Contacts of the strand formed by residues 163 - 168 (chain B) in PDB entry 1XUD
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 163 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B TRP* 4.5 5.6 - - + -
118B LEU* 4.6 10.5 - - + -
119B THR 2.8 13.8 + - - +
120B TYR* 3.1 6.5 - - + +
121B ARG 3.1 23.3 + - - -
142B PHE* 3.8 35.4 - - + -
153B PHE* 4.2 15.7 - - + -
161B ALA 4.2 0.4 - - - -
162B ASP* 1.3 83.5 - - + +
164B MET* 1.3 61.7 + - - +
165B ILE* 3.6 12.7 + - + +
197B GLY* 3.3 26.5 - - - +
198B ASP* 4.0 2.0 - - - -
199B ALA 4.6 1.3 - - - +
224B PHE* 4.5 8.3 - - + -
227B SER* 4.2 16.8 - - - +
228B LEU* 4.8 5.2 - - + -
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Residues in contact with MET 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ARG* 3.6 42.6 - - - +
123B VAL* 4.0 14.8 - - + -
159B GLY 3.7 7.4 - - - +
160B ILE* 4.0 17.0 - - + -
161B ALA 3.3 35.0 - - - +
163B ILE* 1.3 71.6 - - - +
165B ILE* 1.3 60.2 + - - +
166B SER* 5.4 0.4 - - - -
194B ASN 5.8 0.9 - - - +
198B ASP* 2.9 30.8 + - - +
199B ALA 3.0 24.4 + - - +
200B HIS* 4.6 3.3 - - - +
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Residues in contact with ILE 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B TYR* 3.9 15.7 - - + -
121B ARG 2.8 15.9 + - - +
122B ILE* 3.7 6.8 - - + +
123B VAL* 2.8 31.1 + - - +
124B ASN 4.1 0.3 + - - -
138B PHE* 3.5 42.4 - - + -
142B PHE* 3.9 18.4 - - + -
163B ILE* 4.1 13.5 - - + +
164B MET* 1.3 76.1 - - - +
166B SER* 1.3 67.1 + - - +
167B PHE* 5.1 2.0 - - + -
199B ALA* 3.4 4.7 - - + -
201B PHE* 3.9 13.0 - - + -
224B PHE* 3.6 28.9 - - + -
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Residues in contact with SER 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B VAL* 4.1 15.0 - - - -
124B ASN* 3.4 17.0 - - - -
164B MET* 5.1 1.0 + - - -
165B ILE* 1.3 79.2 - - - +
167B PHE* 1.3 68.8 + - - +
168B GLY 4.2 0.3 + - - -
172B HIS* 6.0 0.3 - - - -
199B ALA 3.1 5.9 + - - +
200B HIS* 3.4 27.2 + - - +
201B PHE* 2.9 26.5 + - - -
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Residues in contact with PHE 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ASN* 2.7 54.7 + - - +
125B TYR* 4.0 2.2 - - - -
126B THR* 3.6 43.3 - - + +
134B VAL* 4.4 3.4 - - + -
138B PHE* 3.8 32.8 - + - -
165B ILE* 5.1 2.2 - - + -
166B SER* 1.3 79.2 - - - +
168B GLY* 1.3 58.4 + - - +
201B PHE* 3.3 28.7 - - + +
203B ASP* 3.3 26.7 - - - +
207B TRP* 4.2 8.3 - + - -
216B LEU* 4.0 18.6 - - + -
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Residues in contact with GLY 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B SER 4.2 0.4 + - - -
167B PHE* 1.3 75.8 - - - +
169B ILE* 1.3 66.0 + - - -
172B HIS* 4.4 17.0 - - - -
178B PHE* 3.5 9.7 - - - -
200B HIS* 5.9 1.2 - - - +
201B PHE 2.9 10.5 + - - +
202B ASP* 3.3 5.5 - - - -
203B ASP* 2.9 20.8 + - - +
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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
------------------------------------------------------------
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