Contacts of the strand formed by residues 177 - 181 (chain A) in PDB entry 1XUO
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 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A VAL* 4.5 2.7 - - + -
172A GLN 3.5 6.3 - - - +
173A PHE* 3.9 6.5 - - + -
174A SER 4.6 0.4 - - - -
175A THR 3.9 12.9 + - - -
176A SER* 1.3 100.4 + - - +
178A LYS* 1.3 59.8 + - - +
179A THR 4.4 0.2 - - - -
202A MET* 4.1 1.8 - - - -
207A ASN* 3.5 25.2 + - + +
210A GLY* 3.2 32.5 - - - -
211A ALA* 3.4 26.7 - - + -
214A TYR* 3.8 51.0 + + + -
244A ASP* 4.4 0.5 + - - -
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Residues in contact with LYS 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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171A VAL* 3.3 5.0 - - - +
172A GLN 2.9 33.4 + - - +
177A TYR* 1.3 74.1 - - - +
179A THR* 1.3 74.7 + - - +
180A GLU* 3.2 35.8 + - - +
198A HIS* 4.8 11.3 + - - +
200A LYS* 5.6 5.3 - - - +
202A MET* 3.6 20.1 - - + +
214A TYR* 4.6 0.9 - - - -
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Residues in contact with THR 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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170A ALA 3.7 5.8 - - - +
171A VAL* 4.0 8.0 - - + +
178A LYS* 1.3 79.9 - - - +
180A GLU* 1.3 62.0 + - - +
181A PHE* 3.6 27.3 - - - +
182A ASP* 4.2 13.5 - - + +
214A TYR* 2.7 35.7 + - - -
218A GLU 5.4 0.9 + - - -
219A VAL* 3.8 15.0 - - + +
224A LEU* 5.9 4.5 - - + +
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Residues in contact with GLU 180 (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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136A PHE* 4.0 20.2 - - + -
170A ALA* 2.8 17.9 + - + +
172A GLN* 3.0 31.3 - - - +
178A LYS* 3.2 46.9 + - - +
179A THR* 1.3 72.7 - - - +
181A PHE* 1.3 67.8 + - + +
185A ASP* 4.9 0.5 - - - +
195A LEU 4.3 6.3 - - - +
196A LEU* 4.7 1.8 - - + -
198A HIS 5.0 0.5 - - - +
199A VAL* 3.9 31.2 - - + +
200A LYS 4.6 1.6 + - - +
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Residues in contact with PHE 181 (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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134A PHE* 5.4 0.4 - + - -
158A MET* 3.7 27.4 - - + -
168A PHE* 3.4 25.4 - - + -
169A ALA* 3.4 9.9 - - - +
170A ALA* 3.0 54.7 + - + +
179A THR* 3.6 7.3 - - - +
180A GLU* 1.3 81.2 - - - +
182A ASP* 1.3 70.3 + - - +
185A ASP* 3.6 19.5 - - + +
186A TYR* 4.2 7.9 - - + -
195A LEU* 3.7 49.1 - - + +
196A LEU* 3.9 18.2 - - + -
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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