Contacts of the helix formed by residues 176 - 181 (chain K) in PDB entry 4GUN
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 176 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28K ILE* 3.8 8.9 - - - +
171K ALA 3.6 10.2 + - - -
172K TRP 3.5 21.1 - - - -
173K GLU* 3.4 28.9 + - + +
174K HIS 3.3 0.6 + - - -
175K ALA* 1.3 78.9 - - - +
177K TYR* 1.3 66.1 + + - +
178K LEU 3.4 2.5 - - - -
179K GLN 3.1 4.0 + - - -
180K TYR* 2.8 43.1 + - + +
181K GLN 3.3 23.1 - - - -
182K ASN* 4.8 2.5 + - - -
184K ARG* 3.1 49.4 - - + +
187K TYR* 3.4 46.7 - + + -
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Residues in contact with TYR 177 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I LEU* 3.9 16.6 - - + +
36I HIS* 2.8 38.6 + + - -
174I HIS* 3.7 25.5 + - + +
177I TYR* 4.7 22.9 - - + -
178I LEU* 3.7 37.2 - - + +
173K GLU* 2.9 31.0 + - + +
174K HIS* 4.5 1.8 - - - -
176K TYR* 1.3 86.4 - + - +
178K LEU* 1.3 59.6 + - - +
181K GLN* 2.8 64.2 + - + -
182K ASN* 3.8 2.5 + - - -
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Residues in contact with LEU 178 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177I TYR* 3.8 33.1 - - + +
178I LEU* 4.3 23.6 - - + +
181I GLN* 4.6 15.0 - - + +
25K SER* 5.4 0.4 - - - +
27K GLU* 4.5 21.5 - - + +
28K ILE* 4.0 18.0 - - + +
31K LEU* 3.4 33.2 - - + -
174K HIS 5.7 0.6 + - - -
176K TYR 3.3 1.6 + - - -
177K TYR* 1.3 74.2 - - - +
179K GLN* 1.4 56.3 + - - +
181K GLN* 3.0 16.5 + - - -
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Residues in contact with GLN 179 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K PRO 2.9 26.9 + - - +
23K TYR 3.5 3.6 + - - +
24K ILE* 3.6 1.4 - - - -
25K SER* 3.0 36.2 + - - +
28K ILE* 3.7 16.9 - - + +
176K TYR 3.1 2.2 + - - -
178K LEU* 1.4 78.9 - - - +
180K TYR* 1.3 93.0 + - + +
181K GLN* 3.6 13.4 + - - +
21P GLU* 4.8 10.0 - - - +
22P PRO* 3.7 27.8 - - + +
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Residues in contact with TYR 180 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22K PRO 4.0 1.0 + - - -
23K TYR* 2.7 31.2 + - - -
24K ILE* 5.4 0.7 - - - -
28K ILE* 5.5 1.3 - - + -
176K TYR* 2.8 33.3 + - + +
179K GLN* 1.3 98.9 + - + +
181K GLN* 1.3 70.3 + - - +
183K VAL* 3.1 34.1 + - + +
186K ASP* 3.7 35.0 - - + -
187K TYR* 3.7 31.0 - + + -
190K ALA* 3.2 17.4 - - + +
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Residues in contact with GLN 181 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I LEU* 3.8 30.3 - - + -
178I LEU* 4.2 11.1 - - + +
176K TYR* 3.3 13.2 - - - -
177K TYR* 2.8 56.0 + - + +
178K LEU 3.0 27.3 + - - -
179K GLN 3.6 12.3 + - - +
180K TYR* 1.3 75.1 - - - +
182K ASN* 1.3 70.3 + - - +
183K VAL* 5.4 0.4 - - + -
21P GLU* 5.0 9.4 - - - +
27P GLU* 4.9 16.7 + - - +
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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