Contacts of the helix formed by residues 170 - 176 (chain D) in PDB entry 4G5S
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 THR 170 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D CYS* 4.7 1.1 - - - -
154D TYR* 4.0 0.7 + - - -
161D ARG* 3.3 26.9 + - - +
168D ILE 4.6 3.8 - - - +
169D PRO* 1.3 77.6 - - - +
171D GLN* 1.3 64.7 + - - +
172D GLN* 3.3 10.2 + - - +
173D ASP* 2.8 37.8 + - - +
174D VAL* 3.1 13.5 + - - +
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Residues in contact with GLN 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D ILE* 3.6 44.5 - - + +
60D GLY* 4.7 1.0 - - - -
61D TYR* 3.8 31.3 + - + +
66D CYS* 4.7 6.9 - - - -
170D THR* 1.3 74.1 - - - +
172D GLN* 1.3 55.5 + - - +
174D VAL* 3.3 10.2 + - - +
175D LEU* 2.9 32.3 + - + +
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Residues in contact with GLN 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D TYR* 3.4 25.3 - - + +
170D THR* 3.2 7.0 + - - +
171D GLN* 1.3 76.4 - - - +
173D ASP* 1.3 60.3 + - - +
175D LEU* 3.1 13.6 + - - +
176D ARG* 2.9 46.8 + - + +
327D THR* 2.9 49.2 + - - +
329D THR* 4.5 3.8 + - - -
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Residues in contact with ASP 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D VAL* 4.6 2.5 - - + -
154D TYR* 2.3 39.7 + - - -
155D TYR* 2.5 33.5 + - + -
161D ARG* 2.6 33.9 + - - -
162D ILE* 5.1 0.7 - - - -
167D TYR* 3.2 18.7 + - - +
169D PRO* 4.2 4.3 - - + -
170D THR* 2.8 34.4 + - - +
172D GLN* 1.3 75.9 - - - +
174D VAL* 1.3 61.9 + - - +
176D ARG 3.2 1.2 + - - -
177D THR* 3.1 6.6 + - - +
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Residues in contact with VAL 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D LYS* 3.7 7.2 - - + +
61D TYR* 3.6 35.0 - - + -
66D CYS* 4.3 25.4 - - - -
69D TYR* 3.8 41.1 - - + -
169D PRO* 4.6 5.2 - - + -
170D THR 3.1 13.6 + - - +
171D GLN* 3.5 8.1 - - - +
172D GLN 3.3 0.2 - - - -
173D ASP* 1.3 73.1 - - - +
175D LEU* 1.3 63.5 + - - +
177D THR* 2.3 33.9 + - - -
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Residues in contact with LEU 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D THR* 3.8 34.8 + - + +
51D LYS* 3.7 32.1 + - + -
52D GLN* 3.3 45.1 - - - +
55D ILE* 4.0 13.5 - - + -
61D TYR* 5.9 0.2 - - + -
171D GLN* 2.9 17.0 + - + +
172D GLN* 3.1 32.3 + - - +
174D VAL* 1.3 76.5 - - + +
176D ARG* 1.3 62.6 + - + +
177D THR 3.2 6.2 + - - +
327D THR* 3.8 8.9 - - - +
329D THR* 4.0 5.2 - - - +
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Residues in contact with ARG 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D ASP* 3.8 20.4 + - - +
151D SER* 3.0 35.1 + - - +
154D TYR* 3.5 50.1 - - + +
155D TYR* 3.0 18.9 + - + +
172D GLN* 2.9 34.3 + - - +
173D ASP 3.7 0.2 - - - +
174D VAL 3.1 0.4 - - - -
175D LEU* 1.3 75.1 - - + +
177D THR* 1.3 64.4 + - - +
178D ARG* 3.6 2.6 + - - +
272D ASP* 5.1 8.7 + - - -
273D LEU* 5.6 5.7 - - - +
327D THR* 3.7 38.7 + - - +
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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