Contacts of the strand formed by residues 151 - 156 (chain I) in PDB entry 3IT8
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 151 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93H LEU 5.1 0.2 - - - -
94H LEU* 3.4 18.7 - - + +
95H SER 5.2 0.2 - - - -
120H LEU* 4.1 2.4 - - - +
121H GLY 3.0 40.4 + - - -
15I HIS* 3.4 34.3 - + + +
16I VAL 3.3 11.4 - - - +
17I VAL* 4.7 3.4 - - + -
28I TRP* 3.7 5.4 - - - -
59I TYR* 3.7 13.7 - + - -
60I SER* 2.9 6.8 + - - -
61I GLN* 2.8 77.6 + - + +
119I TYR* 3.6 5.5 - + - -
148I GLY* 3.5 23.3 - - - -
150I VAL* 1.3 79.2 - - - +
152I PHE* 1.3 62.2 + - - +
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Residues in contact with PHE 152 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I ALA 4.5 0.2 - - - -
15I HIS* 3.5 1.5 - - - -
16I VAL* 2.7 45.0 + - + +
28I TRP* 3.6 35.4 - + + -
46I ASN 5.2 1.3 - - - -
48I LEU* 3.4 37.8 - - + +
58I ILE* 4.1 20.9 - - + -
59I TYR* 3.3 17.0 - - - -
60I SER* 4.0 2.9 - - - +
80I ILE* 4.3 5.8 - - + -
132I LEU* 3.9 33.7 - - + -
133I SER 4.1 1.1 - - - -
134I ALA* 3.5 32.8 - - + -
151I TYR* 1.3 77.9 - - - +
153I GLY* 1.3 68.1 + - - +
154I ILE* 4.6 0.4 - - + -
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Residues in contact with GLY 153 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I ALA 2.9 15.0 - - - -
48I LEU* 4.4 2.9 - - - -
58I ILE* 4.0 0.5 - - - +
59I TYR* 2.9 50.6 + - - +
152I PHE* 1.3 78.3 - - - +
154I ILE* 1.3 72.6 + - - +
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Residues in contact with ILE 154 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123H VAL* 5.5 0.2 - - - -
13I VAL* 3.3 6.2 - - - +
14I ALA* 2.8 43.6 + - + +
41I VAL* 4.7 13.7 - - + -
48I LEU* 4.1 22.7 - - + -
50I VAL* 4.0 18.4 - - + -
56I TYR* 4.0 16.6 - - + -
57I LEU 3.0 10.8 - - - +
58I ILE* 3.9 28.5 - - + -
59I TYR* 4.0 3.1 - - - -
132I LEU* 3.9 22.4 - - + -
152I PHE* 4.6 1.1 - - + -
153I GLY* 1.3 81.3 - - - +
155I ILE* 1.3 60.9 + - - +
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Residues in contact with ILE 155 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H LEU* 4.0 17.3 - - + -
123H VAL* 3.9 26.7 - - + -
157H LEU* 3.7 28.3 - - + -
11I LYS* 4.2 14.8 - - + -
12I PRO 3.8 3.4 - - - +
13I VAL* 3.5 28.3 - - + -
56I TYR* 3.5 4.2 - - - -
57I LEU* 2.9 52.9 + - + +
59I TYR* 5.2 0.2 - - + -
154I ILE* 1.3 76.2 - - - +
156I ALA* 1.3 74.8 + - - +
157I LEU* 3.4 5.4 + - + -
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Residues in contact with ALA 156 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I LYS* 3.2 29.5 + - + +
12I PRO* 3.1 45.9 + - + +
54I GLY* 6.5 0.2 - - - -
55I LEU 3.7 6.7 - - - +
56I TYR* 3.7 18.1 - - + -
155I ILE* 1.3 73.0 - - - +
157I LEU* 1.3 61.0 + - - +
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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