Contacts of the strand formed by residues 107 - 113 (chain A) in PDB entry 1ASA
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 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A GLN* 3.6 34.4 + - + +
95A PHE* 4.0 14.4 - - + -
101A LEU* 3.3 11.1 + - + +
105A LYS* 4.4 4.9 - - - +
106A ARG* 1.3 79.6 - - - +
108A ARG* 1.3 70.8 + - - +
271A THR* 4.7 2.9 - - - +
272A LEU 3.3 5.8 - - - +
273A VAL* 3.9 17.9 - - + -
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Residues in contact with ARG 108 (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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81A ASP* 4.1 10.1 + - - -
91A GLN* 4.2 1.8 - - - -
105A LYS* 5.0 3.4 - - - -
107A ALA* 1.3 80.7 - - - +
109A THR* 1.3 63.5 + - - +
270A CYS 3.8 0.5 - - - +
271A THR* 3.4 0.7 - - - -
272A LEU* 2.9 33.9 + - + +
280A VAL* 3.7 27.1 - - + +
281A ASP* 3.1 40.3 + - - +
284A PHE* 3.7 49.3 - - + -
288A LYS* 5.3 3.4 - - - +
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Residues in contact with THR 109 (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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81A ASP* 4.0 11.3 - - - +
86A PHE* 5.3 1.0 - - - -
87A GLY* 3.6 28.4 - - - +
90A THR* 4.8 1.7 - - - -
91A GLN* 2.9 42.0 + - + +
108A ARG* 1.3 76.7 + - - +
110A ALA* 1.3 64.4 + - - +
269A ALA* 4.3 8.5 - - - +
270A CYS 3.3 4.5 - - - -
271A THR* 3.4 27.8 - - + -
284A PHE* 3.7 10.8 - - - -
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Residues in contact with ALA 110 (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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81A ASP* 3.6 10.8 - - - -
109A THR* 1.3 76.5 - - - +
111A GLN* 1.3 64.1 + - - +
112A THR* 4.0 2.7 - - + +
269A ALA* 3.4 4.3 - - - +
270A CYS* 2.8 33.4 + - + -
284A PHE* 3.7 9.3 - - + -
287A MET* 3.5 24.7 - - + -
291A ILE* 3.7 23.1 - - + -
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Residues in contact with GLN 111 (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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78A LEU* 3.5 12.4 - - - +
80A ILE 4.2 3.3 - - - +
81A ASP 2.9 16.7 + - - +
82A GLY* 3.1 9.1 - - - -
83A ILE* 2.9 37.9 - - - +
86A PHE* 3.7 32.3 - - + -
110A ALA* 1.3 73.4 - - - +
112A THR* 1.3 64.1 + - - +
267A VAL* 5.7 0.4 - - + -
268A GLY 3.7 5.8 - - - +
295A TYR* 3.6 7.3 + - - -
298A PRO* 2.9 37.4 - - + +
299A PRO* 3.0 27.0 - - - +
303A ALA* 3.3 16.4 - - + +
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Residues in contact with THR 112 (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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110A ALA* 4.0 12.6 - - + +
111A GLN* 1.3 79.7 - - - +
113A PRO* 1.4 67.5 - - - +
114A GLY 3.1 14.0 + - - -
117A GLY 3.8 4.7 - - - +
118A ALA* 3.3 32.3 + - - +
121A VAL* 4.1 9.4 - - + -
266A ARG 3.4 4.5 - - - +
267A VAL* 3.9 1.2 - - - -
268A GLY 2.9 36.5 + - - +
269A ALA 3.5 0.3 + - - -
270A CYS* 4.2 8.7 - - + -
291A ILE* 5.5 0.2 - - + -
295A TYR* 3.6 13.9 - - - +
298A PRO* 4.7 5.2 - - - +
299A PRO* 5.1 0.8 - - - +
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Residues in contact with PRO 113 (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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112A THR* 1.4 81.9 - - - +
114A GLY* 1.3 59.6 + - - +
116A THR* 4.8 0.2 - - - -
117A GLY* 3.1 27.8 + - - -
266A ARG* 3.2 38.2 + - + +
295A TYR* 3.4 43.3 - - + -
299A PRO* 4.4 15.3 - - + -
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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