D LEU 3.0 12.0 - - - +
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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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105D LYS* 3.1 18.9 + - + +
106D ALA* 3.4 11.3 - - - +
107D ILE 3.0 0.8 - - - -
108D ARG* 1.3 80.7 - - + +
110D GLY* 1.3 60.2 + - - +
131D TYR* 5.6 2.2 - - - +
6L A 4.7 3.8 + - - -
7L A 3.8 25.1 + - - -
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Residues in contact with GLY 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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106D ALA 3.0 7.5 + - - -
107D ILE 2.7 10.1 + - - -
109D ARG* 1.3 75.2 - - - +
111D LEU* 1.3 73.9 + - - +
112D PRO* 4.1 2.4 - - - +
127D MSE 3.9 26.4 - - - +
131D TYR* 5.8 2.5 - - - -
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Residues in contact with LEU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D LEU* 4.3 23.1 - - + -
77D HIS* 3.4 6.4 + - - -
107D ILE* 2.8 17.8 + - + +
108D ARG 3.0 16.7 + - - +
109D ARG 5.3 0.2 - - - -
110D GLY* 1.3 91.1 - - - +
112D PRO* 1.3 83.2 - - + +
119D ILE* 4.3 25.8 - - + -
123D GLU* 4.3 28.7 - - + +
124D ILE* 5.0 11.2 - - + -
127D MSE 4.7 15.0 - - + -
147D LEU* 5.4 7.0 - - + -
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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
------------------------------------------------------------
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