Contacts of the helix formed by residues 155 - 159 (chain H) in PDB entry 2FIE
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 PRO 155 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139H TYR* 3.8 2.3 - - - -
153H LEU 4.2 3.6 - - - +
154H GLN* 1.3 88.4 - - + +
156H GLY* 1.3 55.7 + - - +
157H ARG* 2.7 18.7 + - + +
158H ASN* 2.7 42.3 + - - +
303H LEU 3.6 12.6 - - - +
304H ASP* 4.6 2.9 - - - +
305H VAL 3.7 17.0 - - - +
306H ILE* 4.3 20.0 - - + -
307H PRO* 3.8 4.5 - - + -
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Residues in contact with GLY 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139H TYR* 4.0 7.4 - - - -
155H PRO* 1.3 69.9 - - - +
157H ARG* 1.3 55.5 + - - +
158H ASN 3.0 5.1 + - - -
159H LEU* 3.1 26.7 + - - +
282H ASN* 3.3 26.3 + - - +
286H TYR* 4.2 2.1 - - - -
303H LEU* 3.2 36.8 + - - +
305H VAL 4.3 1.2 + - - -
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Residues in contact with ARG 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155H PRO* 2.7 10.3 + - + +
156H GLY* 1.3 72.5 - - - +
158H ASN* 1.3 64.0 + - - +
159H LEU 3.4 2.2 + - - +
286H TYR* 6.1 1.1 - - - -
289H GLU* 3.4 32.9 + - - -
301H ALA* 4.3 5.7 - - - +
303H LEU* 3.1 28.4 + - - +
304H ASP* 3.3 35.1 + - - +
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Residues in contact with ASN 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139H TYR* 3.8 10.8 - - + -
140H ARG* 4.9 1.9 + - - +
142H LYS* 3.9 24.2 - - - +
154H GLN* 3.8 27.3 + - + +
155H PRO* 2.7 44.3 + - - +
157H ARG* 1.3 79.3 - - - +
159H LEU* 1.3 63.9 + - - +
160H VAL* 3.5 8.3 + - - +
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Residues in contact with LEU 159 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137H GLY* 3.9 7.9 - - - -
138H ILE 3.6 26.9 - - - +
139H TYR* 3.2 36.7 - - + +
156H GLY* 3.1 19.3 + - - +
157H ARG 3.4 2.7 - - - +
158H ASN* 1.3 78.5 - - - +
160H VAL* 1.3 61.4 + - - +
161H ALA 3.9 4.5 - - - +
162H ALA* 4.2 5.4 - - + -
282H ASN* 3.9 20.0 - - + +
283H PRO* 4.3 2.0 - - + -
286H TYR* 3.3 53.9 + - + -
303H LEU* 4.2 1.6 - - + -
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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