Contacts of the helix formed by residues 146 - 151 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A PHE* 3.0 13.3 - - - +
145A ASP* 1.3 76.0 + - - +
147A VAL* 1.3 61.4 + - - +
148A THR* 4.3 4.0 - - - -
149A SER* 2.6 44.4 + - - -
181A THR* 3.7 25.1 - - - -
182A THR 4.7 0.7 - - - -
183A GLU* 2.9 26.7 + - - -
161B ARG* 4.5 1.2 + - - -
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Residues in contact with VAL 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 5.2 0.7 - - + -
76A PHE* 4.0 8.3 - - + -
144A ILE* 3.7 19.6 + - + +
146A SER* 1.3 69.7 - - - +
148A THR* 1.3 67.4 + - - +
150A VAL* 3.2 14.4 - - - +
151A PHE* 2.9 26.8 - - + -
164A LEU* 4.1 22.4 - - + -
167A LEU* 3.8 19.3 - - + -
180A MET* 3.5 34.5 - - + -
181A THR 3.4 14.8 + - - +
182A THR* 4.4 10.8 - - + +
197A GLU* 5.6 0.7 - - + -
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Residues in contact with THR 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A SER* 4.4 1.3 - - - -
147A VAL* 1.3 79.0 - - - +
149A SER* 1.3 56.1 + - - +
151A PHE* 2.8 44.7 + - - +
182A THR* 3.0 31.5 - - - +
183A GLU* 3.9 22.7 + - + +
193A ARG* 3.5 37.9 - - + +
194A TYR* 4.2 12.1 + - + +
197A GLU* 4.3 3.5 + - - +
161B ARG* 4.7 2.2 - - - +
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Residues in contact with SER 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A PHE* 3.2 22.8 - - - +
77A GLU* 5.4 5.9 - - - +
146A SER* 2.6 35.3 + - - -
148A THR* 1.3 77.2 - - - +
150A VAL* 1.3 62.1 + - - +
151A PHE 3.5 6.1 - - - +
161B ARG* 3.6 39.8 + - - +
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Residues in contact with VAL 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A PHE* 4.0 25.0 - - + -
122A ASP* 5.7 2.3 - - - +
147A VAL 3.2 14.7 + - - +
148A THR 3.1 0.2 - - - -
149A SER* 1.3 83.8 + - - +
151A PHE* 1.3 65.6 + - + +
152A GLN* 4.0 3.3 + - - +
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Residues in contact with PHE 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A VAL* 2.9 41.1 - - + -
148A THR* 2.8 26.2 + - - +
149A SER* 3.5 6.2 - - - +
150A VAL* 1.3 76.8 - - + +
152A GLN* 1.3 64.6 + - - +
160A VAL* 4.1 31.0 - - + -
163A GLU* 3.5 33.4 - - + -
164A LEU* 4.1 29.2 - - + -
167A LEU* 5.7 3.6 - - + -
194A TYR* 4.5 22.3 + + + -
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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