Contacts of the helix formed by residues 100 - 115 (chain S) in PDB entry 1T9G
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 GLY 100 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11S LYS* 5.8 3.1 - - - -
99S LEU* 1.3 77.0 - - - +
101S PRO* 1.3 77.5 - - - +
102S LEU 3.1 3.8 + - - -
103S GLN* 3.2 15.1 + - - +
104S VAL* 2.9 28.5 + - - +
129S ASP* 5.5 3.1 - - - -
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Residues in contact with PRO 101 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11S LYS* 5.9 0.4 - - - +
100S GLY* 1.3 81.5 - - - +
102S LEU* 1.3 52.5 + - - +
104S VAL* 3.2 4.0 + - + +
105S ALA* 2.7 37.6 + - - +
129S ASP* 4.6 3.6 - - - +
131S CYS* 3.7 28.3 - - + -
133S GLN* 3.3 40.4 - - + +
134S THR* 3.7 19.8 - - - +
137S MET* 4.3 4.9 - - - -
222S LEU* 6.4 2.2 - - + -
600S AMP 3.7 10.3 - - - +
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Residues in contact with LEU 102 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128R GLU* 4.6 13.5 - - - +
129R VAL 4.1 12.6 - - - +
130R ALA* 3.9 28.9 - - + +
161R GLU* 4.9 3.4 - - - +
100S GLY 3.2 0.8 - - - -
101S PRO* 1.3 75.6 - - - +
103S GLN* 1.3 91.9 + - - +
105S ALA* 3.1 2.6 + - - +
106S ARG* 3.0 39.3 + - - +
137S MET* 3.4 35.0 - - + -
141S PHE* 3.8 20.4 - - + -
219S THR 5.2 4.9 - - - +
220S SER* 6.0 1.8 - - - -
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Residues in contact with GLN 103 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98S ARG 4.4 4.5 - - - +
99S LEU* 3.3 32.5 - - + -
100S GLY* 3.2 23.5 + - - +
102S LEU* 1.3 101.3 - - - +
104S VAL* 1.3 64.7 + - - +
106S ARG* 3.1 9.8 + - - +
107S VAL* 2.8 27.3 + - + +
216S VAL* 4.5 2.9 - - + +
217S ASP 4.6 4.3 + - - +
218S LEU* 3.9 39.9 + - + +
219S THR 4.0 11.1 + - - -
220S SER* 4.6 8.4 + - - -
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Residues in contact with VAL 104 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11S LYS* 5.9 0.9 - - - +
66S CYS* 4.2 10.1 - - + -
99S LEU* 4.2 16.6 - - + -
100S GLY* 2.9 27.5 + - - +
101S PRO* 3.8 3.8 - - + +
103S GLN* 1.3 74.6 - - - +
105S ALA* 1.3 51.0 + - - +
107S VAL* 3.2 8.3 - - - +
108S LEU* 2.6 56.1 + - + +
134S THR* 4.0 7.2 - - + -
600S AMP 3.8 50.7 - - + +
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Residues in contact with ALA 105 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101S PRO 2.7 20.6 + - - +
102S LEU 3.8 0.2 - - - +
104S VAL* 1.3 71.8 - - - +
106S ARG* 1.3 54.7 + - - +
108S LEU* 2.9 3.1 + - - +
109S ALA* 2.7 37.1 + - - +
134S THR* 3.7 4.6 - - + +
137S MET* 3.6 17.3 - - + -
138S THR* 3.1 41.5 - - - +
141S PHE* 3.8 9.2 - - + -
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Residues in contact with ARG 106 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128R GLU* 2.6 44.3 + - - +
102S LEU* 3.0 33.6 + - - +
103S GLN* 3.1 10.1 - - - +
105S ALA* 1.3 75.8 - - - +
107S VAL* 1.3 66.9 + - - +
109S ALA* 3.2 2.4 + - - +
110S LYS* 3.1 18.9 + - - +
141S PHE* 3.4 31.5 - - + -
216S VAL* 3.9 20.0 - - + +
217S ASP* 4.5 17.9 - - - +
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Residues in contact with VAL 107 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66S CYS* 4.0 17.3 - - - -
89S VAL* 4.0 34.1 - - + -
99S LEU* 5.7 3.8 - - + -
103S GLN* 2.8 26.3 + - + +
104S VAL* 3.2 11.2 - - - +
106S ARG* 1.3 75.7 - - - +
108S LEU* 1.3 69.1 + - + +
110S LYS* 3.1 2.8 + - - +
111S LEU* 3.0 30.8 + - + +
211S PRO* 5.0 8.3 - - + -
214S LEU* 5.5 6.5 - - + +
216S VAL* 4.0 23.7 - - + +
218S LEU* 5.9 1.3 - - + -
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Residues in contact with LEU 108 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7S LEU* 4.0 18.3 - - + +
9S ALA* 3.7 22.2 - - + -
64S VAL* 2.9 37.2 - - + -
104S VAL* 2.6 40.9 + - + +
105S ALA 2.9 4.0 + - - +
107S VAL* 1.3 75.1 - - + +
109S ALA* 1.3 56.4 + - - +
111S LEU* 3.3 11.4 - - + +
112S ALA* 2.8 27.7 + - - +
120S VAL* 5.0 6.0 - - + +
122S LEU* 4.0 19.1 - - + -
134S THR* 4.3 4.0 - - + -
138S THR* 3.8 16.3 - - + +
600S AMP 4.5 0.4 - - + +
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Residues in contact with ALA 109 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105S ALA 2.7 19.2 + - - +
106S ARG* 3.7 4.0 - - - +
108S LEU* 1.3 71.2 - - - +
110S LYS* 1.3 58.3 + - - +
112S ALA* 2.8 21.3 + - - +
113S GLU* 3.0 14.5 + - - +
138S THR* 4.0 6.0 - - + +
141S PHE* 3.7 28.3 - - + -
142S LEU* 3.3 28.8 - - + +
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Residues in contact with LYS 110 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106S ARG 3.1 9.3 + - - +
107S VAL 3.7 6.1 - - - +
109S ALA* 1.3 76.9 - - - +
111S LEU* 1.3 58.2 + - - +
113S GLU* 3.2 17.0 + - - +
114S LYS* 3.0 32.0 + - - +
214S LEU* 4.3 24.2 - - + +
216S VAL* 4.5 13.0 - - + -
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Residues in contact with LEU 111 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7S LEU* 4.1 7.3 - - + +
64S VAL* 3.7 33.7 - - + -
87S ILE* 4.4 24.2 - - + -
89S VAL* 4.6 9.9 - - + -
107S VAL* 3.0 27.9 + - + +
108S LEU* 3.3 20.2 - - + +
110S LYS* 1.3 73.6 - - - +
112S ALA* 1.3 64.4 + - - +
114S LYS* 4.4 13.7 - - + -
115S GLU* 3.2 34.7 + - + +
209S ILE* 4.8 13.2 - - + -
214S LEU* 5.5 7.7 - - + +
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Residues in contact with ALA 112 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7S LEU* 4.3 2.9 - - + -
108S LEU 2.8 14.5 + - - +
109S ALA 2.8 17.0 + - - +
111S LEU* 1.3 74.3 - - - +
113S GLU* 1.3 63.6 + - - +
116S LYS 3.2 9.9 + - - -
117S VAL* 3.2 37.6 + - + +
120S VAL* 4.2 9.4 - - + -
142S LEU* 3.8 26.7 - - + -
144S TRP* 4.3 3.1 - - + -
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Residues in contact with GLU 113 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109S ALA* 3.0 12.5 + - - +
110S LYS* 3.5 19.2 - - - +
112S ALA* 1.3 77.1 - - - +
114S LYS* 1.3 66.9 + - + +
116S LYS* 3.2 17.9 + - - +
142S LEU* 4.3 13.2 - - + +
144S TRP* 5.8 2.7 - - + -
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Residues in contact with LYS 114 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110S LYS 3.0 18.3 + - - +
111S LEU* 4.0 13.7 - - + +
113S GLU* 1.3 76.9 - - + +
115S GLU* 1.3 81.8 + - + +
116S LYS* 3.0 18.6 + - - +
207S GLU* 5.3 8.1 + - - -
209S ILE* 4.6 17.9 - - + +
214S LEU* 6.3 3.9 - - + +
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Residues in contact with GLU 115 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5S ARG* 5.1 2.6 - - - +
7S LEU* 6.0 3.6 - - + -
62S ILE* 4.6 9.6 - - + +
85S ARG* 2.8 34.2 + - - +
87S ILE* 3.8 20.6 - - + +
111S LEU* 3.2 22.6 + - + +
112S ALA 4.4 1.1 - - - +
114S LYS* 1.3 98.5 - - + +
116S LYS* 1.3 73.7 + - - +
117S VAL* 3.4 15.9 + - + +
207S GLU* 5.0 5.2 - - - +
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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