Contacts of the strand formed by residues 235 - 239 (chain A) in PDB entry 1AXC
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 LEU 235 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A PHE* 5.4 0.2 - - + -
160A ILE* 4.2 9.2 - - + -
207A PHE* 3.4 40.6 - - + -
212A LEU* 4.1 17.0 - - + -
227A LEU* 4.1 13.0 - - + -
228A SER 3.3 28.3 - - - +
229A MET* 3.4 25.4 - - + +
233A VAL 3.7 1.6 + - - -
234A PRO* 1.3 74.8 - - - +
236A VAL* 1.3 63.9 + - - +
237A VAL* 3.9 23.6 - - + -
249A TYR 3.5 0.6 - - - +
250A TYR* 3.0 9.0 - - - +
251A LEU* 2.9 33.3 + - + +
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Residues in contact with VAL 236 (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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133A TYR* 3.2 41.3 - - + +
226A THR 3.2 5.5 - - - +
227A LEU* 3.3 2.1 - - - -
228A SER* 2.9 40.5 + - - +
234A PRO 4.1 1.8 - - - +
235A LEU* 1.3 80.2 - - - +
237A VAL* 1.3 63.3 + - - +
238A GLU* 4.9 3.5 - - + +
248A LYS* 4.2 24.9 - - + +
249A TYR 3.4 5.4 - - - +
250A TYR* 3.6 33.0 - - + +
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Residues in contact with VAL 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A PHE* 3.8 10.5 - - + -
212A LEU* 4.4 4.3 - - + -
215A PHE* 3.8 29.2 - - + -
225A VAL* 3.3 27.8 - - + -
226A THR 3.5 3.4 - - - -
227A LEU* 3.6 20.9 - - + -
235A LEU* 3.9 18.6 - - + -
236A VAL* 1.3 73.7 - - - +
238A GLU* 1.3 58.5 + - - +
239A TYR* 3.5 15.7 - - + +
248A LYS* 3.5 1.6 - - - -
249A TYR* 2.9 37.2 + - + +
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Residues in contact with GLU 238 (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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224A THR 4.3 0.3 - - - +
225A VAL* 3.6 7.6 - - - -
226A THR* 3.0 44.8 + - - +
236A VAL* 3.9 4.9 - - + -
237A VAL* 1.3 74.2 - - - +
239A TYR* 1.3 72.9 + - - +
240A LYS* 3.1 45.5 + - + +
246A HIS* 3.2 20.7 + - + +
247A LEU 3.6 4.0 - - - +
248A LYS* 3.5 34.0 + - + -
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Residues in contact with TYR 239 (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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141A SER* 4.1 14.6 + - - -
144A PHE* 3.8 20.3 - - - -
215A PHE 3.8 16.8 - - - -
216A THR* 3.7 19.1 - - - +
218A ALA* 3.3 34.8 - - + +
219A THR* 4.0 10.4 + - - -
221A LEU* 4.7 5.8 - - + -
222A SER* 4.5 12.3 - - - -
224A THR 4.4 10.5 - - - -
225A VAL* 3.8 9.1 - - + +
237A VAL* 3.5 22.2 - - + +
238A GLU* 1.3 76.7 - - - +
240A LYS* 1.3 62.2 + - - +
241A ILE* 3.4 1.4 + - - +
246A HIS* 3.2 2.4 - - - -
247A LEU* 2.8 45.2 + - + +
249A TYR* 3.8 23.1 - + - -
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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