Contacts of the helix formed by residues 93 - 101 (chain B) in PDB entry 4F4I
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 TYR 93 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B PHE* 3.5 30.2 - + - -
6B THR* 3.6 18.8 - - + +
8B GLU* 3.1 9.7 + - - +
37B GLU* 4.1 3.8 - - - -
70B ARG* 2.8 47.6 + - + +
73B HIS* 6.1 2.2 - + - -
74B LEU* 3.5 17.3 - - + +
78B VAL* 6.4 0.4 - - + -
90B CYS* 4.7 3.4 - - - -
92B ARG* 1.3 82.1 - - - +
94B ILE* 1.3 80.0 + - + +
95B ASP* 3.1 3.6 + - - +
96B SER* 3.3 10.0 + - - -
120B ILE* 3.2 28.5 - - + +
123B LEU 2.8 25.5 + - - -
125B PRO* 3.6 27.1 - - + -
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Residues in contact with ILE 94 (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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70B ARG* 3.7 12.2 - - - +
93B TYR* 1.3 98.8 - - + +
95B ASP* 1.3 90.1 + - - +
97B SER* 2.9 27.9 + - - -
98B LEU* 3.3 14.0 + - + +
113B ARG* 4.7 9.4 - - + +
116B ASN* 3.3 41.5 - - + +
117B GLU 4.6 1.1 - - - +
120B ILE* 4.4 8.7 - - + -
124B TYR* 4.0 34.1 - - + +
125B PRO* 5.1 0.2 - - + -
177B ARG* 4.3 8.1 - - - +
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Residues in contact with ASP 95 (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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6B THR* 4.8 1.0 + - - -
8B GLU* 3.7 16.7 + - + +
93B TYR* 3.1 1.7 + - - +
94B ILE* 1.3 85.1 - - - +
96B SER* 1.3 65.1 + - - +
98B LEU* 3.6 11.8 + - - +
99B ALA* 3.3 19.2 + - - +
113B ARG* 5.8 0.2 + - - -
125B PRO* 5.2 0.5 - - - +
128B THR* 4.0 6.1 + - - +
167B TYR* 3.9 6.4 - - + -
170B ILE* 3.4 23.5 - - + +
177B ARG* 2.5 49.0 + - - -
178B PHE* 3.4 17.3 - - + -
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Residues in contact with SER 96 (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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8B GLU* 3.2 24.9 + - - -
70B ARG* 4.5 3.4 - - - -
92B ARG* 3.8 21.1 + - - +
93B TYR 3.3 11.9 + - - -
95B ASP* 1.3 76.1 - - - +
97B SER* 1.3 57.2 + - - +
99B ALA* 3.1 2.4 + - - -
100B TYR* 2.9 52.6 + - - -
167B TYR* 3.5 8.3 + - - -
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Residues in contact with SER 97 (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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63B ALA* 6.3 0.7 - - - -
66B PHE* 5.3 6.4 - - - +
70B ARG* 2.7 27.1 + - - -
94B ILE 2.9 15.8 + - - -
96B SER* 1.3 71.2 - - - +
98B LEU* 1.3 59.2 + - - -
100B TYR* 5.0 0.9 - - - -
101B GLN* 2.9 47.3 + - - +
102B GLY 3.1 5.4 + - - -
112B VAL* 3.7 6.0 - - - +
116B ASN* 3.6 21.7 + - - -
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Residues in contact with LEU 98 (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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94B ILE* 3.3 17.6 + - + +
95B ASP* 3.7 10.5 - - - +
96B SER 3.4 0.2 - - - -
97B SER* 1.3 78.2 - - - +
99B ALA* 1.3 58.5 + - - +
102B GLY* 3.2 7.1 + - - +
103B TYR* 2.9 28.4 + - - +
109B VAL* 3.2 37.7 - - + +
112B VAL* 3.9 7.4 - - + +
113B ARG* 3.3 55.0 - - + +
116B ASN* 5.2 1.1 - - - +
170B ILE* 3.3 34.5 - - + -
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Residues in contact with ALA 99 (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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95B ASP 3.3 12.7 + - - +
96B SER 3.1 4.9 + - - +
98B LEU* 1.3 78.1 - - - +
100B TYR* 1.3 60.6 + - + +
103B TYR* 4.1 6.7 - - - +
104B ALA* 3.1 26.5 + - - +
163B VAL* 4.1 15.7 - - + +
166B GLY 4.8 1.8 - - - -
167B TYR* 3.9 35.2 - - + +
170B ILE* 4.0 12.6 - - + -
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Residues in contact with TYR 100 (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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9B GLY 4.3 3.4 + - - -
10B PRO* 3.9 17.2 - - - +
11B GLU* 3.5 23.0 + - - -
96B SER* 2.9 42.9 + - - +
97B SER 4.6 0.2 - - - +
99B ALA* 1.3 80.0 - - + +
101B GLN* 1.3 67.5 + - - +
104B ALA* 3.2 4.9 - - - +
105B ARG* 2.8 42.3 + - + +
159B PHE* 4.5 16.2 - + - -
163B VAL* 3.7 33.5 - - + +
167B TYR* 4.1 13.5 - + - -
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Residues in contact with GLN 101 (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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59B ILE* 4.5 4.3 - - + +
62B GLU* 4.1 22.8 + - + +
63B ALA* 3.7 33.3 - - + +
66B PHE* 4.2 16.2 - - - +
97B SER* 2.9 35.0 + - - +
100B TYR* 1.3 84.2 - - - +
102B GLY* 1.3 62.1 - - - +
105B ARG* 3.6 21.9 - - + +
106B GLY 3.5 7.1 + - - -
107B ILE* 3.2 37.9 + - + +
112B VAL* 4.5 6.3 - - + -
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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