Contacts of the strand formed by residues 174 - 178 (chain E) in PDB entry 6XOX
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 GLN 174 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E ASP 5.0 4.7 - - - +
111E TRP* 4.4 6.7 - - - -
165E PHE* 3.4 5.5 - - - -
166E LEU* 2.8 53.0 + - + +
168E ARG* 3.1 40.1 + - - +
172E SER* 3.1 9.6 + - - +
173E PRO* 1.3 74.5 - - - +
175E LEU* 1.3 69.5 + - - +
176E LEU* 4.9 4.6 - - - +
187E VAL* 5.8 3.7 - - - +
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Residues in contact with LEU 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E SER* 3.3 26.5 - - - +
107E PRO 3.4 19.7 - - - +
108E PHE 3.3 13.9 + - - +
109E ASP* 3.7 20.8 + - + +
163E TYR* 4.5 4.0 - - + -
164E TRP 3.5 9.9 - - - +
165E PHE* 3.6 24.3 - - + -
173E PRO 4.1 0.2 + - - -
174E GLN* 1.3 84.3 - - - +
176E LEU* 1.3 69.4 + - - +
177E ILE 3.7 17.9 - - - +
178E TYR* 4.3 6.7 - - + +
184E ALA* 3.9 16.6 - - + +
187E VAL* 3.7 15.8 - - - +
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Residues in contact with LEU 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E TRP* 2.7 17.4 + - + +
165E PHE 4.0 4.3 - - - +
166E LEU* 3.5 42.6 - - + +
174E GLN* 3.7 4.0 + - - +
175E LEU* 1.3 79.5 - - - +
177E ILE* 1.3 68.4 + - + +
183E LEU* 3.9 1.7 - - - -
184E ALA 3.2 24.4 + - - -
187E VAL* 3.8 16.3 - - + +
188E PRO* 6.0 0.2 - - + -
191E PHE* 3.7 52.3 - - + -
202E LEU* 4.1 19.7 - - + -
215E TYR* 4.2 4.7 - - + -
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Residues in contact with ILE 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E TYR* 3.2 6.4 - - - -
164E TRP* 2.8 46.4 + - + -
175E LEU* 3.7 5.9 - - - +
176E LEU* 1.3 87.9 - - + +
178E TYR* 1.3 62.4 + - - +
180E MET* 3.6 32.5 - - - -
181E SER 3.6 4.3 - - - +
182E ASN 3.3 13.9 - - - +
183E LEU* 4.8 8.1 - - + -
191E PHE* 4.9 3.6 - - + -
192E SER* 3.5 39.5 - - - +
193E GLY* 3.6 6.3 - - - +
202E LEU* 3.7 17.0 - - + -
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Residues in contact with TYR 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E GLY* 4.3 12.0 + - - -
105E SER 3.8 7.9 - - - -
106E SER* 3.2 36.1 - - - +
107E PRO* 4.8 2.2 - - + +
163E TYR* 3.5 17.0 - - + -
175E LEU* 4.3 9.9 - - + -
177E ILE* 1.3 71.8 - - - +
179E ARG* 1.3 96.6 + - - +
180E MET 3.2 2.5 - - - -
182E ASN* 3.0 55.5 + - + +
183E LEU 3.3 25.5 + - - -
184E ALA* 3.9 9.4 - - - -
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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