Contacts of the strand formed by residues 146 - 149 (chain B) in PDB entry 3U1J
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 VAL 146 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A VAL* 4.1 13.9 - - + -
40B VAL* 4.3 17.3 - - + -
85B LEU* 3.8 37.4 - - + +
87B ALA* 3.5 11.7 + - - +
138B PRO* 3.9 25.1 - - + -
139B ILE 3.4 6.5 - - - +
140B ILE* 4.1 7.0 - - + -
145B LYS* 1.3 72.8 - - - +
147B VAL* 1.3 57.7 + - - +
148B GLY 3.4 26.7 - - - +
149B LEU* 4.1 3.1 - - + -
167B GLN* 3.4 14.2 + - - -
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ALA* 3.6 10.3 - - + +
88B GLN 3.7 21.8 - - - +
89B TRP* 3.6 30.4 + - + +
95B VAL* 4.3 9.0 - - + -
139B ILE* 2.8 38.6 + - + +
140B ILE* 4.3 1.3 - - - +
141B ASN* 3.9 29.4 - - + +
145B LYS 3.4 3.1 + - - +
146B VAL* 1.3 73.9 - - - +
148B GLY* 1.3 57.0 + - - +
165B ILE* 3.5 10.1 - - + +
167B GLN* 3.3 25.9 + - - +
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Residues in contact with GLY 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 6.0 0.7 - - - -
139B ILE* 2.8 30.9 + - - -
146B VAL* 3.4 12.5 - - - +
147B VAL* 1.3 80.5 - - - +
149B LEU* 1.3 66.2 + - - +
165B ILE* 3.7 9.6 - - - -
166B ALA 3.1 14.1 - - - -
167B GLN* 4.2 5.4 - - - -
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Residues in contact with LEU 149 (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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40B VAL* 4.1 13.9 - - + -
47B HIS* 4.3 3.1 - - + +
48B THR* 3.6 40.4 - - - +
49B MET* 3.9 18.3 - - + +
76B LEU* 4.1 9.4 - - + -
83B TRP* 4.1 12.8 - - + -
85B LEU* 4.5 5.2 - - + -
136B GLY* 3.5 22.0 - - - +
137B SER 3.7 2.2 - - - +
138B PRO* 4.0 9.4 - - + -
139B ILE* 3.5 4.3 - - - -
146B VAL* 4.1 7.6 - - + -
148B GLY* 1.3 82.7 - - - +
150B TYR* 1.3 62.3 + - - +
151B GLY 4.1 0.2 + - - -
164B GLY 3.6 4.7 - - - +
166B ALA* 2.9 38.7 + - - +
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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