Contacts of the helix formed by residues 88 - 100 (chain L) in PDB entry 1T6V
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 ILE 88 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3L PHE* 3.7 33.0 - - + -
8L LEU* 4.1 8.1 - - + -
11L ALA* 3.9 31.0 - - + +
12L MET* 4.0 20.4 - - + -
14L ARG* 6.0 0.2 - - - +
15L HIS* 4.0 13.2 - - + -
40L THR* 4.5 5.6 - - + -
55L ILE* 4.4 22.4 - - + -
85L SER 5.0 1.3 - - - +
86L SER 3.8 1.3 + - - +
87L ASP* 1.3 73.1 + - - +
89L THR* 1.3 66.8 + - - +
90L ALA 3.4 1.1 - - - -
91L SER* 3.1 9.5 + - - -
92L VAL* 2.9 41.6 + - + +
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Residues in contact with THR 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L HIS* 2.8 29.6 + - + +
87L ASP* 2.5 30.9 + - - -
88L ILE* 1.3 76.8 - - - +
90L ALA* 1.3 61.9 + - - +
92L VAL* 3.2 1.7 + - - +
93L ASN* 3.0 46.5 + - - +
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Residues in contact with ALA 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78L ILE* 4.6 11.0 - - + +
82L ALA* 3.5 40.6 - - + +
83L LEU* 4.0 5.5 - - + +
87L ASP* 4.5 2.8 + - - +
88L ILE 3.4 1.0 - - - -
89L THR* 1.3 78.8 - - - +
91L SER* 1.3 57.9 + - - +
93L ASN* 3.9 4.7 - - - +
94L CYS* 3.0 31.2 + - - +
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Residues in contact with SER 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53L TYR 5.1 0.9 + - - -
54L GLY* 5.0 0.2 - - - -
55L ILE* 3.7 30.3 + - - +
56L LEU* 4.7 5.5 + - - +
58L ILE* 3.9 8.5 - - - +
82L ALA 4.8 1.0 + - - -
83L LEU* 3.5 40.6 + - - +
87L ASP 5.4 0.2 + - - -
88L ILE* 3.1 12.4 + - - -
90L ALA* 1.3 78.7 - - - +
92L VAL* 1.3 57.5 + - - +
94L CYS* 3.4 1.6 + - - +
95L ALA* 2.8 31.3 + - - +
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Residues in contact with VAL 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L MET* 5.1 1.3 - - + -
15L HIS* 3.9 21.3 - - + +
17L LEU* 3.9 29.6 - - + -
55L ILE* 6.1 0.9 - - + -
56L LEU* 5.3 4.9 - - + -
88L ILE* 2.9 47.3 + - + +
89L THR 3.7 3.6 - - - +
91L SER* 1.3 75.4 - - - +
93L ASN* 1.3 62.8 + - - +
95L ALA* 3.1 7.0 + - - +
96L LYS* 2.8 53.1 + - - +
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Residues in contact with ASN 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L HIS* 5.7 2.2 - - - -
89L THR* 3.0 38.8 + - - +
90L ALA* 4.1 5.0 - - - +
92L VAL* 1.3 80.8 - - - +
94L CYS* 1.3 62.4 + - - +
96L LYS* 3.4 22.5 + - - +
97L LYS* 3.2 20.6 + - - +
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Residues in contact with CYS 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58L ILE* 3.9 32.1 - - + -
63L TRP* 4.1 2.0 - - - -
76L CYS* 2.0 52.7 - - + -
78L ILE* 4.2 11.2 - - + -
83L LEU* 4.3 0.4 - - + -
90L ALA 3.0 17.9 + - - +
91L SER 3.8 3.1 - - - +
93L ASN* 1.3 77.9 - - - +
95L ALA* 1.3 57.3 + - - +
97L LYS* 3.0 5.9 + - - +
98L ILE* 2.9 34.7 + - - +
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Residues in contact with ALA 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L LEU* 5.4 2.0 - - + -
28L TRP* 4.2 8.3 - - + -
56L LEU* 4.0 16.6 - - + -
58L ILE* 4.2 2.8 - - + +
91L SER 2.8 21.7 + - - +
92L VAL* 3.5 5.6 - - - +
94L CYS* 1.3 71.8 - - - +
96L LYS* 1.3 58.1 + - - +
98L ILE* 3.3 5.2 + - - +
99L VAL* 2.9 33.6 + - - +
108L TRP* 3.7 31.2 - - + -
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Residues in contact with LYS 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L HIS 2.8 29.6 + - - -
16L GLY* 4.0 11.6 + - - -
17L LEU* 3.9 14.6 - - + -
20L TYR* 3.6 49.3 - - + +
92L VAL* 2.8 28.8 + - - +
93L ASN* 3.6 21.2 + - - +
94L CYS 3.2 0.2 - - - -
95L ALA* 1.3 78.6 - - - +
97L LYS* 1.3 57.9 + - - +
99L VAL* 3.5 4.1 - - - +
100L SER* 2.7 33.6 + - - -
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Residues in contact with LYS 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63L TRP* 4.8 3.8 - - + -
75L LEU 2.7 30.6 + - - +
76L CYS* 4.3 15.4 - - - +
77L ASN* 3.9 12.5 - - - +
93L ASN 3.2 11.5 + - - +
94L CYS 3.0 10.1 + - - +
96L LYS* 1.3 72.1 - - - +
98L ILE* 1.3 70.2 + - - +
100L SER* 3.4 15.2 + - - -
101L ASP* 4.1 2.3 + - - +
88N ALA* 4.3 37.9 - - - +
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Residues in contact with ILE 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58L ILE* 4.0 22.2 - - + -
63L TRP* 3.6 51.9 - - + +
94L CYS* 2.9 27.8 + - - +
95L ALA* 3.6 9.9 - - - +
97L LYS* 1.3 79.8 - - - +
99L VAL* 1.3 59.4 + - - +
100L SER 3.2 1.0 + - - -
101L ASP* 3.1 23.2 + - - +
102L GLY* 5.2 0.2 - - - -
104L GLY 5.0 0.7 - - - +
107L ALA* 3.7 30.3 - - + -
108L TRP* 4.0 10.8 - - + -
87N VAL* 6.1 0.3 - - - +
88N ALA 5.3 0.7 + - - -
101N TYR* 4.1 12.6 - - + -
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Residues in contact with VAL 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L TYR* 3.7 26.2 - - + -
21L ARG* 4.1 13.2 + - + +
23L TYR* 3.7 22.8 - - + -
28L TRP* 3.9 14.4 - - + -
95L ALA 2.9 22.7 + - - +
96L LYS* 3.5 7.4 - - - +
98L ILE* 1.3 73.0 - - - +
100L SER* 1.3 58.7 + - - +
101L ASP 3.2 9.4 + - - +
104L GLY* 3.6 35.4 - - - -
105L MET* 3.7 13.5 - - + +
108L TRP* 4.3 3.6 - - + -
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Residues in contact with SER 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L TYR* 3.5 21.5 + - - -
21L ARG* 3.4 38.1 + - - +
96L LYS 2.7 21.2 + - - -
97L LYS* 3.8 7.6 - - - -
98L ILE 3.1 1.6 - - - -
99L VAL* 1.3 76.5 - - - +
101L ASP* 1.3 60.7 + - - +
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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