Contacts of the strand formed by residues 93 - 97 (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 TYR 93 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82C LYS* 5.2 4.0 - - - +
91C TYR* 3.6 0.6 - - - +
92C ASP* 1.3 98.0 - - + +
94C ILE* 1.3 67.8 - - - +
277C ALA* 3.2 5.7 - - - +
278C ILE* 2.9 51.7 + - + +
280C ASP* 3.9 30.2 + - - -
282C GLU* 3.6 37.4 + - + +
285C PHE* 3.4 50.7 - + + -
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Residues in contact with ILE 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C TYR* 3.8 37.4 + - + +
81C LEU* 3.9 23.3 - - + -
82C LYS* 3.6 42.9 - - + +
85C ALA* 3.5 32.1 - - + -
91C TYR 5.4 1.1 - - - +
92C ASP 5.5 0.2 - - - -
93C TYR* 1.3 82.4 - - - +
95C ILE* 1.3 68.5 + - - +
96C PRO* 4.6 2.2 - - + -
275C LEU* 4.1 9.4 - - + -
276C VAL 3.2 7.6 - - - +
277C ALA* 4.2 6.7 - - + -
278C ILE* 6.3 0.2 - - - -
285C PHE* 3.5 10.9 - - - -
289C ARG* 5.0 1.0 + - - -
299C VAL 5.0 1.2 - - - +
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Residues in contact with ILE 95 (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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94C ILE* 1.3 78.5 - - - +
96C PRO* 1.3 81.2 - - + +
106C ILE* 4.2 11.2 - - + -
275C LEU* 4.1 2.5 - - - -
276C VAL* 2.8 51.8 + - + +
278C ILE* 4.6 1.3 - - + -
285C PHE* 3.9 20.4 - - + +
288C ALA* 3.4 34.8 - - + -
289C ARG* 3.7 20.2 - - + +
292C CYS* 3.6 28.7 - - + -
299C VAL* 4.8 5.8 - - - +
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Residues in contact with PRO 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C TYR* 4.3 12.3 - - + -
81C LEU* 4.4 10.3 - - + -
94C ILE* 4.3 4.7 - - + +
95C ILE* 1.3 98.8 - - + +
97C ALA* 1.3 60.3 + - - +
106C ILE* 4.4 0.2 - - - +
274C GLY 3.8 6.5 - - - +
275C LEU* 4.1 6.4 - - + -
292C CYS* 4.4 2.3 - - - -
299C VAL 3.5 18.2 - - - +
301C TYR 3.7 33.4 - - - +
302C GLY* 3.4 15.7 - - - +
304C LEU* 4.3 12.3 - - + -
309C MET* 4.1 15.0 - - - -
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Residues in contact with ALA 97 (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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95C ILE 4.5 2.2 - - - +
96C PRO* 1.3 76.5 - - - +
98C HIS* 1.3 61.0 + - - +
99C GLN 3.2 4.0 - - - +
102C GLY 4.1 3.4 - - - -
103C ALA* 3.6 39.7 - - + +
106C ILE* 4.2 8.7 - - + -
274C GLY 2.9 32.7 + - - +
275C LEU 4.2 0.4 - - - +
296C GLU* 4.0 2.9 - - - +
302C GLY 3.2 9.0 - - - -
304C LEU* 3.5 8.6 - - - +
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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