Contacts of the helix formed by residues 119 - 123 (chain E) in PDB entry 6K71
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 ASP 119 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E HIS* 2.8 31.5 + - - +
116E GLU* 3.2 12.7 + - + +
118E VAL* 1.3 77.4 - - - +
120E LEU* 1.3 64.5 + - + +
121E PHE 3.1 1.3 - - - -
122E ARG* 3.3 18.4 + - - +
123E ALA* 3.9 7.1 + - - +
191H SER* 5.5 4.8 - - - +
193H THR* 3.5 33.7 - - - +
194H GLN* 5.0 0.2 - - - -
198H ILE* 3.3 24.4 - - - +
212H LEU* 4.0 16.5 - - + +
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Residues in contact with LEU 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116E GLU* 3.0 37.5 + - + +
117E VAL 5.0 4.5 - - - +
118E VAL 4.2 0.2 - - - +
119E ASP* 1.3 77.5 - - + +
121E PHE* 1.3 60.1 + - - +
122E ARG 3.2 1.9 + - - -
123E ALA* 3.6 29.2 + - + +
126E ALA* 5.0 0.2 - - - +
129E ALA* 5.3 2.9 - - + -
165E LYS* 4.6 19.7 - - + -
264E TYR* 4.1 25.0 - - + +
265E SER* 5.2 6.7 - - - +
266E PHE* 4.1 29.6 - - + -
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Residues in contact with PHE 121 (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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2E GLU* 5.6 2.2 - - - -
3E PHE* 5.2 13.7 - + + -
100E ASP* 4.3 20.9 - - + -
102E LEU* 6.0 1.8 - - + -
117E VAL 4.6 2.2 + - - +
118E VAL* 3.3 39.9 - - + +
120E LEU* 1.3 76.9 - - - +
122E ARG* 1.3 76.8 + - + +
123E ALA 3.5 0.2 - - - -
125E ASP* 3.4 12.9 - - - +
126E ALA* 3.3 44.1 + - + -
129E ALA* 4.1 17.2 - - + +
206E CYS* 3.8 16.4 - - + -
207E LEU* 4.1 27.6 - - - -
208E LYS* 4.6 4.5 - - + -
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Residues in contact with ARG 122 (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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2E GLU* 3.6 10.5 + - - -
3E PHE* 3.2 39.1 - - - -
118E VAL 4.3 8.0 + - - +
119E ASP* 3.3 12.4 + - - +
120E LEU 3.2 0.8 - - - -
121E PHE* 1.3 99.4 - - + +
123E ALA* 1.3 66.8 + - - +
124E TYR 3.7 0.7 - - - -
125E ASP* 3.7 13.0 + - - +
193H THR* 5.2 0.2 - - - +
196H MET* 6.1 0.2 - - - -
198H ILE* 3.4 27.8 - - - +
200H SER* 4.0 10.3 + - - -
205H PRO* 4.3 7.6 + - - +
208H VAL* 3.4 32.5 - - - +
209H ARG* 4.8 34.8 + - + +
212H LEU* 4.8 21.5 - - + +
213H GLN* 5.1 1.9 + - - +
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Residues in contact with ALA 123 (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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119E ASP 3.9 3.0 + - - +
120E LEU* 3.6 28.4 + - + +
121E PHE 3.5 2.6 - - - -
122E ARG* 1.3 80.3 - - - +
124E TYR* 1.3 60.5 + - - +
125E ASP 3.6 0.2 - - - +
165E LYS* 4.0 27.8 - - - +
264E TYR* 5.2 3.4 - - + -
209H ARG* 4.9 2.8 + - - -
212H LEU* 6.4 0.2 - - - -
213H GLN* 4.5 8.7 - - - +
216H GLN* 5.1 12.3 + - - +
218H LEU* 4.1 19.3 - - - +
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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