Contacts of the strand formed by residues 174 - 178 (chain A) in PDB entry 6XYU
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 ILE 174 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A VAL* 4.0 19.3 - - + -
99A TRP 3.3 7.9 - - - +
100A ALA* 3.6 7.2 - - + -
101A PRO* 3.6 22.2 - - + +
141A LEU* 3.9 12.1 - - + -
142A PRO 2.7 17.3 + - - +
143A ILE* 3.2 21.3 - - + -
144A LEU* 2.6 34.3 + - - +
173A VAL* 1.3 72.1 - - - +
175A VAL* 1.3 59.8 + - - +
176A ALA* 5.3 1.1 - - + -
218A LEU* 6.1 1.1 - - + -
222A ALA* 6.5 0.2 - - - -
225A PHE* 3.4 27.8 - - + +
226A GLY 4.5 0.2 - - - -
227A GLY* 3.8 24.0 - - - +
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Residues in contact with VAL 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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98A VAL* 3.5 1.6 - - - +
99A TRP* 2.6 43.5 + - + +
144A LEU* 3.1 10.3 - - + +
146A TRP* 5.1 2.0 - - + -
164A ALA* 3.5 26.9 - - + -
167A MET* 3.6 39.5 - - + -
168A ALA* 4.0 11.7 - - - +
173A VAL* 3.9 11.7 - - + +
174A ILE* 1.3 79.6 - - - +
176A ALA* 1.3 67.4 + - - +
235A PHE* 4.3 12.6 - - + -
488A PHE* 4.8 2.5 - - + -
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Residues in contact with ALA 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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97A ASN 3.0 14.1 - - - +
98A VAL* 4.6 3.6 - - + -
99A TRP* 4.4 1.8 - - - -
143A ILE* 4.9 4.7 - - + -
144A LEU 2.7 11.9 + - - +
145A ILE* 3.2 7.4 - - + -
146A TRP* 2.7 33.4 + - - +
174A ILE* 5.3 0.4 - - + -
175A VAL* 1.3 77.7 - - - +
177A SER* 1.3 58.0 + - - +
218A LEU* 3.5 39.9 - - + -
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Residues in contact with SER 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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96A ILE* 3.5 2.4 - - - +
97A ASN* 2.6 48.7 + - - +
99A TRP* 3.3 21.8 - - - -
146A TRP* 3.6 29.6 - - - -
157A ALA* 3.5 15.7 + - - +
162A TYR 5.7 2.2 - - - -
176A ALA* 1.3 74.3 - - - +
178A PHE* 1.3 66.6 + - - +
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Residues in contact with PHE 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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34A TYR* 4.2 0.9 - - + -
95A TYR 3.2 15.0 - - - +
96A ILE* 3.8 14.1 - - + +
97A ASN* 4.3 1.1 - - - +
145A ILE* 3.6 29.8 - - + -
146A TRP 4.1 7.9 + - - +
147A ILE* 4.0 16.7 - - + -
148A TYR* 3.3 19.2 - - - -
157A ALA* 3.6 9.9 - - - +
177A SER* 1.3 84.5 + - - +
179A GLN* 1.3 71.4 + - - +
180A TYR* 4.0 11.4 - + + -
211A GLN* 3.6 48.7 - - + -
214A ALA* 3.5 21.5 - - + -
215A ILE* 4.3 6.7 - - + -
218A LEU* 4.6 3.8 - - + -
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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