Contacts of the strand formed by residues 106 - 111 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LYS* 4.0 24.0 - - + +
95A LEU* 3.8 44.2 + - + +
96A GLN* 3.9 21.6 - - + +
104A VAL 3.9 2.0 + - - -
105A LYS* 1.3 73.0 - - - +
107A GLU* 1.3 63.1 + - - +
108A PHE 3.1 29.4 - - - +
109A SER* 4.3 7.2 - - - -
118A MET* 3.9 12.6 - - + -
119A VAL 3.7 9.2 - - - +
120A MET* 3.7 24.5 - - - +
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Residues in contact with GLU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A THR* 4.7 0.9 + - - -
67A ASN* 5.7 0.7 + - - -
69A TYR* 3.7 30.6 + - + -
105A LYS* 3.8 28.1 - - - +
106A LEU* 1.3 75.9 - - - +
108A PHE* 1.3 79.4 + - + +
119A VAL 2.7 16.4 + - - +
121A GLU* 3.7 34.0 - - - +
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Residues in contact with PHE 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A THR* 3.4 24.5 - - - +
38A ALA* 3.7 28.7 - - + -
42A GLN* 5.8 1.3 - - - -
43A PHE* 3.9 15.0 - + - -
62A HIS* 4.6 14.1 - + - -
65A THR* 6.5 0.2 - - + -
69A TYR* 3.6 33.2 - + - -
106A LEU* 3.1 11.4 - - - +
107A GLU* 1.3 92.6 - - + +
109A SER* 1.3 60.8 + - - +
110A PHE* 4.7 0.4 - - + -
119A VAL* 2.8 42.3 + - + -
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Residues in contact with SER 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ALA 4.2 6.2 + - - -
36A ASN* 3.5 3.4 + - - -
37A THR* 2.9 32.7 + - - +
92A LYS* 3.3 26.7 + - - -
96A GLN* 5.9 0.3 - - - +
106A LEU* 4.3 14.8 - - - -
108A PHE* 1.3 75.5 - - - +
110A PHE* 1.3 66.1 + - - +
117A TYR 3.3 14.1 - - - -
118A MET* 4.6 0.2 - - - -
350A PHE* 4.0 16.3 + - - -
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Residues in contact with PHE 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ASN* 3.3 19.7 - - - +
38A ALA* 3.2 33.0 - - + +
39A HIS* 4.2 2.7 - + - -
40A LEU* 3.3 36.8 - - + -
43A PHE* 3.6 22.0 - + - -
71A MET* 3.4 25.6 - - + -
109A SER* 1.3 82.2 - - - +
111A LYS* 1.3 67.1 + - - +
112A ASP* 6.0 0.7 - - + -
117A TYR* 3.0 56.4 + + + -
119A VAL* 3.7 15.0 - - + -
350A PHE* 3.5 8.8 - - - -
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Residues in contact with LYS 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLN* 3.8 3.1 - - - +
36A ASN* 3.1 24.1 + - - +
76A LYS* 5.0 5.4 - - - +
110A PHE* 1.3 82.5 - - - +
112A ASP* 1.3 64.7 + - - +
115A ASN 3.4 13.5 - - - +
116A LEU* 3.7 17.5 - - + -
117A TYR* 4.3 3.8 - - - -
344A GLY 5.5 0.6 + - - -
347A PHE* 2.9 30.2 + - + +
348A SER* 3.1 18.0 + - - +
350A PHE* 2.9 30.3 + - + +
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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