Contacts of the helix formed by residues 89 - 102 (chain F) in PDB entry 1V8O
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 THR 89 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41E ASN* 3.7 12.6 - - - -
44E TRP* 3.3 31.0 - - + -
83F ALA* 4.3 0.9 - - - -
87F GLY 5.9 0.2 - - - +
88F LEU* 1.3 76.6 - - - +
90F PHE* 1.3 65.5 + - - +
91F TYR* 3.5 8.1 + - - +
92F ASP* 3.2 31.2 + - - +
93F ALA* 2.8 20.6 + - - +
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Residues in contact with PHE 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E ILE* 4.2 6.3 - - + -
37E TYR* 3.8 40.6 - + + -
40E GLY* 3.6 22.4 - - - +
41E ASN* 3.1 27.5 - - - +
44E TRP* 4.0 9.3 - - + -
76F LEU* 3.8 31.2 - - + -
79F VAL* 3.5 32.7 - - + +
80F MSE 3.7 25.4 - - + -
83F ALA* 4.4 3.8 - - + -
89F THR* 1.3 73.7 - - - +
91F TYR* 1.3 58.3 + - - +
93F ALA* 4.4 3.8 - - - -
94F SER* 2.7 44.9 + - - -
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Residues in contact with TYR 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E LEU* 4.9 2.5 - - + +
37E TYR* 3.4 33.4 - - + -
38E GLU* 3.4 30.2 - - + +
41E ASN* 3.4 33.7 - - + +
91E TYR* 5.5 12.8 - + - -
34F LEU* 3.6 26.9 - - + -
38F GLU* 3.6 19.5 - - + +
89F THR* 3.1 8.2 - - - +
90F PHE* 1.3 76.2 - - - +
92F ASP* 1.3 64.5 + - - +
94F SER* 3.2 17.9 - - - -
95F TYR* 3.3 15.8 - - - -
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Residues in contact with ASP 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F GLU* 5.3 1.9 - - - +
88F LEU* 4.0 21.6 - - + +
89F THR* 3.2 22.9 + - - +
91F TYR* 1.3 77.1 - - - +
93F ALA* 1.3 67.0 + - - +
94F SER 3.0 2.9 + - - -
95F TYR* 3.0 18.7 + - - +
96F ALA 3.2 8.8 + - - -
110F ASP* 3.9 15.7 - - - +
112F GLU* 5.9 0.5 - - - +
113F LEU* 3.7 31.2 - - + +
48H ARG* 4.3 10.6 + - - -
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Residues in contact with ALA 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F VAL* 3.7 14.9 - - + +
82F VAL* 4.1 6.0 - - + +
83F ALA* 3.6 36.6 - - + +
88F LEU* 3.9 15.5 - - + +
89F THR 2.8 20.9 + - - +
92F ASP* 1.3 73.6 - - - +
94F SER* 1.3 57.6 + - - +
96F ALA* 3.7 2.2 - - - +
97F TYR* 2.9 31.5 + - - +
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Residues in contact with SER 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E TYR* 3.6 33.3 - - - -
32F LEU* 4.2 9.6 - - - -
34F LEU* 4.6 0.7 - - - -
74F PRO* 4.6 3.4 - - - -
79F VAL* 3.3 20.5 - - - +
90F PHE* 2.7 20.6 + - - -
91F TYR 3.2 11.9 - - - -
92F ASP 3.0 0.4 - - - -
93F ALA* 1.3 74.9 - - - +
95F TYR* 1.3 65.5 + - - +
97F TYR* 3.8 0.9 - - - +
98F VAL* 3.0 29.5 + - - +
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Residues in contact with TYR 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F LEU* 3.7 18.7 - - + +
7F VAL 4.1 2.7 - - - -
8F ASP* 3.4 36.5 - - + -
32F LEU* 3.6 23.6 - - + -
34F LEU* 3.8 9.5 - - + -
35F THR* 2.9 35.2 + - - +
38F GLU* 2.7 31.3 + - - -
91F TYR 3.3 26.0 - - - -
92F ASP* 3.0 12.9 + - - +
94F SER* 1.3 75.7 - - - +
96F ALA* 1.3 65.1 + - - +
99F ALA* 2.8 28.6 + - - +
106F LEU* 3.9 20.6 - - + -
113F LEU* 4.3 7.2 - - + -
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Residues in contact with ALA 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F VAL* 4.3 2.9 - - + -
86F ARG* 4.2 14.4 - - - +
88F LEU* 4.1 14.1 - - + -
92F ASP 3.2 9.3 + - - +
93F ALA* 3.7 7.6 - - - +
95F TYR* 1.3 77.1 - - - +
97F TYR* 1.3 58.1 + - - +
99F ALA* 3.8 0.3 - - - +
100F GLU* 2.8 37.0 + - - +
106F LEU* 4.0 1.0 - - - +
113F LEU* 4.0 4.5 - - + +
117F THR* 3.6 32.1 - - + +
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Residues in contact with TYR 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F PRO* 3.8 17.7 - - + -
75F PRO* 3.6 24.0 - - + +
78F GLU* 3.1 47.8 + - + +
79F VAL* 4.4 9.4 - - + -
82F VAL* 4.1 23.7 - - + +
86F ARG* 6.3 0.4 - - - +
93F ALA 2.9 21.4 + - - +
94F SER 3.8 2.2 - - - +
96F ALA* 1.3 70.6 - - - +
98F VAL* 1.3 63.1 + - + +
100F GLU* 4.8 2.7 - - - -
101F SER* 2.7 61.3 + - - -
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Residues in contact with VAL 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F LEU* 3.6 13.9 - - + -
32F LEU* 3.6 15.7 - - + -
71F LEU* 3.5 34.1 - - + -
72F GLU 4.5 4.3 - - - +
74F PRO* 3.0 39.5 - - + -
94F SER 3.0 15.1 + - - +
97F TYR* 1.3 80.0 - - + +
99F ALA* 1.3 59.2 + - - +
101F SER* 4.5 2.0 - - - -
102F SER* 2.8 38.9 + - - +
104F LEU* 4.7 0.7 - - + -
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Residues in contact with ALA 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F LEU* 3.7 11.4 - - + +
95F TYR 2.8 22.8 + - - +
96F ALA* 3.8 2.0 - - - +
98F VAL* 1.3 75.1 - - - +
100F GLU* 1.3 62.9 + - - +
103F GLY 3.2 0.9 + - - -
104F LEU* 2.8 45.7 + - - +
106F LEU* 3.5 35.0 - - + +
117F THR* 4.6 2.7 - - + -
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Residues in contact with GLU 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F ARG* 2.7 46.7 + - - -
96F ALA 2.8 20.5 + - - +
97F TYR* 3.9 3.3 - - - +
99F ALA* 1.3 75.3 - - - +
101F SER* 1.3 62.4 + - - +
103F GLY* 3.2 10.0 + - - -
104F LEU 4.9 1.6 - - - -
116F LYS 4.2 0.2 - - - +
117F THR* 3.9 3.7 - - + -
118F LYS* 3.1 63.0 + - + +
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Residues in contact with SER 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F TYR* 2.7 53.0 + - - -
98F VAL* 3.8 2.5 - - - -
100F GLU* 1.3 71.5 - - - +
102F SER* 1.3 61.1 + - - +
103F GLY* 2.9 10.6 + - - -
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Residues in contact with SER 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F LEU* 5.1 2.5 - - - +
98F VAL* 2.8 27.8 + - - +
101F SER* 1.3 71.1 + - - +
103F GLY* 1.3 64.0 + - - +
104F LEU* 3.1 27.8 + - - +
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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
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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