Contacts of the helix formed by residues 327 - 342 (chain A) in PDB entry 2OAT
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 PRO 327 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A GLN* 4.2 9.2 - - - +
108A LEU* 4.0 19.1 - - + +
109A THR 3.6 23.3 - - - +
110A LEU* 4.1 7.6 - - - +
111A THR* 4.3 3.8 - - - +
117A ASN* 3.3 39.5 - - + +
119A VAL* 3.6 28.6 - - + +
325A GLY 3.6 0.4 - - - +
326A ASN* 1.3 83.5 - - + +
328A LEU* 1.3 60.0 + - - +
330A CYS* 3.4 1.5 + - + -
331A ARG* 3.1 24.3 + - - +
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Residues in contact with LEU 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 3.6 24.7 - - + +
104A GLN* 3.8 12.5 - - + +
105A VAL* 3.3 45.3 - - + +
109A THR* 3.8 28.2 + - + +
299A TYR* 4.0 7.6 - - + -
326A ASN* 3.0 9.9 + - - +
327A PRO* 1.3 75.9 - - - +
329A GLY* 1.3 67.2 + - - +
331A ARG* 3.4 2.6 + - - +
332A VAL* 3.1 26.6 + - - +
101B LEU* 4.0 8.5 - - + -
298B LEU 3.5 24.9 - - - +
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Residues in contact with GLY 329 (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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299A TYR* 3.9 28.6 - - - -
301A VAL* 3.7 12.8 - - - +
326A ASN* 2.7 21.9 + - - -
328A LEU* 1.3 74.0 - - - +
330A CYS* 1.3 63.3 + - - +
332A VAL* 3.3 5.8 + - - +
333A ALA* 3.0 24.1 + - - +
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Residues in contact with CYS 330 (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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119A VAL* 3.6 20.9 - - + -
120A LEU* 3.4 39.0 - - - -
123A TYR* 3.7 24.5 - - + -
301A VAL* 5.9 0.7 - - - -
325A GLY* 3.7 9.0 - - - -
326A ASN 3.1 20.9 + - - +
327A PRO 4.3 0.2 - - - -
328A LEU 3.2 0.6 - - - -
329A GLY* 1.3 76.6 - - - +
331A ARG* 1.3 57.8 + - - +
333A ALA* 3.1 7.9 + - - +
334A ILE* 2.8 34.0 + - - +
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Residues in contact with ARG 331 (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 ALA* 3.7 17.8 - - + +
103A SER* 6.2 0.2 - - - -
104A GLN* 3.3 44.7 + - + +
118A ASN* 3.8 20.8 + - - -
119A VAL* 3.9 15.3 - - + +
122A GLU* 3.3 37.6 + - - -
327A PRO 3.1 13.3 + - - +
328A LEU 3.8 4.7 - - - +
329A GLY 3.3 0.2 - - - -
330A CYS* 1.3 77.8 - - - +
332A VAL* 1.3 62.2 + - + +
334A ILE* 3.5 17.6 + - - +
335A ALA* 3.3 20.8 + - - +
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Residues in contact with VAL 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ILE* 3.6 18.3 - - + +
100A ALA* 4.4 4.3 - - - -
101A LEU* 3.2 45.1 - - + -
295A SER* 3.7 33.2 - - - +
298A LEU* 4.3 3.6 - - + -
299A TYR* 4.1 12.1 - - + -
328A LEU 3.1 17.1 + - - +
329A GLY* 3.7 8.1 - - - +
330A CYS 3.2 0.4 - - - -
331A ARG* 1.3 75.8 - - - +
333A ALA* 1.3 54.7 + - - +
335A ALA 3.4 0.9 + - - -
336A ALA* 2.8 33.4 + - - +
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Residues in contact with ALA 333 (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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123A TYR* 3.5 25.8 - - + -
294A LEU* 3.3 22.7 - - + +
301A VAL* 4.3 13.5 - - + -
329A GLY 3.0 17.6 + - - +
330A CYS* 3.1 5.6 + - - +
332A VAL* 1.3 76.0 - - - +
334A ILE* 1.3 66.2 + - - +
336A ALA* 3.2 1.0 + - - +
337A LEU* 3.0 30.3 + - - +
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Residues in contact with ILE 334 (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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119A VAL* 4.8 2.5 - - + +
122A GLU* 4.1 14.8 - - + +
123A TYR* 3.8 42.0 - - + +
126A TYR* 4.1 22.4 - - + -
330A CYS 2.8 23.1 + - - +
331A ARG* 3.9 28.7 - - - +
332A VAL 3.4 0.2 - - - -
333A ALA* 1.3 77.3 - - - +
335A ALA* 1.3 61.8 + - - +
337A LEU* 3.3 2.6 + - - +
338A GLU* 3.0 47.1 + - + +
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Residues in contact with ALA 335 (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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96A LYS* 4.0 20.9 - - - +
97A ILE* 4.0 8.7 - - - -
100A ALA* 3.7 28.9 - - + -
331A ARG 3.3 4.1 + - - +
332A VAL 3.6 7.2 - - - +
333A ALA 3.2 0.6 - - - -
334A ILE* 1.3 79.0 - - - +
336A ALA* 1.3 61.7 + - - +
338A GLU* 3.2 12.6 + - - +
339A VAL* 3.0 26.7 + - - +
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Residues in contact with ALA 336 (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 GLN* 3.1 33.4 + - - +
97A ILE* 3.7 15.0 - - + +
293A ALA 3.8 0.4 - - - +
294A LEU 3.4 23.8 - - - +
295A SER 3.7 16.2 - - - -
332A VAL 2.8 18.0 + - - +
333A ALA 3.2 0.2 + - - -
335A ALA* 1.3 73.1 - - - +
337A LEU* 1.3 62.0 + - - +
339A VAL* 3.6 1.9 + - - +
340A LEU* 3.4 14.4 + - - +
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Residues in contact with LEU 337 (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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123A TYR* 4.4 3.8 - - + -
126A TYR* 3.4 40.4 - - + +
127A ILE* 4.2 18.8 - - + -
130A LEU* 4.3 16.6 - - + -
131A PHE* 4.5 4.3 - - + -
269A LEU* 4.0 24.5 - - + -
275A TRP* 3.8 6.8 - - + -
294A LEU* 3.9 29.4 - - + +
333A ALA 3.0 22.6 + - - +
336A ALA* 1.3 74.4 - - - +
338A GLU* 1.3 66.2 + - - +
340A LEU* 3.3 11.2 + - + +
341A GLU* 3.1 22.3 + - - +
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Residues in contact with GLU 338 (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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96A LYS* 3.0 32.7 + - - +
126A TYR* 3.5 23.4 - - + +
334A ILE* 3.0 35.7 + - - +
335A ALA* 3.2 7.5 + - - +
337A LEU* 1.3 78.0 - - - +
339A VAL* 1.3 52.4 + - - +
341A GLU* 3.2 3.9 + - - +
342A GLU* 2.8 49.3 + - - +
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Residues in contact with VAL 339 (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 GLN* 3.6 26.2 - - + -
94A HIS* 3.4 46.2 - - + +
96A LYS* 4.2 13.5 - - + -
97A ILE* 4.1 8.7 - - + -
335A ALA 3.0 19.6 + - - +
336A ALA 3.8 5.6 - - - +
338A GLU* 1.3 74.4 - - - +
340A LEU* 1.3 59.4 + - - +
342A GLU* 4.7 3.4 - - - +
343A GLU* 2.9 44.6 + - - +
345A LEU* 3.9 6.9 - - + +
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Residues in contact with LEU 340 (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 ASN* 4.4 8.3 - - + -
90A GLN* 3.7 28.5 - - + +
269A LEU* 3.7 46.9 - - + +
270A ALA* 4.0 13.1 - - + +
275A TRP* 3.7 24.2 - - + -
293A ALA 4.7 0.2 - - - +
336A ALA 3.4 15.9 + - - +
337A LEU* 3.3 14.2 + - + +
339A VAL* 1.3 81.3 - - - +
341A GLU* 1.3 59.3 + - - +
344A ASN* 3.4 1.4 + - - -
345A LEU* 3.3 37.3 + - + +
346A ALA 4.8 1.6 + - - -
418A LEU* 4.5 0.2 - - + -
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Residues in contact with GLU 341 (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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126A TYR* 4.4 13.8 + - - +
130A LEU* 4.4 13.8 - - - +
275A TRP* 3.8 30.9 + - + -
337A LEU 3.1 12.3 + - - +
338A GLU* 3.7 8.1 - - - +
340A LEU* 1.3 73.6 - - - +
342A GLU* 1.3 68.9 + - + +
344A ASN* 3.2 21.8 + - - +
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Residues in contact with GLU 342 (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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96A LYS* 3.1 33.8 + - - +
338A GLU* 2.8 33.1 + - - +
339A VAL* 4.4 2.6 + - - +
341A GLU* 1.3 78.5 - - + +
343A GLU* 1.3 62.9 + - + +
344A ASN* 3.3 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
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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