Contacts of the helix formed by residues 95 - 99 (chain A) in PDB entry 3H44
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 GLY 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A ILE* 1.3 80.1 - - - +
96A SER* 1.3 60.9 + - - -
97A LEU 3.2 2.7 - - - -
98A SER* 2.8 28.9 + - - -
107A SER* 3.3 14.5 + - - -
142A THR* 4.1 0.7 - - - -
143A SER 3.5 9.6 - - - -
144A GLY 3.2 11.0 + - - -
145A GLU* 3.7 4.6 - - - +
146A HIS 3.9 3.6 - - - -
147A THR* 4.1 3.1 - - - -
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Residues in contact with SER 96 (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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95A GLY* 1.3 70.3 - - - -
97A LEU* 1.3 59.5 + - - +
98A SER 3.0 0.4 - - - -
99A ASP* 2.9 44.3 + - - +
107A SER* 3.3 12.4 + - - -
142A THR* 4.1 6.9 + - - +
143A SER 3.2 18.1 + - - -
144A GLY* 4.2 4.2 - - - -
217A LYS* 3.9 10.4 - - - +
219A GLY* 3.6 28.3 - - - -
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Residues in contact with LEU 97 (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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96A SER* 1.3 79.0 + - - +
98A SER* 1.3 52.4 + - - +
144A GLY* 3.0 29.1 + - - +
145A GLU* 3.9 9.2 - - + -
206A LYS* 4.7 9.6 - - - +
213A HIS* 6.4 0.2 - - + -
214A PRO* 3.4 36.4 - - + +
215A PHE* 3.8 15.9 - - + +
217A LYS* 2.8 28.0 + - + -
288A PHE* 3.9 30.4 - - + -
366A GLY 5.5 0.7 - - - +
367A ALA* 3.8 29.6 - - + -
370A PHE* 5.3 3.6 - - + -
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Residues in contact with SER 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ILE* 3.7 21.9 - - - +
95A GLY 2.8 14.6 + - - -
97A LEU* 1.3 77.0 - - - +
99A ASP* 1.3 63.8 + - - -
100A PRO* 3.4 2.3 - - - +
217A LYS* 4.4 0.4 - - - +
244A PHE* 3.3 16.2 - - - -
248A TYR* 4.4 20.6 + - - -
286A PRO* 3.7 26.3 - - - +
288A PHE* 5.4 1.0 - - - -
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Residues in contact with ASP 99 (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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95A GLY 3.8 0.2 + - - -
96A SER* 2.9 30.7 + - - +
98A SER* 1.3 75.3 - - - +
100A PRO* 1.4 74.6 - - + +
101A PRO* 3.4 1.0 - - - +
103A ILE 4.2 1.1 - - - +
104A ALA* 4.0 2.4 - - - -
105A GLY* 2.6 36.2 + - - +
106A LEU 3.6 2.5 - - - -
107A SER* 3.0 36.6 + - - -
217A LYS* 2.6 36.8 + - + +
218A PHE 3.9 6.2 - - - +
219A GLY* 4.1 0.2 - - - -
244A PHE* 4.5 1.1 - - - -
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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