Contacts of the strand formed by residues 327 - 333 (chain F) in PDB entry 2AJQ
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 327 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267F PRO* 4.0 16.4 - - + -
287F PRO* 4.1 10.1 + - + +
288F ARG 4.0 14.8 - - - +
289F ILE* 3.7 6.4 - - - +
326F TYR* 1.3 73.4 - - - +
328F PRO* 1.3 77.3 - - + +
329F VAL* 3.3 10.3 - - + +
31I TRP* 4.7 5.4 - - + -
32I CYS* 3.1 31.5 - - - +
33I GLY 4.3 1.7 + - - -
34I PRO* 3.4 11.8 - - - +
75I ILE* 2.8 30.4 + - - -
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Residues in contact with PRO 328 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267F PRO* 3.2 5.0 - - - +
268F LYS 3.1 38.3 + - - +
269F GLY* 4.4 0.7 - - - -
270F GLY* 3.8 24.0 - - - +
288F ARG 4.2 1.6 - - - +
290F LYS* 3.7 34.8 - - + +
326F TYR* 3.3 17.2 - - + +
327F THR* 1.3 87.7 - - + +
329F VAL* 1.3 63.7 + - - +
73I ARG* 3.9 14.4 - - - +
74I GLY* 4.2 1.3 - - - -
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Residues in contact with VAL 329 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265F TYR* 4.0 22.7 - - + -
266F GLN 3.3 12.8 - - - +
268F LYS* 4.4 1.5 + - - +
327F THR* 3.3 15.0 - - + +
328F PRO* 1.3 82.3 - - - +
330F GLU* 1.3 62.6 + - - +
31I TRP* 4.1 17.7 - - + -
72I ILE* 4.2 8.8 - - + +
73I ARG* 3.2 33.0 + - - +
74I GLY* 3.3 25.8 - - - +
75I ILE* 4.0 17.5 - - + +
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Residues in contact with GLU 330 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265F TYR* 3.3 7.6 - - - -
266F GLN* 3.0 58.8 + - + +
267F PRO 4.5 0.7 - - - +
268F LYS* 3.0 53.8 + - + +
329F VAL* 1.3 75.1 - - - +
331F HIS* 1.3 59.9 + - - +
332F VAL* 3.4 26.4 + - + +
73I ARG* 3.4 19.7 - - - +
964Z G 5.2 2.1 + - - -
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Residues in contact with HIS 331 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263F SER* 3.1 31.7 + - - -
264F TRP* 3.0 32.2 + - - -
265F TYR* 3.7 30.3 - + + +
330F GLU* 1.3 76.2 - - - +
332F VAL* 1.3 64.3 + - - +
333F VAL* 5.8 3.2 - - + +
64I PRO* 4.9 2.4 + - - +
68I PRO* 3.8 30.8 - - + +
72I ILE 5.8 0.8 + - - +
73I ARG* 6.1 0.2 - - - +
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Residues in contact with VAL 332 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263F SER* 2.9 26.4 - - - -
264F TRP* 2.9 51.7 + - + +
266F GLN* 3.9 14.1 - - + +
330F GLU* 3.4 40.1 + - + +
331F HIS* 1.3 75.4 - - - +
333F VAL* 1.3 61.1 + - - +
334F PHE 3.9 0.2 + - - -
341F HIS* 4.0 17.3 - - + +
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Residues in contact with VAL 333 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258F THR* 5.5 8.3 - - + -
262F GLY 4.2 0.9 - - - +
263F SER* 3.7 15.7 - - - -
264F TRP* 4.7 0.7 - - - -
331F HIS* 5.8 2.9 - - + +
332F VAL* 1.3 76.9 - - - +
334F PHE* 1.3 72.0 + - - +
335F ASN* 3.2 5.4 + - + +
341F HIS* 3.8 10.4 - - - -
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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
------------------------------------------------------------
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