Contacts of the helix formed by residues 138 - 143 (chain E) in PDB entry 4B2Q
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 ILE 138 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E THR* 3.3 3.5 + - - +
137E GLY* 1.3 85.8 - - - +
139E LYS* 1.3 66.2 + - - +
140E VAL* 3.5 24.7 - - + +
141E VAL* 3.0 30.4 + - + +
142E ASP* 3.0 19.4 + - - +
166E PHE* 3.4 35.0 - - + -
169E GLU* 4.4 13.0 - - + -
170E LEU* 4.4 11.2 - - + -
173E ASN* 4.6 7.0 - - - +
346E PRO* 4.6 14.8 - - + -
348E VAL* 5.7 0.2 - - + -
416E GLN* 3.3 15.3 - - + +
418E PHE* 5.0 3.6 - - + -
432E VAL 5.3 1.1 - - - -
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Residues in contact with LYS 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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138E ILE* 1.3 66.7 - - - +
140E VAL* 1.3 59.3 + - - +
141E VAL 2.9 10.7 + - - -
142E ASP 4.7 0.4 - - - +
143E LEU* 3.1 29.1 + - - +
413E PHE* 2.8 62.4 + - + -
414E LEU* 4.2 5.2 - - - +
415E SER 3.7 10.7 + - - -
416E GLN* 3.2 13.0 + - - -
432E VAL* 3.6 36.3 - - + +
437E THR* 3.7 21.8 - - + +
440E SER* 5.5 1.1 - - - +
441E PHE* 4.2 12.3 - - + -
460E VAL 3.2 24.9 + - - -
461E GLY 4.6 1.8 + - - +
462E GLY* 6.3 0.4 - - - -
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Residues in contact with VAL 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138E ILE* 3.3 13.6 - - + -
139E LYS* 1.3 75.5 - - - +
141E VAL* 1.3 56.9 + - + +
144E LEU* 3.2 42.8 - - + +
145E ALA* 3.8 2.3 + - - +
344E ILE* 6.3 1.3 - - + -
346E PRO* 4.8 11.7 - - + +
348E VAL* 3.3 44.5 - - + +
350E PRO* 5.1 2.2 - - + -
353E SER* 5.5 0.3 - - - -
414E LEU* 3.0 46.2 - - + +
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Residues in contact with VAL 141 (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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136E THR* 3.4 20.0 - - + +
138E ILE* 3.2 35.4 - - + +
139E LYS 2.9 1.8 + - - -
140E VAL* 1.3 79.5 - - + +
142E ASP* 1.3 69.6 + - - +
143E LEU 2.9 3.0 + - - -
144E LEU 3.1 10.6 + - - -
145E ALA 3.1 20.4 + - - +
146E PRO* 3.1 11.8 - - + -
147E TYR* 3.3 40.6 - - + +
166E PHE* 4.6 9.4 - - + -
170E LEU* 5.6 0.9 - - + -
333E THR* 5.4 4.7 - - + +
348E VAL* 5.7 2.2 - - + -
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Residues in contact with ASP 142 (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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133E ILE* 4.9 6.6 - - - +
134E LEU 4.0 4.0 - - - +
135E GLU* 3.5 12.3 - - - +
136E THR* 3.3 23.6 + - - -
137E GLY* 3.6 17.0 + - - -
138E ILE 3.0 21.7 + - - +
139E LYS 4.7 0.4 - - - +
141E VAL* 1.3 80.2 - - - +
143E LEU* 1.3 57.0 + - - +
146E PRO* 4.1 16.0 - - - +
367E HIS* 3.0 25.3 + - - -
432E VAL 4.2 7.1 - - - +
433E ARG* 5.0 0.5 - - - -
434E LEU* 3.6 32.6 + - + +
437E THR* 5.0 6.3 + - + +
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Residues in contact with LEU 143 (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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139E LYS 3.1 15.2 + - - +
141E VAL 3.0 1.0 - - - -
142E ASP* 1.3 80.9 - - - +
144E LEU* 1.3 69.5 + - + +
146E PRO* 4.9 0.2 - - - -
358E LEU* 4.2 0.5 - - - +
367E HIS* 4.1 12.8 - - + +
370E VAL* 4.2 14.4 - - + -
371E ALA* 3.1 55.1 - - + +
374E VAL* 4.0 14.4 - - + -
414E LEU* 5.0 1.6 - - + -
434E LEU* 5.4 0.2 - - - -
437E THR* 3.9 13.5 - - + -
438E VAL* 5.2 7.2 - - + -
441E PHE* 3.5 51.4 - - + -
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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