Contacts of the strand formed by residues 108 - 115 (chain E) in PDB entry 4DOH
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 TYR 108 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45E PHE* 5.2 2.2 - - + -
73E TYR* 4.9 3.1 - + + -
74E PHE 3.4 10.3 - - - +
75E ILE* 3.7 31.0 - - + -
100E GLU 3.6 18.1 + - - -
101E THR* 3.3 40.5 - - + -
102E SER 3.9 0.2 + - - -
103E ASP* 2.8 50.1 + - - +
106E HIS* 3.4 19.7 + + + +
107E GLN* 1.3 78.0 - - - +
109E TYR* 1.3 69.8 + - - +
128E ARG* 3.6 5.5 - - - +
129E PHE* 2.9 43.7 + + + +
131E PRO* 3.7 14.8 - - + -
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Residues in contact with TYR 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C GLN* 4.4 9.2 + - - +
57C ASP* 4.6 2.6 + - - -
60C ILE* 3.8 31.1 - - + +
45E PHE* 4.6 3.6 - - - -
73E TYR* 3.6 4.3 - - - +
74E PHE* 3.0 45.4 + + + +
76E TYR* 3.9 26.4 - + + -
81E TRP* 4.1 7.9 - - + -
108E TYR* 1.3 82.1 - - - +
110E ALA* 1.3 65.3 + - - +
125E GLU* 4.6 11.9 - - + -
126E SER* 3.5 27.1 - - - -
127E GLY* 4.1 1.1 - - - -
128E ARG* 3.0 58.7 + - + +
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Residues in contact with ALA 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E ILE* 5.7 0.7 - - - -
45E PHE* 3.7 22.2 - - + -
54E LEU* 4.1 20.9 - - + -
72E GLN 3.2 13.5 - - - +
73E TYR* 4.4 0.9 - - - -
81E TRP* 3.9 4.0 - - - -
97E LEU* 4.2 9.6 - - + -
109E TYR* 1.3 76.9 - - - +
111E ARG* 1.3 64.3 + - - +
125E GLU* 3.6 3.5 - - - +
126E SER* 2.8 33.2 + - - +
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Residues in contact with ARG 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E ILE* 5.6 0.9 - - - -
54E LEU* 5.3 0.9 - - - -
71E VAL* 3.1 6.6 - - - +
72E GLN* 2.7 61.4 + - + +
81E TRP* 3.4 58.4 - - + +
110E ALA* 1.3 75.3 - - - +
112E VAL* 1.3 63.2 + - - +
123E TRP* 3.5 51.0 - - + +
124E ALA 2.7 24.0 - - - +
125E GLU* 3.9 6.7 - - - -
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Residues in contact with VAL 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E PRO* 3.9 12.3 - - + +
43E ILE* 4.3 15.9 - - + -
54E LEU* 4.9 1.1 - - + -
56E TRP* 3.9 42.0 - - + +
69E TYR* 3.9 15.0 - - + -
70E THR 3.2 17.0 - - - +
71E VAL* 4.0 7.4 - - + -
111E ARG* 1.3 78.8 - - - +
113E ARG* 1.3 62.9 + - - +
123E TRP* 3.6 4.4 - - - -
124E ALA* 2.7 51.7 + - + +
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Residues in contact with ARG 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E PRO* 4.0 7.4 - - - -
69E TYR* 3.1 4.4 - - - -
70E THR* 2.9 54.0 + - - +
112E VAL* 1.3 76.5 - - - +
114E ALA* 1.3 60.2 + - - +
115E ILE* 4.1 4.8 - - + +
120E CYS* 4.2 32.0 - - - +
121E SER 3.3 5.6 - - - +
122E LYS 3.0 28.9 + - - +
123E TRP* 3.6 37.0 - - + +
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Residues in contact with ALA 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E LYS 4.2 7.6 - - - +
40E PRO* 3.8 7.2 - - + +
59E PRO* 3.8 20.0 - - + -
67E VAL* 4.4 10.3 - - + -
68E THR 3.1 6.1 - - - +
69E TYR* 3.4 27.1 - - + -
113E ARG* 1.3 75.4 - - - +
115E ILE* 1.3 63.3 + - - +
119E LYS 4.5 0.3 - - - +
120E CYS* 3.6 3.3 - - - +
121E SER* 3.3 26.0 + - - +
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Residues in contact with ILE 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E LYS* 4.1 2.4 - - + +
67E VAL* 3.3 11.1 - - - +
68E THR* 2.5 56.4 + - - +
69E TYR 4.3 0.4 - - - +
70E THR* 4.4 15.5 - - + +
89E ASN* 3.1 33.9 - - - +
113E ARG* 4.1 13.5 - - - +
114E ALA* 1.3 80.0 - - - +
116E TRP* 1.3 72.9 + - - +
117E GLY 5.1 4.0 - - - +
119E LYS 4.0 3.8 - - - -
120E CYS* 3.8 20.9 - - - -
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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