Contacts of the strand formed by residues 133 - 140 (chain E) in PDB entry 5IJ7
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 PHE 133 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 4.3 11.0 - - + -
83E PHE* 3.8 7.3 - - - -
102E VAL* 3.8 22.6 - - + -
103E GLY* 3.9 11.3 + - - +
104E SER 2.9 9.7 + - - +
105E ASN* 3.5 39.0 - - - -
106E ARG 3.6 10.3 - - - +
107E VAL* 4.0 15.5 - - + -
126E ASP* 3.4 25.8 - - + -
131E GLU* 3.6 21.1 - - + -
132E ASN* 1.3 79.9 - - - +
134E TYR* 1.3 61.0 + - - +
135E THR 4.8 0.2 - - - +
151E VAL* 3.8 19.7 - - + -
152E ALA* 3.7 27.4 - - - +
153E GLY 4.1 0.4 - - - -
157E ILE 5.2 1.3 - - - -
159E ARG* 4.4 7.2 - - + -
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Residues in contact with TYR 134 (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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83E PHE* 3.4 48.6 - + - +
84E GLY* 3.8 1.0 + - - -
102E VAL* 3.7 5.4 - - - -
132E ASN* 3.6 27.8 + - - +
133E PHE* 1.3 82.1 - - - +
135E THR* 1.3 60.8 + - - +
152E ALA 3.0 4.4 + - - -
153E GLY* 3.9 5.2 - - - -
154E SER* 3.4 34.0 - - - -
178E ALA* 4.1 10.7 - - + +
179E ILE 3.6 23.8 - - - +
180E ASN* 3.9 14.1 - - - +
350E TRP* 6.6 0.2 - + - -
351E TYR* 3.4 25.6 + + + +
353E ARG* 4.7 2.3 + - - -
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Residues in contact with THR 135 (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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84E GLY* 5.1 2.7 - - - -
102E VAL* 3.7 10.3 - - - +
133E PHE* 4.8 0.2 - - - +
134E TYR* 1.3 81.5 - - - +
136E CYS* 1.3 72.7 + - - +
151E VAL* 3.4 3.5 - - - +
152E ALA 3.2 34.2 + - - +
179E ILE* 4.1 7.4 - - + +
180E ASN 3.7 14.5 + - - +
181E GLU* 3.7 20.8 + - - +
182E LEU* 3.4 43.6 + - + +
353E ARG* 5.5 1.5 + - - -
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Residues in contact with CYS 136 (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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84E GLY* 4.9 3.3 - - - -
85E VAL 4.7 2.5 - - - -
86E GLN* 3.2 47.9 - - - +
100E ALA* 4.2 22.2 - - - -
102E VAL* 3.8 16.6 - - + +
135E THR* 1.3 82.2 + - - +
137E ALA* 1.3 64.3 + - - +
149E LEU* 4.1 6.5 - - + -
150E ALA 3.0 15.3 - - - +
151E VAL* 3.7 14.8 - - + +
182E LEU* 4.2 5.5 - - - +
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Residues in contact with ALA 137 (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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86E GLN* 4.5 8.3 - - - +
136E CYS* 1.3 77.9 - - - +
138E TRP* 1.3 59.2 + - - +
149E LEU* 3.5 6.2 - - - -
150E ALA* 2.8 32.4 + - + +
182E LEU* 3.7 27.1 - - + +
183E LYS* 4.4 3.8 - - - -
184E PHE* 3.5 27.6 - - + +
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Residues in contact with TRP 138 (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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68A VAL* 4.4 3.1 - - + -
86E GLN* 3.0 33.9 + - + +
87E PHE 3.4 19.5 - - - +
88E ASN* 3.6 33.2 - - + +
89E TRP 5.2 0.4 - - - +
90E HIS* 3.3 23.4 - - + +
98E VAL* 3.9 21.3 - - + -
99E PHE 4.2 0.7 - - - -
100E ALA* 3.6 26.7 - - + +
109E LEU* 3.8 24.5 - - + -
137E ALA* 1.3 73.5 - - - +
139E THR* 1.3 61.8 + - - +
147E PRO* 4.2 16.2 - - + -
148E LEU 3.3 19.3 - - - -
149E LEU* 3.6 24.7 - - + +
163E PRO* 4.3 10.8 - - + -
184E PHE* 3.6 12.5 - - - +
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Residues in contact with THR 139 (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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90E HIS* 3.5 17.9 + - - -
138E TRP* 1.3 75.3 - - - +
140E TYR* 1.3 70.7 + - - +
147E PRO* 3.4 6.8 - - - +
148E LEU* 2.8 51.6 + - + +
160E ILE* 5.4 0.9 - - + -
184E PHE* 3.4 39.2 - - + +
189E PRO* 2.7 32.9 + - - +
206E ILE* 5.4 2.7 - - + -
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Residues in contact with TYR 140 (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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63A ARG* 3.4 47.0 + - - -
65A ILE* 3.6 32.8 - - + -
90E HIS* 3.5 29.8 - + + -
139E THR* 1.3 82.5 + - - +
141E ASP* 1.3 70.5 + - - +
142E SER* 3.7 12.4 + - - -
145E SER* 5.6 0.2 - - - -
146E HIS 3.3 9.4 - - - +
147E PRO* 4.6 0.7 - - + -
148E LEU* 4.2 7.8 - - - +
187E ARG 4.4 4.9 + - - -
189E PRO* 3.4 54.3 - - + +
190E ASN* 5.0 2.4 - - - +
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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