Contacts of the strand formed by residues 259 - 263 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B TYR* 3.7 9.1 - - - -
107B LEU* 4.4 13.5 - - + -
219B PHE* 3.7 22.9 - - + -
220B VAL 3.3 2.9 + - - +
221B VAL* 3.5 4.2 - - + -
222B MET 2.8 22.5 + - - -
257B ALA* 3.5 7.0 - - - +
258B ASP* 1.3 81.0 - - - +
260B LEU* 1.4 63.5 + - - +
277B ALA 3.3 14.8 - - - +
278B ILE* 4.1 12.3 - - + +
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Residues in contact with LEU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PHE* 3.7 37.2 - - + -
91B TYR* 4.0 4.9 - - + -
107B LEU* 4.7 0.9 - - - +
221B VAL* 4.3 2.0 - - - -
222B MET 3.3 16.2 - - - +
224B SER* 3.6 6.5 - - - +
254B TYR* 3.8 24.5 - - + -
259B ALA* 1.4 75.3 - - - +
261B THR* 1.3 75.2 + - - +
262B MET* 3.9 20.0 - - + -
275B LEU* 4.0 8.1 - - + +
276B VAL* 3.6 7.8 - - - +
277B ALA* 2.8 47.7 + - + +
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Residues in contact with THR 261 (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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100B GLY 5.1 1.1 - - - -
103B ALA* 4.2 26.0 - - + +
104B GLU* 4.4 12.5 + - - +
107B LEU* 3.8 23.8 - - + -
108B PHE* 4.2 14.7 - - + -
135B THR* 6.0 0.2 - - - +
221B VAL* 3.9 10.2 - - + +
222B MET 3.2 2.5 + - - +
223B ASP* 3.6 22.6 - - - +
224B SER* 2.8 26.3 + - - -
260B LEU* 1.3 77.1 - - - +
262B MET* 1.3 62.6 + - - +
275B LEU 3.6 5.2 - - - -
276B VAL* 4.9 1.1 - - + +
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Residues in contact with MET 262 (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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89B PHE* 3.5 34.8 - - + -
100B GLY* 3.8 8.0 - - - -
103B ALA* 4.4 2.2 - - - +
223B ASP* 5.5 0.4 - - - -
224B SER* 3.6 23.6 - - - +
225B ALA 4.5 0.4 - - - +
227B PHE* 3.6 19.3 - - + -
260B LEU* 3.9 11.4 - - + -
261B THR* 1.3 76.3 - - - +
263B SER* 1.3 71.2 + - - +
264B ALA* 4.6 7.0 - - - -
268B PRO* 3.8 23.8 - - + -
274B GLY* 3.1 6.8 - - - -
275B LEU* 2.8 52.3 + - + +
312B MET* 5.8 1.1 - - - +
316B LEU* 4.2 8.7 - - + -
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Residues in contact with SER 263 (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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100B GLY* 3.7 10.1 - - - +
223B ASP* 5.7 0.4 + - - -
225B ALA* 3.7 19.9 - - - +
262B MET* 1.3 79.9 - - - +
264B ALA* 1.3 60.0 + - - +
265B LYS* 3.1 11.5 + - - +
266B LLP 2.5 79.2 + - - +
268B PRO* 4.0 2.4 - - - +
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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