Contacts of the strand formed by residues 106 - 111 (chain L) in PDB entry 3E8E
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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92L LYS* 4.4 10.5 - - + +
95L LEU* 4.1 43.4 + - + +
96L GLN* 4.2 21.6 - - + -
104L VAL 3.9 2.8 + - - -
105L LYS* 1.3 79.1 - - - +
107L GLU* 1.3 63.9 + - - +
108L PHE* 3.3 24.7 - - - +
109L SER* 4.3 19.1 - - - +
118L MET* 3.6 26.0 - - + -
119L VAL 3.4 10.8 - - - +
120L MET* 4.2 6.7 - - + +
351L G98 5.1 0.9 - - + -
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Residues in contact with GLU 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37L THR* 4.3 2.4 + - - +
69L TYR* 3.5 34.9 + - + -
105L LYS* 3.9 13.5 - - - +
106L LEU* 1.3 80.0 - - - +
108L PHE* 1.3 93.0 + - + +
119L VAL* 2.5 18.5 + - + +
120L MET 4.2 2.2 - - - -
121L GLU* 3.7 23.9 - - - +
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Residues in contact with PHE 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37L THR* 3.3 33.4 - - - +
38L ALA* 4.0 16.8 - - + -
42L GLN* 6.0 0.2 - - - -
43L PHE* 3.9 24.0 - + - -
62L HIS* 4.7 13.0 - + - -
69L TYR* 4.5 19.3 - + - -
106L LEU* 3.3 11.6 - - - +
107L GLU* 1.3 106.4 - - + +
109L SER* 1.3 60.0 + - - +
110L PHE* 4.8 1.6 - - + -
119L VAL* 2.7 46.3 + - + -
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Residues in contact with SER 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34L ALA* 3.9 14.2 + - - +
35L GLN* 4.7 1.2 - - - -
36L ASN 3.3 6.7 + - - -
37L THR* 3.0 31.7 + - - +
92L LYS* 3.7 37.2 - - - +
96L GLN* 5.7 1.0 - - - +
106L LEU* 4.3 8.8 - - - +
108L PHE* 1.3 73.2 - - - +
110L PHE* 1.3 64.5 + - - +
117L TYR 3.3 11.4 - - - -
118L MET* 4.6 1.8 - - - -
350L PHE* 4.3 5.8 - - - -
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Residues in contact with PHE 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36L ASN* 3.6 17.0 - - - +
38L ALA* 3.0 35.2 - - + +
39L HIS* 3.8 5.8 - - - -
40L LEU* 3.4 34.8 - - + -
43L PHE* 3.9 19.1 - + - -
71L MET* 3.9 12.1 - - + -
108L PHE* 4.8 0.2 - - + -
109L SER* 1.3 81.5 - - - +
111L LYS* 1.3 70.6 + - - +
112L ASP* 5.3 0.9 - - - -
117L TYR* 2.8 67.7 + + + +
119L VAL* 4.1 12.1 - - + -
350L PHE* 3.4 9.7 - - - -
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Residues in contact with LYS 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L ASN* 4.5 7.6 + - - +
76L LYS* 4.9 8.1 - - - +
110L PHE* 1.3 85.3 - - - +
112L ASP* 1.3 69.5 + - - +
115L ASN 3.4 14.6 - - - +
116L LEU* 4.1 19.7 - - + -
117L TYR* 4.0 4.5 - - - -
341L GLU* 6.0 2.0 - - - -
344L GLY 4.9 3.0 + - - -
347L PHE* 2.5 40.2 + - + +
348L SER* 3.8 10.9 + - - +
350L PHE* 3.3 24.1 + - + +
194P ARG* 5.5 4.2 - - - +
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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