Contacts of the helix formed by residues 173 - 179 (chain A) in PDB entry 1SHZ
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 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A ASN* 5.9 2.0 - - - -
171A GLY* 2.8 4.5 + - - -
172A GLU* 1.3 83.8 - - - +
174A VAL* 1.3 64.9 + - - +
175A LYS 3.1 3.3 + - - -
176A TYR* 3.4 12.5 + - - +
177A PHE* 3.3 19.1 - - - -
198A LEU* 2.8 51.9 + - - +
200A ARG* 5.6 3.6 - - - -
475A GDP 3.8 16.0 + - - -
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Residues in contact with VAL 174 (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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91A ASN* 3.8 30.1 - - + +
92A VAL* 5.3 3.3 - - - +
95A GLY* 4.2 15.3 - - - -
99A LEU* 5.6 1.6 - - + -
162A TYR* 4.5 7.0 - - + -
170A LEU* 4.1 25.4 - - + -
171A GLY* 3.1 22.7 - - - +
173A SER* 1.3 79.5 - - - +
175A LYS* 1.3 62.4 + - - +
177A PHE* 3.5 9.0 + - - +
178A LEU* 3.0 48.4 + - + +
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Residues in contact with LYS 175 (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 TRP* 4.5 11.8 - - + -
162A TYR* 3.3 47.3 - - + +
172A GLU 3.9 8.0 + - - +
173A SER 3.1 0.2 - - - -
174A VAL* 1.3 81.0 - - - +
176A TYR* 1.3 63.8 + - - +
177A PHE 3.1 0.4 - - - -
178A LEU* 3.4 8.1 + - - +
179A ASP* 2.8 53.4 + - - +
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Residues in contact with TYR 176 (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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172A GLU 4.6 1.2 + - - +
173A SER* 3.4 11.9 + - - +
174A VAL 3.4 0.6 - - - -
175A LYS* 1.3 79.5 - - - +
177A PHE* 1.3 86.1 + + - +
179A ASP* 3.9 3.7 + - - +
180A ASN* 2.7 51.3 + - + +
183A LYS* 4.5 3.6 + - - -
192A SER* 4.3 0.9 + - - -
194A GLN* 4.3 8.5 - - + +
195A ASP* 2.6 30.7 + - - -
198A LEU* 3.4 43.7 - - + +
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Residues in contact with PHE 177 (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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88A ILE* 3.7 36.3 - - + -
91A ASN* 4.2 20.0 - - + -
92A VAL* 3.7 23.1 - - + -
173A SER* 3.3 23.5 + - - -
174A VAL* 3.5 7.3 + - - +
175A LYS 3.1 0.4 - - - -
176A TYR* 1.3 102.2 - + - +
178A LEU* 1.3 61.3 + - - +
179A ASP 3.0 2.0 - - - -
180A ASN* 2.8 20.9 + - + +
181A LEU* 3.1 17.1 + - - +
184A LEU* 4.4 13.8 - - + +
195A ASP* 3.7 34.8 - - - -
198A LEU* 4.0 15.7 - - + -
199A ALA 4.2 2.9 - - - -
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Residues in contact with LEU 178 (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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92A VAL* 3.8 31.2 - - + +
95A GLY 6.1 0.2 - - - -
96A MET* 4.1 19.3 - - + +
99A LEU* 4.6 4.9 - - + -
149A ILE* 3.8 20.9 - - + -
153A TRP* 3.0 69.3 + - + -
174A VAL* 3.0 41.0 + - + +
175A LYS 3.4 1.1 + - - +
177A PHE* 1.3 75.8 - - - +
179A ASP* 1.3 60.1 + - - +
180A ASN 3.3 0.6 + - - -
181A LEU* 3.6 18.1 + - + +
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Residues in contact with ASP 179 (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 TRP* 3.4 18.9 + - - -
175A LYS* 2.8 47.6 + - - +
176A TYR* 4.2 6.6 - - - +
177A PHE 3.0 1.4 - - - -
178A LEU* 1.3 78.5 - - - +
180A ASN* 1.3 64.4 + - - +
181A LEU 3.5 1.3 + - - -
182A ASP* 5.2 1.0 + - - +
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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