Contacts of the strand formed by residues 106 - 111 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92I LYS* 4.1 17.0 - - + +
95I LEU* 3.9 35.2 + - + +
96I GLN* 3.8 33.7 - - + +
104I VAL 3.8 3.0 + - - -
105I LYS* 1.3 81.2 - - - +
107I GLU* 1.3 61.5 + - - +
108I PHE 3.2 26.9 - - - +
109I SER* 4.6 4.7 - - - +
118I MET* 3.6 28.5 - - + -
119I VAL 3.6 8.7 - - - +
120I MET* 4.2 5.8 - - + -
351I G98 5.2 0.4 - - + -
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Residues in contact with GLU 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I THR* 4.4 2.3 + - - +
69I TYR* 3.6 32.8 + - + -
105I LYS* 3.9 20.1 - - - +
106I LEU* 1.3 77.7 - - - +
108I PHE* 1.3 90.9 + - + +
119I VAL 2.6 17.0 + - - +
120I MET* 4.1 3.1 - - - -
121I GLU* 3.6 22.3 - - - +
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Residues in contact with PHE 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I THR* 3.3 34.3 - - - +
38I ALA* 3.7 17.9 - - + -
42I GLN* 5.8 1.1 - - - -
43I PHE* 3.8 26.2 - + - -
62I HIS* 4.9 15.3 - + - -
69I TYR* 4.3 19.7 - + - -
106I LEU* 3.2 13.8 - - - +
107I GLU* 1.3 101.0 - - + +
109I SER* 1.3 59.2 + - - +
119I VAL* 2.8 43.2 + - + -
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Residues in contact with SER 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I ALA 4.5 5.0 + - - -
35I GLN* 4.7 0.9 - - - -
36I ASN 3.2 7.6 + - - -
37I THR* 3.0 29.8 + - - -
92I LYS* 3.5 31.8 + - - +
106I LEU* 4.6 5.8 - - - +
108I PHE* 1.3 78.9 - - - +
110I PHE* 1.3 66.2 + - - +
117I TYR 3.2 15.5 - - - -
118I MET* 4.1 13.0 - - - -
350I PHE* 4.3 2.5 + - - -
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Residues in contact with PHE 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36I ASN* 4.0 18.6 - - - +
38I ALA* 3.3 46.2 - - + +
39I HIS* 3.7 3.4 - + - -
40I LEU* 3.4 35.2 - - + -
43I PHE* 3.9 13.5 - + - -
71I MET* 4.5 4.0 - - + -
109I SER* 1.3 82.2 - - - +
111I LYS* 1.3 64.7 + - - +
112I ASP* 5.9 0.4 - - + -
117I TYR* 2.7 78.2 + + + +
119I VAL* 4.1 10.3 - - + -
350I PHE* 3.7 8.5 - - - -
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Residues in contact with LYS 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ARG* 5.5 3.8 - - - +
35I GLN* 5.5 0.2 + - - -
36I ASN* 5.2 3.6 + - - +
76I LYS* 4.9 6.3 - - - +
110I PHE* 1.3 82.2 - - - +
112I ASP* 1.3 67.3 + - - +
115I ASN 3.2 14.6 - - - +
116I LEU* 3.9 15.9 - - + -
117I TYR* 4.1 3.6 - - - -
341I GLU* 5.8 4.0 - - - -
344I GLY 5.2 1.2 + - - -
347I PHE* 2.5 31.3 + - + +
348I SER* 3.4 16.4 + - - +
350I PHE* 2.9 30.4 + - + +
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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