Contacts of the helix formed by residues 76 - 91 (chain B) 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 76 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B HIS* 3.7 6.7 - - - -
75B LEU* 1.4 76.4 - - - +
77B THR* 1.3 65.0 + - - -
78B PHE 3.3 2.2 - - - -
79B ASP* 3.2 16.8 + - - +
80B ALA* 3.1 17.2 + - - +
320B ASP* 3.4 15.5 - - - -
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Residues in contact with THR 77 (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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65B HIS* 3.6 9.8 - - + -
76B GLY* 1.3 68.8 - - - -
78B PHE* 1.3 63.8 + - - -
80B ALA* 3.2 1.0 + - - -
81B CYS* 2.9 27.7 + - - -
254B LYS* 3.1 62.8 - - + +
257B PRO* 4.2 17.0 - - + -
258B VAL* 3.9 11.9 - - + -
316B ALA* 4.1 4.0 - - + -
319B VAL* 3.6 15.6 - - + +
320B ASP* 2.8 11.5 + - - -
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Residues in contact with PHE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PHE* 4.4 15.9 - + - -
20B GLN* 3.4 37.9 - - - +
77B THR* 1.3 75.4 - - - +
79B ASP* 1.3 63.6 + - - +
81B CYS* 3.4 3.0 - - + +
82B LEU* 3.0 26.3 + - + +
312B TYR* 5.9 1.1 - + - -
313B GLN* 3.8 51.4 - - + -
316B ALA* 3.6 15.5 - - + +
317B TRP* 4.3 9.9 - + + +
320B ASP* 2.9 21.7 + - + +
12C PHE* 3.6 42.4 - + + -
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Residues in contact with ASP 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLN* 5.1 1.0 - - - +
20B GLN* 3.0 38.6 + - - +
23B PHE* 4.4 13.9 - - + -
75B LEU* 3.7 30.7 - - + +
76B GLY* 3.2 24.3 + - - +
78B PHE* 1.3 79.0 - - - +
80B ALA* 1.3 56.0 + - - +
82B LEU* 3.5 8.4 + - - +
83B ILE* 3.0 36.5 + - - +
320B ASP* 5.7 0.2 - - - -
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Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B THR* 4.2 18.3 - - - +
65B HIS* 3.7 31.4 - - + +
76B GLY 3.1 6.2 + - - +
77B THR 3.2 5.8 + - - +
79B ASP* 1.3 74.6 - - - +
81B CYS* 1.3 53.0 + - - +
83B ILE* 3.3 7.3 + - - +
84B SER* 2.7 40.0 + - - -
102B SER* 5.9 0.4 - - - +
258B VAL* 3.9 11.4 - - + -
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Residues in contact with CYS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B THR 2.9 20.7 + - - +
78B PHE* 3.4 7.4 - - + +
80B ALA* 1.3 74.7 - - - +
82B LEU* 1.3 59.0 + - - +
84B SER* 3.1 4.0 + - - -
85B GLU* 2.8 27.9 + - - +
257B PRO* 3.4 46.9 - - - -
258B VAL* 3.7 8.0 - - - +
261B ALA* 3.4 12.9 - - - +
312B TYR* 3.4 24.5 - - + -
316B ALA* 4.1 6.5 - - + -
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PHE* 3.3 36.3 - - + -
20B GLN* 3.8 35.0 - - + +
23B PHE* 5.1 3.8 - - + -
24B GLN* 3.4 34.8 - - + +
78B PHE* 3.0 21.7 + - + +
79B ASP* 3.7 7.9 - - - +
81B CYS* 1.3 76.5 - - - +
83B ILE* 1.3 68.2 + - + +
85B GLU* 4.0 2.7 + - - +
86B GLU* 3.5 18.5 + - - +
312B TYR* 4.1 13.8 - - + +
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Residues in contact with ILE 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE* 4.3 31.9 - - + +
24B GLN* 5.8 0.9 - - - +
27B ALA* 4.3 8.5 - - + +
60B GLY 4.9 1.6 - - - +
61B LEU* 3.9 45.1 - - + +
64B THR* 4.1 24.9 - - + -
75B LEU* 4.5 8.5 - - + -
79B ASP 3.0 24.6 + - - +
80B ALA* 3.6 5.2 - - - +
82B LEU* 1.3 74.9 - - + +
84B SER* 1.3 69.0 + - - +
86B GLU* 3.0 17.3 + - - +
87B LEU* 3.2 22.0 + - + +
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Residues in contact with SER 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ALA* 2.7 23.1 + - - -
81B CYS* 3.6 4.0 - - - -
83B ILE* 1.3 73.9 - - - +
85B GLU* 1.3 56.7 + - - +
87B LEU* 3.2 11.9 + - - +
88B ALA* 2.8 30.9 + - - +
95B GLN* 3.0 27.9 + - - -
99B GLU* 6.1 0.2 - - - -
258B VAL* 3.4 28.4 + - - +
261B ALA* 4.7 0.9 - - - -
262B GLY 4.0 2.3 + - - -
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Residues in contact with GLU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B CYS 2.8 13.6 + - - +
82B LEU* 4.4 4.9 - - - +
83B ILE 3.1 0.6 + - - -
84B SER* 1.3 71.2 - - - +
86B GLU* 1.3 62.3 + - + +
88B ALA 3.2 1.0 + - - -
89B TYR* 2.9 32.8 + - + +
261B ALA* 3.7 18.0 - - + +
264B VAL* 2.8 19.4 - - - +
265B GLY* 3.4 17.3 - - - +
268B GLN* 4.5 3.4 - - + +
309B ARG* 2.4 45.9 + - - -
312B TYR* 2.8 30.8 + - - +
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Residues in contact with GLU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLN* 3.5 26.3 - - - +
27B ALA* 3.8 22.7 - - + -
28B ARG* 2.7 56.3 + - - +
31B ALA* 3.0 19.4 - - - +
32B ARG* 4.2 7.6 + - - -
82B LEU* 3.5 17.8 - - - +
83B ILE 3.0 5.6 + - - +
85B GLU* 1.3 81.5 - - - +
87B LEU* 1.3 65.9 + - - +
89B TYR* 3.5 16.4 + - - +
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Residues in contact with LEU 87 (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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27B ALA* 4.3 10.8 - - + +
30B PHE* 3.8 33.4 - - + -
31B ALA* 4.1 3.8 - - - -
35B ILE* 4.3 12.0 - - + +
61B LEU* 4.2 15.0 - - + +
83B ILE* 3.2 29.8 + - + +
84B SER* 3.8 9.2 - - - +
86B GLU* 1.3 76.6 - - - +
88B ALA* 1.3 58.1 + - - +
90B GLY* 2.9 17.8 + - - -
91B CYS 3.0 14.5 + - - +
95B GLN* 3.7 18.4 - - + +
98B ILE* 4.2 32.5 - - + -
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Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B SER 2.8 21.2 + - - +
85B GLU 3.7 3.8 - - - +
87B LEU* 1.3 69.7 - - - +
89B TYR* 1.3 66.7 + - - +
90B GLY 3.0 1.7 + - - -
91B CYS* 3.4 15.0 + - - -
92B THR* 3.5 19.5 + - + +
95B GLN* 3.7 13.7 - - + +
262B GLY* 3.1 36.1 - - - +
265B GLY* 4.0 0.4 - - - -
266B LEU* 4.1 7.6 + - - +
269B ARG* 5.4 0.2 - - - +
365B LEU* 6.0 1.0 - - - +
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Residues in contact with TYR 89 (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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31B ALA* 5.7 0.9 - - + -
32B ARG* 3.0 42.0 + - + +
36B ILE* 3.7 24.2 - - + -
85B GLU* 2.9 14.1 + - + +
86B GLU* 3.5 15.7 - - - +
88B ALA* 1.3 77.2 - - - +
90B GLY* 1.3 50.9 + - - +
265B GLY* 3.8 12.5 - - - +
268B GLN* 3.7 14.4 - - + -
269B ARG* 2.8 77.8 + - - +
272B ASP* 2.7 38.0 + - - +
276B LYS* 4.9 6.1 + - - -
365B LEU* 5.8 0.3 - - - +
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Residues in contact with GLY 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ALA* 4.2 10.3 - - - -
35B ILE* 3.6 13.4 - - - +
36B ILE* 3.7 21.9 - - - +
39B ALA* 4.4 5.9 - - - +
86B GLU 3.6 2.4 + - - -
87B LEU 2.9 7.7 + - - -
89B TYR* 1.3 79.3 - - - +
91B CYS* 1.3 63.1 + - - +
269B ARG* 3.0 19.2 + - - -
364B LYS* 5.0 2.1 + - - -
365B LEU* 6.0 0.9 - - - +
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Residues in contact with CYS 91 (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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35B ILE* 3.6 19.0 - - + +
39B ALA* 3.8 13.7 - - + -
43B ASP* 6.2 0.2 - - - -
87B LEU 3.0 11.8 + - - +
88B ALA 3.6 6.1 - - - -
90B GLY* 1.3 79.2 - - - +
92B THR* 1.3 58.3 + - - +
93B GLY* 3.1 21.5 - - - -
94B VAL* 3.3 23.2 - - + +
95B GLN* 3.1 21.1 + - - +
219B CYS* 4.6 5.6 - - - -
364B LYS* 3.5 25.8 - - - +
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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