Contacts of the strand formed by residues 259 - 263 (chain C) in PDB entry 1AX4
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 ALA 259 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C TYR* 3.8 8.7 - - - -
107C LEU* 4.3 15.7 - - + -
219C PHE* 3.7 23.1 - - + -
220C VAL 3.3 2.5 + - - +
221C VAL* 3.5 3.1 - - + -
222C MET 2.9 22.1 + - - -
257C ALA* 3.5 7.4 - - - +
258C ASP* 1.3 81.8 - - - +
260C LEU* 1.3 64.5 + - - +
277C ALA 3.2 13.2 - - - +
278C ILE* 4.2 11.0 - - + -
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Residues in contact with LEU 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C PHE* 3.7 40.4 - - + -
91C TYR* 4.0 7.9 - - + -
107C LEU* 4.6 0.3 - - - +
221C VAL* 4.3 1.8 - - - -
222C MET 3.3 15.0 - - - +
224C SER* 3.7 7.2 - - - +
254C TYR* 3.8 18.2 - - + -
259C ALA* 1.3 77.8 - - - +
261C THR* 1.3 68.0 + - - +
262C MET* 3.8 30.3 - - + -
275C LEU* 4.0 7.9 - - + +
276C VAL* 3.5 7.8 - - - +
277C ALA* 2.8 52.5 + - + +
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Residues in contact with THR 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C GLY 5.1 0.9 - - - -
103C ALA* 4.2 26.0 - - + +
104C GLU* 4.5 12.5 + - - +
107C LEU* 3.7 29.2 - - + -
108C PHE* 4.2 14.1 - - + -
188C VAL* 5.8 0.2 - - - +
221C VAL* 3.9 10.3 - - + +
222C MET 3.2 2.7 + - - +
223C ASP* 3.6 21.8 - - - +
224C SER* 2.8 25.5 + - - -
260C LEU* 1.3 73.8 - - - +
262C MET* 1.3 63.5 + - - +
275C LEU 3.6 4.7 - - - -
276C VAL* 4.9 1.1 - - + -
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Residues in contact with MET 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C PHE* 3.6 26.2 - - + -
100C GLY* 3.8 7.8 - - - -
103C ALA* 4.4 2.1 - - - +
223C ASP* 5.5 0.2 - - - -
224C SER* 3.8 21.1 - - - +
225C ALA* 4.5 0.9 - - - +
227C PHE* 3.5 29.6 - - + -
260C LEU* 3.8 11.0 - - + -
261C THR* 1.3 79.1 - - - +
263C SER* 1.3 70.8 + - - +
264C ALA* 4.5 6.7 - - - -
268C PRO* 3.8 23.8 - - + -
274C GLY* 3.2 6.4 - - - -
275C LEU* 2.8 52.4 + - + +
312C MET* 5.8 1.1 - - - +
316C LEU* 4.1 8.7 - - + -
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Residues in contact with SER 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C GLY* 3.7 10.4 - - - +
223C ASP* 5.7 0.4 + - - -
225C ALA* 3.7 21.5 - - - +
262C MET* 1.3 77.7 - - - +
264C ALA* 1.3 59.7 + - - +
265C LYS* 3.1 9.8 + - - +
266C LLP 2.6 79.4 + - - +
268C PRO* 4.0 1.0 - - - +
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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