Contacts of the helix formed by residues 93 - 111 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92C ILE* 1.3 87.0 - - - +
94C GLN* 1.3 89.3 + - + +
95C LYS* 2.8 14.5 + - + +
96C THR* 2.8 17.2 + - - +
97C LEU* 3.3 1.7 + - - -
234C SER* 4.5 14.2 + - - +
20L A 3.0 27.9 + - - +
21L A 2.3 42.4 + - - +
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Residues in contact with GLN 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ILE 3.7 2.6 + - - -
93C LYS* 1.3 93.6 + - + +
95C LYS* 1.3 56.2 + - - +
97C LEU* 3.1 15.9 - - - +
98C ILE* 2.7 30.7 - - + +
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Residues in contact with LYS 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C LYS* 2.8 16.0 + - + +
94C GLN* 1.3 74.3 + - - +
96C THR* 1.3 69.0 + - - +
97C LEU 3.1 1.1 - - - -
98C ILE* 3.0 9.6 + - + +
99C ASN* 2.9 32.0 + - - +
7K G 5.1 0.6 + - - -
20L A 5.8 0.9 - - + -
21L A 4.3 28.5 - - + +
22L G 2.9 42.9 + - - +
23L C 3.6 14.8 - - - +
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Residues in contact with THR 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C ILE* 2.9 24.9 - - + -
93C LYS* 2.8 10.9 + - - +
95C LYS* 1.3 73.5 - - - +
97C LEU* 1.3 61.8 + - - +
99C ASN* 2.9 19.4 + - - +
100C TYR* 3.0 39.9 + - + +
19L A 3.2 29.1 - - + +
20L A 2.5 41.0 + - + +
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Residues in contact with LEU 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C LEU* 5.7 5.2 - - + -
88C ALA* 4.8 21.8 - - + +
92C ILE* 3.9 13.0 - - + +
93C LYS 3.3 3.9 + - - +
94C GLN* 3.1 17.0 - - - +
96C THR* 1.3 76.8 - - - +
98C ILE* 1.3 97.7 + - + +
100C TYR* 3.0 15.2 + - - +
101C MSE 2.8 47.7 + - + +
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Residues in contact with ILE 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C GLN* 2.7 33.2 - - + +
95C LYS* 3.0 11.5 + - + +
97C LEU* 1.3 98.6 - - + +
99C ASN* 1.3 58.3 + - - +
101C MSE 3.6 10.8 - - + -
102C SER* 2.3 40.5 + - - +
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Residues in contact with ASN 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C LYS* 2.9 25.5 + - - +
96C THR* 3.2 7.6 - - - +
98C ILE* 1.3 72.9 - - - +
100C TYR* 1.3 69.0 + - + +
102C SER* 2.7 14.9 + - - -
103C LYS* 2.5 37.9 + - - +
8K C 4.1 10.1 - - - +
20L A 3.9 16.2 - - - +
21L A 2.7 54.4 + - - +
22L G 4.3 4.2 + - - -
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Residues in contact with TYR 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C TYR* 5.4 2.9 - - - -
87C LEU* 3.7 31.0 - - + -
90C ARG* 4.7 8.1 - - - -
92C ILE* 4.5 12.8 - - + -
96C THR* 3.2 28.4 - - + +
97C LEU* 3.0 10.5 + - - +
99C ASN* 1.3 79.8 - - + +
101C MSE 1.3 58.4 + - + +
103C LYS* 2.8 28.6 + - + +
104C ILE* 3.0 17.2 + - + +
142C LEU* 6.3 2.9 - - + -
146C THR* 4.9 21.3 - - + +
149C ASP* 5.8 0.7 - - - -
18L T 3.2 19.0 - + + +
19L A 2.4 46.1 + + - -
20L A 5.3 1.8 - - - -
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Residues in contact with MSE 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C GLU* 3.3 37.9 - - + +
87C LEU* 6.2 1.3 - - - -
97C LEU* 2.8 45.1 + - + +
98C ILE* 3.0 17.0 + - + +
100C TYR* 1.3 73.1 - - + +
102C SER* 1.3 62.1 + - - +
104C ILE* 3.1 29.8 - - - +
105C LYS* 3.0 23.3 + - - +
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Residues in contact with SER 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ILE* 2.3 36.2 + - - +
99C ASN* 2.7 11.4 + - - -
101C MSE 1.3 72.0 - - - +
103C LYS* 1.3 78.2 + - - +
105C LYS* 3.2 13.0 - - - +
106C ALA* 2.8 19.8 + - - +
7K G 5.5 10.5 + - - -
8K C 5.1 10.8 + - - -
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Residues in contact with LYS 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ASN* 2.5 58.9 + - - +
100C TYR* 2.8 13.8 + - + +
102C SER* 1.3 82.8 + - - +
104C ILE* 1.3 70.5 + - - +
106C ALA* 2.5 27.6 + - - +
107C ILE* 2.9 7.6 + - + +
139C SER* 6.5 0.2 - - - -
142C LEU* 4.2 29.8 - - + +
143C ILE* 4.5 23.3 - - + +
146C THR* 4.6 16.8 - - - +
8K C 4.6 9.9 - - - +
9K T 5.0 8.5 + - - -
20L A 5.7 3.4 - - - +
21L A 5.8 0.2 - - - +
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Residues in contact with ILE 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C LEU* 4.6 22.7 - - + -
83C TYR* 4.6 22.2 - - + -
84C GLU* 3.7 23.3 - - + +
87C LEU* 5.1 4.3 - - + -
100C TYR* 3.0 11.4 + - + +
101C MSE 3.1 50.3 - - - +
103C LYS* 1.3 71.4 - - - +
105C LYS* 1.3 56.9 - - - +
107C ILE* 2.3 44.5 + - + +
108C ARG* 2.9 23.4 + - + +
146C THR* 5.5 3.9 - - + +
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Residues in contact with LYS 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C MSE 3.0 9.2 + - - +
102C SER* 3.2 15.0 - - - +
104C ILE* 1.3 79.0 - - - +
106C ALA* 1.3 67.8 + - - +
107C ILE 2.9 0.2 + - - -
108C ARG* 3.0 28.8 + - + +
109C ARG* 3.2 12.4 + - - +
6K A 4.5 20.0 + - - -
7K G 3.5 36.4 + - - +
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Residues in contact with ALA 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C SER 2.8 10.2 + - - +
103C LYS* 2.5 26.6 + - - +
105C LYS* 1.3 72.7 - - - +
107C ILE* 1.3 60.9 + - + +
109C ARG* 3.2 11.0 + - - +
110C GLY* 3.1 16.3 + - - -
127C MSE 5.3 2.3 - - - +
131C TYR* 4.7 17.2 + - + +
143C ILE* 4.6 20.4 - - + -
8K C 6.1 1.6 - - - +
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Residues in contact with ILE 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C LEU* 4.9 9.2 - - + -
77C HIS* 6.2 0.4 - - + -
80C LEU* 5.0 13.0 - - + -
103C LYS* 2.9 22.7 + - + +
104C ILE* 2.3 34.1 + - + +
106C ALA* 1.3 64.2 - - - +
108C ARG* 1.3 68.1 + - - +
109C ARG 3.0 1.8 - - - -
110C GLY* 2.8 12.9 + - - +
111C LEU* 2.8 28.7 + - + +
127C MSE 5.0 8.5 - - - -
143C ILE* 4.1 25.1 - - + +
146C THR* 5.3 2.2 - - + -
147C LEU* 4.2 48.0 - - + +
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Residues in contact with ARG 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C HIS* 2.8 60.1 + - + +
80C LEU* 4.2 5.6 - - + +
81C ASP* 2.5 44.5 + - - +
84C GLU* 3.7 21.6 + - - -
104C ILE* 2.9 14.5 + - + +
105C LYS* 3.3 31.0 - - + +
107C ILE* 1.3 76.6 - - - +
109C ARG* 1.3 59.8 + - + +
111C LEU 2.8 24.9 - - - +
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Residues in contact with ARG 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C LYS* 3.2 7.3 + - + +
106C ALA* 3.2 12.7 + - - +
107C ILE 3.0 0.4 - - - -
108C ARG* 1.3 78.7 - - + +
110C GLY* 1.3 59.8 + - - +
131C TYR* 5.1 12.2 + - - +
7K G 4.3 25.5 + - - -
8K C 5.4 6.7 + - - -
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Residues in contact with GLY 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C ALA 3.1 8.1 + - - -
107C ILE 2.8 6.0 + - - -
109C ARG* 1.3 80.0 - - - +
111C LEU* 1.3 75.1 + - - +
112C PRO* 4.1 1.4 - - - +
127C MSE 4.0 28.8 - - - +
131C TYR* 5.6 3.4 - - - -
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Residues in contact with LEU 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C LEU* 4.1 19.5 - - + -
77C HIS* 3.2 7.3 + - - -
107C ILE* 2.8 20.9 + - + +
108C ARG 2.8 21.0 - - - +
110C GLY* 1.3 88.1 - - - +
112C PRO* 1.3 89.5 - - + +
113C ASP 3.8 0.2 + - - -
119C ILE* 4.0 28.9 - - + -
123C GLU* 4.3 25.4 - - + +
124C ILE* 4.6 12.6 - - + -
127C MSE 4.9 12.3 - - + -
147C LEU* 5.4 5.4 - - + -
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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
------------------------------------------------------------
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