Contacts of the strand formed by residues 151 - 156 (chain T) in PDB entry 3L9J
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 T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15T HIS* 3.5 35.9 - + + +
16T VAL 3.1 13.9 - - - +
17T VAL* 4.4 3.4 - - + -
28T TRP* 3.5 5.2 - - - -
59T TYR* 3.7 24.7 - + - -
60T SER* 2.8 19.9 + - - -
61T GLN* 2.7 62.3 + - + +
119T TYR* 3.4 19.4 - + - -
148T GLY* 3.4 31.0 - - - -
150T VAL* 1.3 78.5 - - - +
152T PHE* 1.3 61.0 + - - +
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Residues in contact with PHE 152 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15T HIS* 3.5 1.6 + - - -
16T VAL* 2.7 40.5 + - + +
28T TRP* 3.5 37.2 - + + -
46T ASN 5.0 1.3 - - - -
47T GLN 5.1 0.2 - - - -
48T LEU* 3.7 28.9 - - + +
58T ILE* 5.5 0.9 - - + -
59T TYR* 3.4 19.5 - - - -
60T SER* 4.1 3.1 - - - +
80T ILE* 4.3 16.6 - - + -
132T LEU* 3.5 43.5 - - + -
133T SER* 4.0 1.6 - - - -
134T ALA* 3.6 33.0 - - + -
151T TYR* 1.3 78.0 - - - +
153T GLY* 1.3 63.7 + - - +
154T ILE* 4.7 3.8 - - + -
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Residues in contact with GLY 153 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14T ALA 3.0 16.2 - - - -
48T LEU* 4.5 2.5 - - - -
58T ILE* 3.5 0.2 - - - -
59T TYR* 2.9 54.4 + - - +
152T PHE* 1.3 76.7 - - - +
154T ILE* 1.3 70.4 + - - +
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Residues in contact with ILE 154 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13T VAL* 3.3 3.9 - - - +
14T ALA* 2.9 43.8 + - + +
41T VAL* 3.9 32.3 - - + -
48T LEU* 3.9 14.4 - - + -
50T VAL* 4.9 9.0 - - + -
56T TYR* 3.9 23.3 - - + -
57T LEU 3.1 9.6 - - - +
58T ILE* 3.9 13.0 - - + -
59T TYR* 4.0 0.4 - - - -
132T LEU* 3.6 32.5 - - + -
152T PHE* 4.7 2.5 - - + -
153T GLY* 1.3 80.4 - - - +
155T ILE* 1.3 66.8 + - - +
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Residues in contact with ILE 155 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11T LYS* 4.5 12.8 - - + +
12T PRO 3.8 3.6 - - - +
13T VAL* 4.5 16.6 - - + +
56T TYR* 3.4 4.3 - - - -
57T LEU* 2.8 61.3 + - + +
59T TYR* 4.5 14.1 - - + -
154T ILE* 1.3 80.0 - - - +
156T ALA* 1.3 77.0 + - - +
157T LEU* 3.4 8.1 + - + +
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Residues in contact with ALA 156 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11T LYS* 2.9 29.5 - - + +
12T PRO* 2.8 42.6 + - + +
55T LEU 3.6 2.0 - - - +
56T TYR* 3.5 30.0 - - + -
155T ILE* 1.3 75.9 - - - +
157T LEU* 1.3 62.9 + - - +
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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