Contacts of the strand formed by residues 274 - 278 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A PRO* 3.9 3.8 - - - +
97A ALA* 2.9 31.0 + - - +
99A GLN* 3.8 12.6 - - - -
262A MET 3.1 13.9 - - - -
264A ALA* 3.9 3.1 - - - -
273A GLY* 1.3 75.5 - - - -
275A LEU* 1.3 63.3 - - - +
304A LEU* 4.2 0.2 - - - +
312A MET* 3.5 15.3 - - - +
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Residues in contact with LEU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 4.1 28.0 - - + -
85A ALA* 4.7 19.5 - - + -
89A PHE* 4.8 4.7 - - + -
94A ILE* 4.0 15.3 - - + -
95A ILE 3.8 13.5 - - - +
96A PRO* 4.1 5.8 - - + -
97A ALA* 4.2 3.5 - - - +
103A ALA* 3.6 4.0 - - - +
260A LEU* 4.0 12.9 - - + +
261A THR* 3.6 3.6 - - - -
262A MET* 2.9 55.3 + - + +
274A GLY* 1.3 76.3 - - - +
276A VAL* 1.3 80.3 + - - +
277A ALA* 4.5 3.6 - - + +
312A MET* 4.6 8.1 - - - -
316A LEU* 5.1 4.5 - - + -
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Residues in contact with VAL 276 (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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94A ILE* 3.2 4.9 - - - +
95A ILE* 2.8 52.2 + - + +
97A ALA* 5.1 0.2 - - + -
103A ALA* 3.5 39.9 - - + +
106A ILE* 4.3 16.6 - - + -
107A LEU* 4.5 16.2 - - + -
260A LEU 3.5 10.5 - - - +
261A THR* 4.7 2.5 - - + -
275A LEU* 1.3 74.0 - - - +
277A ALA* 1.3 63.4 + - - +
278A ILE* 4.0 27.6 - - + -
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Residues in contact with ALA 277 (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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85A ALA* 4.7 4.9 - - + -
91A TYR* 3.9 13.9 - - + -
93A TYR 3.1 11.2 - - - +
94A ILE* 4.1 11.9 - - + -
259A ALA* 3.2 5.2 - - - +
260A LEU* 2.8 60.5 + - + +
275A LEU* 4.7 5.8 - - + -
276A VAL* 1.3 75.0 - - - +
278A ILE* 1.3 61.7 + - - +
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Residues in contact with ILE 278 (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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91A TYR* 3.6 2.6 - - - +
92A ASP 3.3 2.6 + - - -
93A TYR* 2.8 36.4 + - + +
94A ILE* 6.3 0.2 - - - -
95A ILE* 4.6 1.8 - - + -
107A LEU* 4.7 2.2 - - + -
219A PHE* 5.3 1.3 - - + -
258A ASP 4.0 8.1 - - - +
259A ALA* 4.1 10.8 - - + -
276A VAL* 4.0 20.9 - - + -
277A ALA* 1.3 78.6 - - - +
279A ARG* 1.3 68.3 + - - +
280A ASP 4.0 0.4 - - - +
281A ASN* 3.5 40.2 - - + +
284A ILE* 4.1 17.5 - - + +
285A PHE* 3.6 35.9 - - + +
288A ALA* 4.5 6.3 - - + -
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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