Contacts of the strand formed by residues 274 - 278 (chain D) 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 GLY 274 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96D PRO* 3.8 3.1 - - - +
97D ALA* 2.9 33.3 + - - +
99D GLN* 3.8 12.3 - - - -
262D MET 3.2 12.8 - - - -
264D ALA* 4.0 3.1 - - - -
273D GLY* 1.3 74.8 - - - -
275D LEU* 1.3 64.1 + - - +
304D LEU* 4.3 0.2 - - - +
312D MET* 3.5 16.2 - - - +
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Residues in contact with LEU 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D LEU* 4.1 33.9 - - + -
85D ALA* 4.7 18.4 - - + -
89D PHE* 4.8 7.6 - - + -
94D ILE* 4.1 15.9 - - + -
95D ILE 3.8 15.5 - - - +
96D PRO* 4.1 2.5 - - + -
97D ALA* 4.2 2.9 - - - +
103D ALA* 3.6 5.2 - - - +
260D LEU* 4.0 12.8 - - + +
261D THR* 3.5 3.5 - - - -
262D MET* 2.8 56.5 + - + +
274D GLY* 1.3 75.6 - - - +
276D VAL* 1.3 76.9 + - - +
277D ALA* 4.2 3.4 - - + +
312D MET* 4.6 7.6 - - - -
316D LEU* 5.1 4.5 - - + -
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Residues in contact with VAL 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ILE* 3.3 4.3 - - - +
95D ILE* 2.8 52.4 + - + +
97D ALA* 5.2 0.2 - - + -
103D ALA* 3.4 39.0 - - + +
106D ILE* 4.2 18.4 - - + -
107D LEU* 4.5 17.0 - - + -
260D LEU 3.5 9.9 - - - +
261D THR* 4.8 1.1 - - + -
275D LEU* 1.3 74.3 - - - +
277D ALA* 1.3 62.6 + - - +
278D ILE* 4.0 28.0 - - + -
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Residues in contact with ALA 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D ALA* 4.7 4.7 - - + -
91D TYR* 3.9 15.3 - - + -
93D TYR 3.2 9.4 - - - +
94D ILE* 4.2 11.9 - - + -
259D ALA* 3.3 4.5 - - - +
260D LEU* 2.8 59.1 + - + +
275D LEU* 4.7 5.8 - - + -
276D VAL* 1.3 76.4 - - - +
278D ILE* 1.3 62.2 + - - +
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Residues in contact with ILE 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D TYR* 3.9 2.9 - - - -
92D ASP 3.5 2.4 + - - -
93D TYR* 2.9 36.3 + - + +
94D ILE* 6.3 0.2 - - - -
95D ILE* 4.7 1.6 - - + -
107D LEU* 4.7 2.2 - - + -
219D PHE* 5.2 1.1 - - + -
258D ASP 4.0 8.3 - - - +
259D ALA* 4.1 11.2 - - + -
276D VAL* 4.0 20.0 - - + -
277D ALA* 1.3 77.7 - - - +
279D ARG* 1.3 68.4 + - - +
281D ASN* 3.6 39.5 - - + +
284D ILE* 4.1 15.7 - - + -
285D PHE* 3.6 37.5 - - + +
288D ALA* 4.5 7.4 - - + -
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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