Contacts of the strand formed by residues 103 - 108 (chain B) in PDB entry 1EE8
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 ARG 103 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ALA 4.8 3.1 + - - -
32B ARG* 3.4 40.3 - - - +
33B TYR* 4.2 2.2 - - - -
34B ARG* 6.3 0.2 - - - -
65B VAL 4.4 0.4 - - - -
67B HIS* 2.9 43.5 + - + +
95B PHE* 3.9 2.3 - - - -
100B ARG 3.0 23.4 + - - -
101B PHE* 3.2 18.4 + - - +
102B GLY* 1.3 98.8 + - - +
104B LEU* 1.3 71.5 + - - +
105B PHE* 3.5 30.7 - - + -
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Residues in contact with LEU 104 (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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25B VAL* 4.0 25.6 - - + -
32B ARG 3.1 7.9 + - - +
33B TYR* 3.6 31.0 - - + -
34B ARG 2.8 26.0 + - - -
36B THR* 4.1 7.4 - - + -
64B LEU* 4.4 15.9 - - + -
65B VAL 3.2 4.3 - - - +
66B ALA* 3.7 24.0 - - + -
74B PHE* 4.6 6.5 - - + -
84B ALA* 4.1 15.7 - - + -
86B LEU* 4.5 7.0 - - + -
95B PHE* 3.8 15.5 - - + -
103B ARG* 1.3 81.5 - - - +
105B PHE* 1.3 67.7 + - - +
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Residues in contact with PHE 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ARG 5.2 0.7 - - - -
34B ARG* 3.4 26.9 - - + -
53B PHE* 4.9 1.3 - + - -
63B GLU 3.4 2.6 - - - +
64B LEU* 3.5 3.5 - - - +
65B VAL* 2.8 51.5 + - + +
67B HIS* 4.8 8.1 - - + -
103B ARG* 3.5 36.6 - - + -
104B LEU* 1.3 80.7 - - - +
106B GLY* 1.3 62.5 + - - +
107B VAL* 3.5 7.8 + - + -
114B GLU* 4.2 19.3 - - + -
115B ILE* 3.8 49.1 - - + -
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Residues in contact with GLY 106 (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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34B ARG 2.8 12.4 + - - +
35B ASN* 3.4 37.2 + - - +
36B THR* 4.5 1.5 - - - +
38B LEU* 3.7 15.3 - - - +
39B ALA* 5.1 3.4 - - - -
62B VAL* 5.3 0.2 - - - -
63B GLU 3.7 5.6 - - - -
64B LEU* 4.4 9.7 - - - +
105B PHE* 1.3 71.2 - - - +
107B VAL* 1.3 63.4 + - - +
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Residues in contact with VAL 107 (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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35B ASN* 6.1 0.4 - - - +
38B LEU* 3.8 9.5 - - - +
62B VAL* 3.2 6.1 - - - +
63B GLU* 2.8 48.6 + - + +
65B VAL* 4.0 19.3 - - + -
105B PHE* 4.0 19.1 - - + +
106B GLY* 1.3 80.2 - - - +
108B ARG* 1.3 71.7 + - - +
111B ASP* 3.5 25.6 - - + +
112B TYR* 4.3 6.5 - - + -
114B GLU* 6.1 4.9 - - + -
115B ILE* 4.3 8.1 - - + -
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Residues in contact with ARG 108 (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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24A GLN* 5.2 8.0 - - - +
25A VAL 5.3 2.8 + - - -
36A THR* 5.6 1.6 + - - -
37A ALA* 3.4 25.1 - - - +
40A GLU* 2.8 38.8 + - + +
38B LEU* 4.2 5.2 - - + +
61B GLY 3.7 12.8 - - - +
62B VAL* 4.4 6.1 - - + +
107B VAL* 1.3 79.1 - - - +
109B ARG* 1.3 72.2 + - - +
110B GLY 3.1 0.5 + - - -
111B ASP* 2.9 32.2 + - + +
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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