Contacts of the strand formed by residues 106 - 111 (chain B) in PDB entry 4AE6
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 LEU 106 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B LYS* 4.0 13.7 - - + +
95B LEU* 3.8 32.0 + - + +
96B GLN* 3.8 35.6 - - + +
104B VAL 3.7 3.6 + - - -
105B LYS* 1.3 74.4 - - - +
107B GLU* 1.3 64.1 + - - +
108B PHE 3.4 25.6 - - - +
109B SER* 4.6 6.7 - - - +
118B MET* 3.7 26.5 - - + -
119B VAL 3.9 2.9 - - - +
120B MET* 3.6 24.9 - - + +
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Residues in contact with GLU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B THR* 4.5 1.4 + - - -
69B TYR* 3.6 40.7 + - + -
105B LYS* 3.0 35.0 - - + +
106B LEU* 1.3 76.5 - - - +
108B PHE* 1.3 77.3 + - + +
119B VAL 2.8 13.6 + - - +
121B GLU* 3.9 19.1 - - - +
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Residues in contact with PHE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B THR* 3.4 21.3 - - - +
38B ALA* 3.8 26.2 - - + -
43B PHE* 3.8 15.5 - + - -
62B HIS* 3.7 24.7 - + - -
65B THR* 6.0 0.9 - - + -
69B TYR* 3.7 37.5 - + - -
106B LEU* 3.4 12.0 - - - +
107B GLU* 1.3 93.7 - - + +
109B SER* 1.3 58.7 + - - +
110B PHE* 4.9 0.4 - - + -
119B VAL* 2.8 45.4 + - + -
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Residues in contact with SER 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ALA 4.5 3.3 + - - -
36B ASN* 3.4 4.4 + - - -
37B THR* 2.8 33.5 + - - +
92B LYS* 3.2 31.3 + - - -
106B LEU* 4.6 5.9 - - - +
108B PHE* 1.3 74.9 - - - +
110B PHE* 1.3 67.5 + - - +
117B TYR 3.3 12.3 - - - -
118B MET* 4.5 3.8 - - - -
350B PHE* 3.8 18.6 + - - -
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Residues in contact with PHE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ASN* 3.8 19.1 - - - +
38B ALA* 3.3 31.9 - - + +
39B HIS* 4.1 2.9 - + - -
40B LEU* 3.2 42.0 - - + -
43B PHE* 3.7 28.0 - + - -
71B MET* 4.6 3.1 - - - -
108B PHE* 4.9 0.2 - - + -
109B SER* 1.3 83.3 - - - +
111B LYS* 1.3 64.8 + - - +
112B ASP* 5.9 0.9 - - + -
117B TYR* 2.7 84.8 + + + +
119B VAL* 3.9 14.6 - - + -
350B PHE* 3.4 7.9 - - - -
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Residues in contact with LYS 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLN* 4.5 1.2 + - - -
36B ASN* 3.4 22.7 + - - +
76B LYS* 5.0 6.7 - - - +
110B PHE* 1.3 82.1 - - - +
112B ASP* 1.3 65.5 + - - +
115B ASN 3.2 14.1 - - - +
116B LEU* 3.8 17.3 - - + -
117B TYR* 4.1 3.8 - - - -
341B GLU* 6.0 1.6 - - - -
344B GLY 5.2 1.4 + - - -
347B PHE* 2.7 33.2 + - + +
348B SER* 3.4 14.5 + - - +
350B PHE* 3.1 30.8 + - + +
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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