Contacts of the strand formed by residues 199 - 206 (chain A) in PDB entry 4A8W
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 199 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ILE* 4.3 0.7 - - - -
198A ALA* 1.3 75.0 - - - +
200A TYR* 1.3 59.7 + - - +
201A VAL 3.9 0.4 + - - -
273A MET* 3.7 33.4 - - + -
274A GLY 3.4 3.8 - - - -
275A GLY* 3.5 32.8 - - - -
276A PRO* 4.5 2.4 - - + +
279A LEU* 5.5 0.4 - - + +
280A ASN* 4.8 2.2 + - - -
360A SER* 2.6 34.2 + - - -
363A LEU* 3.6 31.9 - - + -
364A PRO 3.0 12.6 + - - +
365A VAL* 3.5 4.0 - - + -
366A TYR* 2.8 27.4 + - - +
392A SER* 3.5 22.7 - - - -
394A GLY 3.8 15.9 - - - -
395A GLN* 3.3 20.8 - - - +
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Residues in contact with TYR 200 (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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18A PHE* 4.1 4.5 - + - -
27A ALA* 2.7 44.2 + - + +
30A ARG* 4.6 8.0 - - - +
152A CYS* 4.6 8.7 - - + -
153A ILE* 4.3 8.7 - - + -
156A PHE* 3.6 36.6 - + + -
198A ALA 4.0 0.2 + - - -
199A TYR* 1.3 72.0 - - - +
201A VAL* 1.3 76.5 + - - +
202A VAL* 3.4 13.5 + - + +
273A MET* 3.4 2.6 - - - -
274A GLY 2.9 36.3 + - - +
366A TYR* 3.8 30.7 - + + -
368A GLY* 5.2 6.0 - - - -
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Residues in contact with VAL 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A PRO* 4.3 13.0 - - + -
200A TYR* 1.3 81.1 - - - +
202A VAL* 1.3 61.9 + - - +
203A TYR* 3.8 40.3 + - + +
271A THR* 4.5 10.5 - - + -
272A ALA 3.6 9.0 - - - +
273A MET* 3.9 24.9 - - + +
365A VAL* 4.1 12.8 - - + -
366A TYR 2.9 28.1 + - - +
367A VAL* 4.2 7.4 - - - -
368A GLY* 3.9 15.4 + - - -
369A ALA 5.2 0.2 + - - -
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Residues in contact with VAL 202 (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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200A TYR* 4.2 19.1 - - + +
201A VAL* 1.3 74.3 - - - +
203A TYR* 1.3 72.5 + - - +
204A ARG* 4.6 10.1 - - + -
271A THR* 3.8 0.7 - - - -
272A ALA* 2.8 56.0 + - + +
273A MET* 4.4 5.2 - - - +
274A GLY* 4.7 2.5 - - - +
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Residues in contact with TYR 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ALA* 3.6 16.4 - - + -
99A THR 2.6 30.0 + - - -
101A PRO* 3.9 6.9 - - - +
201A VAL* 3.8 17.8 - - + +
202A VAL* 1.3 81.6 - - - +
204A ARG* 1.3 60.6 + - - +
205A ALA 4.3 0.3 + - - -
269A ARG* 3.2 35.5 + - + +
270A ARG 3.4 5.4 - - - +
271A THR* 3.4 33.0 - - + -
367A VAL* 3.7 21.0 - - + +
368A GLY 5.1 0.2 - - - -
369A ALA 4.0 20.0 - - - -
370A PRO* 3.7 29.7 - - + +
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Residues in contact with ARG 204 (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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202A VAL* 3.7 11.9 + - + -
203A TYR* 1.3 74.6 - - - +
205A ALA* 1.3 62.0 + - - +
269A ARG* 3.5 4.3 - - - -
270A ARG* 2.8 44.9 + - + +
272A ALA* 3.8 25.8 - - + -
529A GLU* 2.7 40.7 + - - +
530A TYR* 3.0 22.3 + - + +
543A LYS* 5.0 5.3 - - - +
626A ASN* 3.2 38.6 + - - +
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Residues in contact with ALA 205 (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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203A TYR 4.3 0.4 + - - -
204A ARG* 1.3 74.7 - - - +
206A GLN* 1.3 60.0 + - - +
207A SER* 3.5 2.1 + - - +
267A GLU* 3.7 32.5 - - + +
268A ARG 3.6 6.7 - - - +
269A ARG* 4.5 8.6 - - + +
270A ARG* 5.8 0.2 - - - -
529A GLU* 3.3 43.8 + - + +
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Residues in contact with GLN 206 (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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89A HIS* 5.9 0.3 - - - -
204A ARG 3.7 0.6 + - - -
205A ALA* 1.3 71.4 - - - +
207A SER* 1.4 62.9 + - - +
208A THR* 3.2 22.1 + - - +
209A ASP* 4.6 3.9 + - - +
267A GLU* 4.2 0.5 - - - +
268A ARG* 3.0 70.8 + - + +
270A ARG* 3.0 42.1 + - + +
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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