Contacts of the helix formed by residues 93 - 111 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ILE* 1.3 82.4 - - - +
94A GLN* 1.3 61.7 + - + +
95A LYS* 2.8 19.2 + - + +
96A THR* 2.8 20.4 + - - +
97A LEU* 3.3 1.3 + - - -
234A SER* 4.7 14.3 - - - +
20J A 2.6 38.0 + - - +
21J A 2.8 43.6 + - - +
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Residues in contact with GLN 94 (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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92A ILE 3.6 3.5 + - - -
93A LYS* 1.3 77.7 - - + +
95A LYS* 1.3 56.7 + - - +
97A LEU* 3.2 20.1 - - - +
98A ILE* 2.6 25.3 - - + +
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Residues in contact with LYS 95 (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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93A LYS* 2.8 9.3 + - + +
94A GLN* 1.3 74.7 - - - +
96A THR* 1.3 70.1 + - - +
97A LEU 3.0 1.3 - - - -
98A ILE* 2.8 32.4 + - + -
99A ASN* 2.9 39.4 + - - +
6I T 5.1 12.2 - - - +
7I G 5.4 0.8 + - - -
8I C 5.7 0.4 - - - +
20J A 6.0 0.4 - - + -
21J A 4.4 26.5 - - + +
22J G 4.2 18.1 + - - -
23J C 4.5 10.3 - - - +
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Residues in contact with THR 96 (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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92A ILE* 3.4 11.2 - - + -
93A LYS* 3.1 13.7 + - - +
95A LYS* 1.3 75.4 - - - +
97A LEU* 1.3 65.4 + - - +
99A ASN* 2.9 19.7 + - - +
100A TYR* 3.0 27.7 + - + -
19J A 2.8 44.2 - - + +
20J A 2.8 43.0 + - + +
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Residues in contact with LEU 97 (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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87A LEU* 5.8 3.8 - - + +
88A ALA* 4.8 23.3 - - + +
92A ILE* 3.7 19.7 - - + +
93A LYS 3.3 2.5 + - - +
94A GLN* 3.2 28.0 - - - +
96A THR* 1.3 74.3 - - - +
98A ILE* 1.3 72.5 + - + +
100A TYR* 3.0 15.1 + - - +
101A MSE 2.7 46.9 + - + +
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Residues in contact with ILE 98 (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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94A GLN* 2.6 32.8 - - + +
95A LYS* 2.8 32.6 + - + +
97A LEU* 1.3 85.9 - - + +
99A ASN* 1.3 73.2 + - - +
101A MSE 3.5 13.7 - - + -
102A SER* 2.7 24.1 + - - +
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Residues in contact with ASN 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LYS* 2.9 34.6 + - - +
96A THR* 2.9 9.5 + - - +
98A ILE* 1.3 80.6 - - - +
100A TYR* 1.3 66.7 + - - +
102A SER* 2.8 21.5 + - - -
103A LYS* 3.1 18.5 - - - +
8I C 4.3 6.5 - - - +
20J A 4.0 15.2 - - - +
21J A 2.7 51.1 + - - +
22J G 3.9 2.6 + - - -
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Residues in contact with TYR 100 (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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83A TYR* 4.7 5.8 - + + -
87A LEU* 4.7 22.9 - - + -
90A ARG* 4.6 2.0 + - - -
92A ILE* 4.3 14.6 - - + -
96A THR* 3.0 32.5 + - + -
97A LEU* 3.1 10.3 - - - +
99A ASN* 1.3 78.7 - - - +
101A MSE 1.3 54.3 + - + +
103A LYS* 2.7 31.8 + - + +
104A ILE* 3.0 19.2 + - + +
145A SER* 5.5 2.9 - - - -
146A THR* 3.3 34.0 - - + +
149A ASP* 5.2 3.3 + - + -
18J A 2.7 26.5 - + + +
19J A 2.3 36.6 + + - -
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Residues in contact with MSE 101 (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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84A GLU* 3.4 45.5 - - + +
87A LEU* 6.1 0.9 - - - -
97A LEU* 2.7 37.0 + - + +
98A ILE* 2.9 23.1 + - + +
100A TYR* 1.3 72.6 - - + +
102A SER* 1.3 64.2 + - - +
104A ILE* 3.0 34.9 - - - +
105A LYS* 3.1 8.5 + - - +
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Residues in contact with SER 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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98A ILE* 2.7 17.8 + - - +
99A ASN* 2.8 6.2 + - - -
101A MSE 1.3 73.4 - - - +
103A LYS* 1.3 98.7 + - - +
105A LYS* 3.3 10.8 + - - +
106A ALA* 2.8 18.9 + - - +
7I G 5.5 18.4 - - - -
8I C 5.3 3.0 - - - -
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Residues in contact with LYS 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ASN* 3.1 30.6 + - - +
100A TYR* 2.7 13.5 + - + +
102A SER* 1.3 109.5 + - - +
104A ILE* 1.3 71.1 + - - +
106A ALA* 2.3 30.1 + - + +
107A ILE* 2.8 6.3 + - + +
139A SER* 5.4 3.4 - - - +
142A LEU* 3.9 39.0 - - + -
143A ILE* 4.5 15.9 - - + +
146A THR* 4.4 17.9 - - - +
8I C 4.8 15.4 - - - +
9I T 5.0 10.3 + - - +
20J A 6.3 0.4 - - - +
21J A 5.8 0.4 - - - +
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Residues in contact with ILE 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 5.1 13.9 - - + +
83A TYR* 4.6 24.5 - - + -
84A GLU* 4.1 19.5 - - + +
87A LEU* 5.1 7.6 - - + -
100A TYR* 3.0 15.4 + - + +
101A MSE 3.0 48.9 - - + +
103A LYS* 1.3 74.9 - - - +
105A LYS* 1.3 61.4 + - + +
107A ILE* 2.2 54.4 + - + +
108A ARG* 2.9 21.6 + - + +
146A THR* 6.0 2.6 - - + -
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Residues in contact with LYS 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A MSE 3.1 7.4 + - - +
102A SER* 3.3 13.7 - - - +
103A LYS 3.1 0.4 - - - -
104A ILE* 1.3 86.5 - - + +
106A ALA* 1.3 68.6 + - - +
107A ILE 2.7 0.3 + - - -
108A ARG* 2.8 27.1 + - + +
109A ARG* 3.2 14.1 + - + +
6I T 5.0 8.1 + - - -
7I G 3.5 34.9 + - - +
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Residues in contact with ALA 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 SER 2.8 9.8 + - - +
103A LYS* 2.3 33.7 + - - +
105A LYS* 1.3 69.8 - - - +
107A ILE* 1.3 63.5 + - + +
109A ARG* 3.1 24.3 + - - +
110A GLY* 3.1 17.0 + - - -
127A MSE 5.3 2.2 - - - +
131A TYR* 4.8 10.5 + - + -
143A ILE* 4.6 21.8 - - + -
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Residues in contact with ILE 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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76A LEU* 5.9 3.6 - - + -
80A LEU* 4.8 23.6 - - + -
83A TYR* 6.4 1.8 - - + -
103A LYS* 3.4 8.1 - - + +
104A ILE* 2.2 45.2 + - + +
106A ALA* 1.3 69.7 - - + +
108A ARG* 1.3 66.5 + - - +
110A GLY* 2.6 14.4 + - - +
111A LEU* 2.9 26.7 + - + +
127A MSE 5.0 9.9 - - - -
143A ILE* 4.7 17.0 - - + +
146A THR* 5.3 2.9 - - - -
147A LEU* 4.5 43.1 - - + +
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Residues in contact with ARG 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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77A HIS* 2.9 67.7 + - + +
80A LEU* 4.5 12.6 - - + +
81A ASP* 2.5 44.2 + - - +
84A GLU* 4.4 14.1 + - - -
104A ILE* 2.9 18.2 + - + +
105A LYS* 2.8 23.3 + - + +
107A ILE* 1.3 73.0 - - - +
109A ARG* 1.3 56.7 + - + +
111A LEU 2.9 15.1 - - - +
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Residues in contact with ARG 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 LYS* 3.2 9.6 + - + +
106A ALA* 3.1 28.5 + - - +
107A ILE 3.0 0.8 - - - -
108A ARG* 1.3 76.2 - - + +
110A GLY* 1.3 62.3 + - - +
111A LEU 3.5 0.2 - - - -
131A TYR* 3.0 29.3 + - - +
7I G 4.0 26.1 + - - -
8I C 3.0 36.6 + - - -
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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 ALA 3.1 8.8 + - - -
107A ILE 2.6 14.3 + - - -
109A ARG* 1.3 76.7 - - - +
111A LEU* 1.3 75.2 + - - +
112A PRO* 4.1 0.9 - - - +
127A MSE 4.0 24.8 - - - +
131A TYR* 5.7 2.7 - - - -
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU* 4.7 11.2 - - + -
77A HIS* 2.9 28.0 + - - +
107A ILE* 2.9 19.2 + - + +
108A ARG 2.9 5.7 - - - +
109A ARG 3.5 0.4 - - - -
110A GLY* 1.3 102.1 - - - +
112A PRO* 1.3 77.7 - - + +
113A ASP 3.8 0.2 + - - -
119A ILE* 4.2 25.4 - - + -
123A GLU* 4.4 21.5 - - + +
124A ILE* 4.9 19.1 - - + +
127A MSE 4.5 17.5 - - + -
147A LEU* 5.7 4.9 - - + -
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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
------------------------------------------------------------
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