Contacts of the helix formed by residues 93 - 111 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ILE* 1.3 77.4 - - - +
94B GLN* 1.3 76.2 + - - +
95B LYS* 2.7 6.4 + - + +
96B THR* 2.7 34.9 + - - +
97B LEU* 3.3 5.0 + - - +
234B SER* 4.4 16.1 + - - +
20K A 2.8 34.5 + - - +
21K A 2.8 34.0 + - - +
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Residues in contact with GLN 94 (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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92B ILE 3.7 8.0 + - - -
93B LYS* 1.3 77.9 - - - +
95B LYS* 1.3 61.3 + - - +
97B LEU* 3.3 32.1 - - - +
98B ILE* 3.6 13.5 + - - +
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Residues in contact with LYS 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LYS* 2.7 7.8 + - + +
94B GLN* 1.3 73.2 - - - +
96B THR* 1.3 65.9 + - - +
97B LEU 3.1 1.8 - - - -
98B ILE* 2.9 18.3 + - + +
99B ASN* 2.9 34.8 + - - +
5J C 6.2 0.2 - - - -
6J A 4.2 24.6 - - - +
7J A 5.5 2.0 - - - +
20K A 6.5 0.4 - - + -
21K A 5.2 26.0 - - + +
22K C 4.3 21.5 - - + +
23K T 4.5 13.1 + - - +
24K T 5.4 0.2 + - - -
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Residues in contact with THR 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ILE* 4.2 15.9 - - + -
93B LYS* 2.7 35.3 + - - +
95B LYS* 1.3 72.5 - - - +
97B LEU* 1.3 65.4 + - - +
99B ASN* 2.9 19.2 + - - +
100B TYR* 2.8 43.7 - - + +
19K A 4.6 6.5 - - - -
20K A 3.6 36.9 + - + +
21K A 5.8 0.6 - - - -
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 3.8 38.8 - - + +
88B ALA* 4.2 13.7 - - + +
92B ILE* 4.3 16.7 - - + +
93B LYS 3.3 4.0 + - - +
94B GLN* 3.3 26.7 - - - +
96B THR* 1.3 82.4 - - - +
98B ILE* 1.3 54.2 + - + +
100B TYR* 3.0 9.4 + - + +
101B MSE 2.8 56.8 + - + +
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLN* 3.6 11.6 + - + +
95B LYS* 2.9 21.4 + - + +
97B LEU* 1.3 76.7 - - + +
99B ASN* 1.3 74.0 + - - +
101B MSE 3.3 14.3 - - + +
102B SER* 2.8 22.5 + - - -
5J C 5.4 10.3 - - - +
6J A 5.6 18.2 - - + +
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Residues in contact with ASN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LYS* 2.9 26.7 + - - +
96B THR* 3.0 15.0 - - - +
98B ILE* 1.3 79.1 - - - +
100B TYR* 1.3 76.9 + - + +
102B SER* 2.8 9.4 + - - -
103B LYS* 2.8 35.4 + - - +
8J G 3.6 13.3 + - - -
20K A 4.8 4.8 - - - +
21K A 3.0 47.4 - - - +
22K C 4.2 3.0 - - - +
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Residues in contact with TYR 100 (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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83B TYR* 5.1 4.7 - + + -
87B LEU* 4.8 20.4 - - + -
90B ARG* 6.3 1.3 - - - -
92B ILE* 5.7 7.0 - - + -
96B THR* 2.8 42.8 - - + +
97B LEU* 3.1 11.7 - - + +
99B ASN* 1.3 88.3 - - + +
101B MSE 1.3 55.4 + - + +
103B LYS* 2.5 43.6 + - - +
104B ILE* 2.9 15.3 + - + +
146B THR* 3.8 26.2 - - + +
149B ASP* 5.9 1.3 - - - -
18K T 4.3 3.1 - - - +
19K A 3.0 42.2 + + - -
20K A 5.2 7.0 - - - -
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Residues in contact with MSE 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLU* 3.7 45.3 - - + +
87B LEU* 5.2 3.6 - - - -
88B ALA* 6.5 1.1 - - + -
97B LEU* 2.8 45.6 + - + +
98B ILE* 3.0 18.8 + - + +
100B TYR* 1.3 72.7 - - + +
102B SER* 1.3 64.8 + - - +
104B ILE* 3.0 33.0 - - - +
105B LYS* 3.1 11.7 + - - +
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Residues in contact with SER 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ILE* 2.8 12.4 + - - -
99B ASN* 3.2 12.1 - - - -
101B MSE 1.3 77.1 - - - +
103B LYS* 1.3 73.4 + - - +
105B LYS* 3.3 9.8 + - - +
106B ALA* 2.8 18.5 + - - +
6J A 5.5 2.9 - - - -
7J A 4.0 40.7 + - - +
8J G 5.6 1.8 + - - -
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Residues in contact with LYS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ASN* 2.8 50.9 + - - +
100B TYR* 2.5 28.7 + - + +
102B SER* 1.3 74.8 - - - +
104B ILE* 1.3 72.8 + - + +
106B ALA* 2.5 25.5 + - - +
107B ILE* 2.8 8.3 + - + +
139B SER* 6.1 1.1 - - - +
142B LEU* 4.0 41.1 - - + +
143B ILE* 5.0 14.6 - - + -
146B THR* 4.5 16.8 - - + +
8J G 5.4 4.8 + - - -
9J T 4.8 10.9 + - - -
21K A 5.2 0.2 - - - +
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Residues in contact with ILE 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 4.6 18.6 - - + -
83B TYR* 4.4 25.4 - - + -
84B GLU* 3.8 27.1 - - + +
87B LEU* 4.7 4.5 - - + -
100B TYR* 3.3 10.8 - - + +
101B MSE 3.0 41.5 - - + +
103B LYS* 1.3 76.9 - - + +
105B LYS* 1.3 58.9 + - + +
107B ILE* 2.2 49.7 + - + +
108B ARG* 2.9 13.3 + - + +
146B THR* 4.9 6.1 - - + -
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Residues in contact with LYS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B MSE 3.1 9.0 + - - +
102B SER* 3.5 12.1 - - - +
104B ILE* 1.3 79.9 - - + +
106B ALA* 1.3 68.9 + - - +
108B ARG* 2.6 44.7 + - + +
109B ARG* 3.1 27.6 + - + +
6J A 3.5 26.7 + - - -
7J A 4.8 14.4 + - - +
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Residues in contact with ALA 106 (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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102B SER 2.8 12.3 + - - +
103B LYS* 2.5 22.0 + - - +
105B LYS* 1.3 74.8 - - - +
107B ILE* 1.3 62.0 + - + +
109B ARG* 3.0 19.3 + - - +
110B GLY* 3.0 10.0 + - - -
127B MSE 5.5 2.0 - - - +
131B TYR* 4.2 29.8 + - + +
143B ILE* 4.9 9.9 - - + -
8J G 5.9 1.8 - - - +
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Residues in contact with ILE 107 (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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76B LEU* 5.0 4.7 - - + -
80B LEU* 4.7 17.0 - - + -
103B LYS* 3.3 9.2 - - + +
104B ILE* 2.2 39.9 + - + +
106B ALA* 1.3 69.2 - - - +
108B ARG* 1.3 53.6 + - - +
110B GLY* 2.6 24.2 + - - +
111B LEU* 2.9 31.6 + - + +
127B MSE 5.0 9.2 - - - -
143B ILE* 4.4 17.9 - - + +
146B THR* 4.8 5.4 - - + -
147B LEU* 3.5 50.7 - - + +
150B ALA* 6.4 0.7 - - + -
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Residues in contact with ARG 108 (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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76B LEU* 5.7 2.0 - - - -
77B HIS* 3.4 43.4 + - + +
80B LEU* 5.4 9.3 - - + +
81B ASP* 2.9 39.0 + - - +
84B GLU* 3.9 18.7 + - - -
104B ILE* 2.9 15.3 + - + +
105B LYS* 2.6 39.9 + - + +
107B ILE* 1.3 70.7 - - - +
109B ARG* 1.3 63.9 + - + +
111B LEU 3.0 22.9 - - - +
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Residues in contact with ARG 109 (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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105B LYS* 4.0 29.2 + - - +
106B ALA* 3.0 12.3 + - - +
108B ARG* 1.3 77.7 - - + +
110B GLY* 1.3 60.0 + - - +
111B LEU 5.1 0.2 - - - -
131B TYR* 6.0 0.9 - - - +
7J A 3.0 32.5 + - - -
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Residues in contact with GLY 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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106B ALA 3.0 7.2 + - - -
107B ILE 2.6 14.7 + - - -
109B ARG* 1.3 75.4 - - - +
111B LEU* 1.3 70.6 + - - +
112B PRO* 4.0 3.6 - - - +
127B MSE 4.4 23.5 - - - +
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU* 3.7 24.7 - - + -
77B HIS* 3.0 16.6 + - - -
107B ILE* 2.9 26.5 + - + +
108B ARG 3.0 7.5 - - - +
110B GLY* 1.3 92.1 - - - +
112B PRO* 1.3 79.9 - - + +
119B ILE* 4.7 17.5 - - + -
123B GLU* 4.2 30.1 - - + +
124B ILE* 4.8 11.4 - - + -
127B MSE 4.7 14.4 - - + -
147B LEU* 5.1 8.3 - - + -
151B PHE* 6.5 0.9 - - + -
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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