Contacts of the strand formed by residues 149 - 154 (chain E) in PDB entry 5JLH
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 GLY 149 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E LEU* 4.4 5.6 - - - -
148E THR* 1.3 76.8 - - - +
150E ILE* 1.3 60.4 + - - -
151E VAL* 3.9 4.2 + - - +
162E VAL 4.0 1.2 - - - +
164E ILE* 2.8 38.2 + - - +
292E LEU* 3.4 9.6 - - - -
295E ASN* 3.3 21.1 - - - -
297E VAL* 5.2 0.7 - - - -
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Residues in contact with ILE 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149E GLY* 1.3 73.4 - - - -
151E VAL* 1.3 63.7 + - - +
152E MET* 3.5 2.3 + - + -
161E THR* 3.7 20.2 - - + -
162E VAL 3.7 2.0 - - - -
163E PRO* 3.9 19.7 - - + -
277E THR* 4.0 10.8 - - + -
280E SER* 3.5 31.9 - - - -
281E ILE* 3.7 25.1 - - + -
292E LEU* 3.6 19.5 - - + +
295E ASN 3.6 3.2 + - - -
296E THR* 3.2 31.1 - - + +
297E VAL 2.9 19.0 + - - -
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Residues in contact with VAL 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E ALA* 3.7 28.1 - - + +
138E VAL* 5.8 0.2 - - - -
140E SER* 3.2 22.2 - - - +
141E LEU* 3.9 35.2 - - + -
149E GLY 4.7 1.1 - - - +
150E ILE* 1.3 75.2 - - - +
152E MET* 1.3 62.8 + - - +
153E ASP* 3.7 1.0 + - + -
160E HIS 3.9 0.3 - - - +
161E THR* 3.4 5.1 - - - +
162E VAL 3.0 33.8 + - - +
164E ILE* 5.8 1.1 - - + -
297E VAL* 3.2 22.9 - - + +
299E SER* 4.1 13.7 - - - +
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Residues in contact with MET 152 (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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150E ILE* 3.5 3.2 + - + +
151E VAL* 1.3 71.0 - - - +
153E ASP* 1.3 59.0 + - - +
154E SER* 4.7 8.5 - - - +
159E THR* 3.4 28.3 - - + -
160E HIS 3.7 2.2 - - - +
161E THR* 3.6 22.4 - - + -
273E ILE* 3.6 38.6 - - + +
276E THR* 4.9 1.3 - - - +
277E THR* 4.3 16.6 - - + +
296E THR* 5.0 5.4 - - + -
297E VAL 2.8 7.4 + - - +
298E LEU* 3.5 29.7 - - + +
299E SER* 2.8 29.8 + - - +
303E THR* 4.8 7.2 - - + -
312E MET* 5.1 5.4 - - + -
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Residues in contact with ASP 153 (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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108E PRO* 4.3 2.6 - - - +
136E GLN* 3.0 39.2 - - - +
137E ALA* 4.4 9.9 + - + +
151E VAL* 3.7 9.8 - - + -
152E MET* 1.3 72.8 - - - +
154E SER* 1.3 61.5 + - - +
155E GLY 3.8 9.5 + - - -
159E THR* 3.2 2.1 - - - +
160E HIS* 2.5 67.2 + - + +
299E SER* 3.4 18.3 + - - +
300E GLY* 4.8 1.0 - - - -
338E VAL* 5.3 1.2 - - - +
402E MG 4.0 7.4 - - - -
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Residues in contact with SER 154 (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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152E MET* 3.9 6.1 + - - +
153E ASP* 1.3 76.4 + - - +
155E GLY* 1.3 60.5 + - - +
159E THR* 3.0 31.9 - - - +
260E LEU* 5.7 2.6 - - - +
299E SER 3.4 4.6 + - - -
300E GLY* 3.2 23.2 - - - -
302E THR* 3.0 26.2 + - - +
303E THR* 3.4 20.8 - - - +
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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