Contacts of the strand formed by residues 234 - 239 (chain X) in PDB entry 2AE0
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 VAL 234 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121X TYR 4.5 1.6 + - - +
133X ARG* 5.5 0.4 - - - +
160X ASP* 3.6 43.6 + - + +
163X GLY* 5.1 1.3 - - - -
180X TYR* 3.9 17.9 - - + -
182X GLY 3.8 7.4 - - - +
183X LYS* 4.5 13.5 - - + -
232X SER* 5.2 2.2 - - - +
233X PHE* 1.3 100.6 - - - +
235X PHE* 1.3 76.2 + - - +
236X PHE* 3.6 33.0 - - + -
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Residues in contact with PHE 235 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121X TYR* 3.5 11.7 - - + -
122X ARG 3.4 15.3 - - - -
123X MET* 3.8 37.9 - - + +
124X PRO* 3.7 17.0 - - + -
129X ARG* 3.6 24.7 - - + -
136X ILE* 4.3 7.9 - - + -
141X LEU* 3.7 28.0 - - + -
181X ALA* 3.0 20.8 + - - -
182X GLY 2.9 18.8 + - - +
183X LYS 4.0 4.7 - - - -
184X ASN* 3.8 20.4 - - + -
233X PHE* 3.8 21.5 - + - -
234X VAL* 1.3 82.0 - - - +
236X PHE* 1.3 64.4 + - - +
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Residues in contact with PHE 236 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120X ILE* 3.8 25.6 - - + -
121X TYR 2.9 14.3 + - - +
122X ARG* 3.1 26.2 - - - +
123X MET 3.9 0.3 + - - -
147X LEU* 3.6 8.2 - - + +
156X ASN 5.4 0.2 - - - -
159X MET* 3.7 38.6 - - + -
160X ASP* 3.5 21.3 - - - -
163X GLY 3.5 34.8 - - - -
164X SER* 4.5 1.3 - - - -
178X PHE* 4.1 13.7 - - + -
179X SER 3.2 11.9 - - - +
180X TYR 4.4 0.2 - - - -
181X ALA* 3.5 8.0 - - - +
234X VAL* 3.6 29.8 - - + -
235X PHE* 1.3 75.7 - - - +
237X LYS* 1.3 63.1 + - - +
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Residues in contact with LYS 237 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122X ARG* 5.3 0.7 - - + -
147X LEU* 4.6 1.1 - - - -
178X PHE* 3.3 6.3 - - - -
179X SER* 2.9 46.6 + - - +
180X TYR 3.6 20.0 + - - -
181X ALA* 3.9 15.4 + - + +
236X PHE* 1.3 76.6 - - - +
238X PRO* 1.3 82.7 - - + +
239X GLN* 4.6 5.2 - - - -
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Residues in contact with PRO 238 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122X ARG* 5.8 1.6 - - + -
147X LEU* 4.6 13.9 - - + -
177X PHE 3.8 1.3 - - - +
178X PHE* 3.8 25.1 - - + -
237X LYS* 1.3 99.1 - - + +
239X GLN* 1.3 60.3 + - - +
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Residues in contact with GLN 239 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177X PHE* 2.9 52.0 + - + +
179X SER* 2.7 35.2 + - - +
237X LYS* 4.6 6.9 - - - -
238X PRO* 1.3 77.5 - - - +
240X SER* 1.3 81.2 + - - +
241X PHE 3.4 1.4 + - - -
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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