Contacts of the helix formed by residues 153 - 157 (chain A) in PDB entry 4I2C
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 TYR 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A SER* 2.9 7.5 + - - +
152A GLN* 1.4 102.9 + - + +
154A ALA* 1.3 58.6 + - - +
155A CYS* 3.9 16.2 - - - -
156A GLN* 3.0 35.3 + - - +
157A ARG* 3.5 15.3 - - - +
459A ASP* 3.6 18.6 - - + -
462A ARG* 3.7 33.4 + - + -
463A TYR* 3.6 24.7 - + + -
466A HIS* 3.9 14.9 + - - +
467A GLU* 2.7 44.3 + - + +
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Residues in contact with ALA 154 (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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153A TYR* 1.3 70.8 - - - +
155A CYS* 1.4 56.3 + - - +
156A GLN 3.1 0.7 - - - -
157A ARG* 3.1 51.7 + - - +
159A THR* 4.9 2.1 + - - -
196A SER* 4.2 1.3 - - - +
455A GLN* 4.2 2.2 - - + +
456A PHE* 3.5 18.1 - - - -
459A ASP* 2.7 27.1 + - + +
510A ALA* 3.6 26.5 - - + -
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Residues in contact with CYS 155 (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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153A TYR* 3.2 10.4 - - - -
154A ALA* 1.4 76.1 - - - +
156A GLN* 1.4 58.7 + - - +
157A ARG 3.5 1.1 - - - -
456A PHE* 3.5 15.8 + - + +
459A ASP* 3.7 12.6 - - - +
460A LEU* 3.8 34.5 - - + +
463A TYR* 3.6 35.4 - - - -
495A PHE* 4.6 0.5 - - - -
500A LEU* 4.0 21.8 - - + +
501A ASP 4.7 1.2 - - - +
503A ILE* 3.4 20.8 - - - +
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Residues in contact with GLN 156 (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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151A SER* 2.7 42.4 + - - +
153A TYR* 3.0 19.4 + - + +
155A CYS* 1.4 75.4 - - - +
157A ARG* 1.3 64.3 + - - +
463A TYR* 3.5 29.2 + - + -
499A GLY 5.6 1.4 + - - -
500A LEU* 3.5 21.4 - - + +
503A ILE* 4.8 5.6 - - - -
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Residues in contact with ARG 157 (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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150A ILE* 3.7 15.7 - - + -
151A SER 3.0 29.4 + - - +
152A GLN* 3.3 22.0 + - - +
153A TYR 3.5 11.8 - - - +
154A ALA* 3.1 38.3 + - - +
156A GLN* 1.3 80.8 - - - +
158A ARG* 1.3 63.4 + - - +
159A THR* 3.9 5.5 + - - +
193A ARG* 4.7 1.8 + - - +
196A SER* 2.9 35.6 + - - -
197A VAL* 3.7 21.3 - - - +
200A SER* 3.6 32.9 + - - +
216A CYS* 4.9 2.4 - - - -
459A ASP* 4.3 3.2 + - - -
503A ILE* 3.8 13.5 - - - +
507A GLU 4.0 5.5 - - - +
510A ALA* 5.0 0.4 - - - +
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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