Contacts of the helix formed by residues 91 - 96 (chain A) in PDB entry 2FY5
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 91 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ARG 3.7 0.8 + - - -
90A LEU* 1.3 73.4 - - - +
92A LEU* 1.3 63.9 + - - +
93A PRO* 3.5 1.4 - - + -
95A ASN* 2.9 29.1 + - - +
96A SER* 4.9 0.4 - - - -
237A SER 3.3 25.8 - - - +
238A ASP* 3.7 21.8 - - - +
239A GLY* 3.8 5.7 - - - +
240A ARG* 4.7 0.4 - - - +
387A ILE* 3.8 21.8 - - + -
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Residues in contact with LEU 92 (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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90A LEU 4.5 2.9 - - - +
91A ALA* 1.3 69.2 - - - +
93A PRO* 1.3 74.4 - - + +
96A SER* 2.9 35.1 + - - +
97A SER* 2.9 23.2 + - - +
163A ARG* 3.4 34.1 - - - +
236A THR 5.2 0.6 + - - +
238A ASP 4.9 0.8 + - - -
240A ARG* 3.3 41.8 - - - +
304A TYR* 3.8 32.5 - - + +
305A ASP* 4.3 0.7 - - - +
323A GLU* 4.2 15.9 - - + +
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Residues in contact with PRO 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ALA* 3.4 16.7 - - + +
92A LEU* 1.3 93.2 - - + +
94A VAL* 1.3 64.7 + - + +
95A ASN* 2.7 19.8 + - - -
97A SER* 5.0 2.2 - - - -
236A THR 4.8 0.2 - - - +
237A SER* 3.9 20.0 - - - +
290A LEU 4.2 10.3 - - - +
291A HIS* 4.8 1.8 - - + -
304A TYR* 3.5 43.7 - - + +
384A LEU* 4.8 7.4 - - + -
387A ILE* 4.0 15.9 - - + +
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Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU 3.2 2.2 + - - -
93A PRO* 1.3 72.1 - - - +
95A ASN* 1.3 62.4 + - - +
96A SER 3.3 2.8 + - - -
97A SER 4.4 10.8 + - - +
290A LEU* 4.4 16.8 + - + +
291A HIS* 4.2 15.0 - - + -
387A ILE* 3.5 24.0 - - + -
391A LEU* 4.1 38.1 - - + -
552A TYR* 4.7 1.4 - - - +
553A GLY* 2.9 48.9 + - - +
578A PHE* 4.2 18.8 - - + -
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Residues in contact with ASN 95 (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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88A ASN* 5.0 7.7 + - - +
90A LEU* 3.6 43.1 - - + +
91A ALA 2.9 30.5 + - - +
93A PRO 2.7 15.6 + - - -
94A VAL* 1.3 74.5 - - - +
96A SER* 1.3 59.1 + - - +
387A ILE* 4.2 12.9 - - - +
552A TYR* 6.5 0.2 - - - -
553A GLY 5.0 1.4 - - - +
554A PRO 4.3 14.7 - - - +
555A VAL* 4.8 10.6 - - - +
578A PHE* 4.0 20.5 - - - -
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Residues in contact with SER 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR* 3.5 27.3 - - - -
88A ASN* 5.4 8.7 - - - -
90A LEU 5.9 0.7 - - - -
92A LEU* 2.9 33.1 + - - +
94A VAL 3.3 1.5 - - - -
95A ASN* 1.3 83.1 - - - +
97A SER* 1.3 61.5 + - - +
98A PRO* 3.1 15.1 - - - +
163A ARG* 4.2 4.2 + - - -
323A GLU* 4.7 1.2 + - - -
324A HIS* 3.6 17.6 - - - +
552A TYR* 5.1 5.0 - - - +
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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