Contacts of the helix formed by residues 146 - 151 (chain E) in PDB entry 7V3X
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 SER 146 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E PHE* 3.3 23.1 - - - +
77E GLU* 5.5 0.6 - - - +
144E ILE* 4.5 0.7 - - - -
145E ASP* 1.3 74.6 + - - +
147E VAL* 1.3 64.7 + - - +
148E THR* 4.1 3.1 + - - -
149E SER* 3.3 21.8 + - - -
181E THR* 3.5 33.7 - - - -
182E THR* 4.4 1.6 - - - -
183E GLU* 3.7 22.2 + - - -
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Residues in contact with VAL 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E PHE* 4.4 9.4 - - - -
144E ILE* 4.1 10.0 + - + +
146E SER* 1.3 70.3 - - - +
148E THR* 1.3 64.7 + - - +
150E VAL* 3.0 25.2 + - - +
151E PHE* 4.2 12.6 + - + -
167E LEU* 5.2 3.8 - - + -
180E MET* 3.2 35.4 - - + -
181E THR 3.2 12.7 + - - +
182E THR* 4.8 3.6 - - - +
197E GLU* 6.6 0.2 - - + -
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Residues in contact with THR 148 (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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146E SER* 4.1 1.3 + - - -
147E VAL* 1.3 77.3 - - - +
149E SER* 1.3 63.3 + - - +
151E PHE* 3.0 29.8 + - - +
181E THR 4.2 0.2 + - - -
182E THR* 3.4 36.3 - - + +
183E GLU* 3.4 21.5 + - + +
193E ARG* 3.8 37.9 - - + +
194E TYR* 4.7 14.8 + - + +
197E GLU* 4.9 3.5 + - - +
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Residues in contact with SER 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E PHE* 4.3 15.0 - - - -
77E GLU* 5.2 11.2 - - - -
146E SER* 3.3 20.3 + - - -
147E VAL 3.2 0.8 + - - -
148E THR* 1.3 76.1 - - - +
150E VAL* 1.3 67.6 + - - +
151E PHE 3.0 8.5 + - - -
183E GLU* 5.3 5.8 + - - -
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Residues in contact with VAL 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E PHE* 3.6 27.3 - - + -
147E VAL 3.0 15.0 + - - +
149E SER* 1.3 78.1 - - - +
151E PHE* 1.3 75.8 + - + +
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Residues in contact with PHE 151 (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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147E VAL* 4.3 13.2 - - + -
148E THR* 3.0 15.6 + - - +
149E SER* 3.6 9.1 - - - +
150E VAL* 1.3 97.3 - - + +
155E ASP* 3.5 35.8 - - + +
160E VAL* 2.9 57.4 - - + -
163E GLU* 4.0 27.4 - - + -
164E LEU* 4.5 7.9 - - + -
194E TYR* 4.0 25.6 - + + +
197E GLU* 6.3 0.2 - - + -
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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