Contacts of the strand formed by residues 100 - 106 (chain A) in PDB entry 2AY6
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 THR 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A LEU* 5.1 1.9 - - + +
95A LEU* 3.9 20.5 - - + +
96A LYS* 2.7 26.9 + - - +
97A SER* 2.9 15.2 + - - +
99A THR* 1.3 79.6 + - - +
101A ALA* 1.3 65.5 + - - +
102A THR* 3.9 17.2 + - - +
271A LEU* 4.4 10.8 - - + -
272A ALA 3.4 5.4 - - - +
273A LEU* 4.5 18.1 - - + +
280A ARG* 3.2 22.4 + - - +
284A GLN* 4.8 0.2 - - - +
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Residues in contact with ALA 101 (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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100A THR* 1.3 73.9 - - - +
102A THR* 1.3 65.7 + - - +
270A LEU 3.8 0.3 - - - +
271A LEU* 3.4 2.6 - - - -
272A ALA* 2.7 43.8 + - + +
280A ARG* 3.9 8.7 - - + +
283A ALA* 4.0 5.6 - - + -
284A GLN* 3.6 26.9 - - - +
287A MET* 3.5 22.9 - - - -
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Residues in contact with THR 102 (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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74A SER* 4.0 0.9 - - - +
80A GLN* 3.0 60.2 + - + +
100A THR* 3.9 8.9 + - - +
101A ALA* 1.3 77.4 - - - +
103A LEU* 1.3 64.7 + - - +
269A CYS* 4.4 12.1 - - + -
270A LEU 3.4 4.3 - - - +
271A LEU* 3.3 29.6 - - + +
284A GLN* 3.1 24.7 + - - -
287A MET* 4.1 2.5 - - - -
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Residues in contact with LEU 103 (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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74A SER* 3.7 17.5 - - - -
102A THR* 1.3 76.7 - - - +
104A ALA* 1.3 69.1 + - - +
105A THR* 3.5 6.1 + - + +
114A GLN* 4.1 28.0 - - + +
269A CYS* 2.9 8.0 - - - -
270A LEU* 2.8 39.9 + - + +
287A MET* 3.7 52.7 - - + +
288A ALA* 4.2 0.9 - - - +
290A LEU* 5.4 1.1 - - + -
291A ASN* 3.3 38.4 - - - +
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Residues in contact with ALA 104 (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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74A SER 2.9 19.0 + - - +
75A GLY* 3.7 16.8 - - - -
79A PHE* 4.2 19.7 - - + -
80A GLN* 4.9 1.6 - - + +
102A THR* 5.1 0.4 - - - +
103A LEU* 1.3 73.5 - - - +
105A THR* 1.3 60.8 + - - +
268A GLY 3.7 6.5 - - - +
269A CYS* 4.1 3.8 - - - -
291A ASN* 3.5 22.3 + - - +
295A TYR* 4.3 0.2 + - - -
298A PRO* 3.7 18.1 - - + +
299A PRO 6.0 0.9 - - - +
303A ALA* 5.5 5.4 - - + -
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Residues in contact with THR 105 (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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103A LEU* 3.5 26.9 - - + +
104A ALA* 1.3 80.4 - - - +
106A VAL* 1.3 61.4 + - - +
107A GLY 2.9 20.8 + - - -
110A GLY 3.9 4.7 - - - +
111A ALA* 3.5 33.8 + - + +
114A GLN* 4.4 4.3 - - + -
266A ARG 3.5 5.9 - - - +
267A THR* 4.1 0.5 - - - -
268A GLY 2.9 30.8 + - - +
269A CYS* 3.1 2.1 + - - -
270A LEU* 4.1 3.8 - - + +
295A TYR* 4.1 6.5 - - - +
298A PRO* 4.9 0.6 - - - +
299A PRO* 4.5 7.3 - - - +
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Residues in contact with VAL 106 (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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105A THR* 1.3 70.7 - - - +
107A GLY* 1.3 65.1 + - - +
110A GLY* 3.1 17.5 + - - -
266A ARG* 3.4 30.7 - - + -
295A TYR* 3.6 38.5 + - + -
299A PRO* 3.7 22.2 - - + -
106B VAL* 4.3 6.7 - - + -
295B TYR* 3.6 38.6 - - + +
297B PHE 4.1 1.8 - - - +
299B PRO* 4.2 9.9 - - + -
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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