Contacts of the helix formed by residues 1384 - 1390 (chain B) in PDB entry 1XTB
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 THR1384 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A ILE* 3.8 4.5 - - - +
185A ASN* 3.5 12.2 + - - -
186A ILE* 3.6 22.3 - - + +
216A GLU* 3.3 31.2 + - - +
1340B TYR* 3.9 1.8 - - + -
1383B GLY* 1.3 68.9 + - - -
1385B ASN* 1.3 69.0 + - - +
1386B GLY 3.2 3.1 - - - -
1387B GLN* 2.8 44.8 + - - +
1388B HIS* 3.3 5.3 - - - -
1424B LEU* 3.8 10.5 - - + -
1427B ASN* 3.8 19.5 - - + -
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Residues in contact with ASN1385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ILE* 4.0 15.3 - - + +
157A GLY* 5.3 1.4 + - - -
160A ASP* 4.2 5.2 - - - +
184A SER* 2.9 29.5 + - - -
185A ASN* 3.2 44.3 - - - +
1342B GLN* 4.4 3.6 + - - -
1381B GLU* 5.7 3.8 - - + -
1382B PRO* 3.5 13.3 + - + +
1383B GLY 3.4 0.6 - - - -
1384B THR* 1.3 77.4 + - - +
1386B GLY* 1.3 64.1 + - - +
1388B HIS* 2.9 15.6 + - - +
1389B ALA* 3.2 12.8 + - - +
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Residues in contact with GLY1386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1381B GLU* 5.2 1.7 - - - +
1382B PRO 3.3 11.1 + - - -
1383B GLY* 4.5 0.4 - - - -
1384B THR 3.1 1.4 + - - -
1385B ASN* 1.3 78.3 - - - +
1387B GLN* 1.3 56.0 + - - +
1389B ALA* 2.8 21.6 + - - -
1390B PHE* 3.0 33.6 + - - -
1391B TYR* 3.0 26.4 + - - -
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Residues in contact with GLN1387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A GLU* 4.4 4.0 - - - +
357A GLU* 4.9 0.3 - - - +
514A VAL* 4.1 21.1 - - - +
518A LYS* 6.2 0.5 - - - +
1340B TYR* 2.7 38.7 + - - +
1384B THR* 2.8 22.1 + - - +
1386B GLY* 1.3 75.1 - - - +
1388B HIS* 1.3 64.4 + - + +
1389B ALA 3.5 0.2 - - - -
1391B TYR* 3.4 38.5 + - + +
1392B GLN 5.2 0.7 + - - -
1427B ASN* 3.0 30.2 - - - +
1431B GLN* 3.4 28.4 + - - +
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Residues in contact with HIS1388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ILE* 3.3 32.0 - - + +
157A GLY* 3.8 19.3 - - - +
214A THR* 4.0 6.7 - - + -
216A GLU* 2.8 37.0 + - - -
353A GLN* 3.0 19.6 - - - +
357A GLU* 3.1 14.3 - - - +
514A VAL* 5.6 0.9 - - - -
518A LYS* 4.6 16.0 - - - -
2002A S6P 2.7 38.1 + - - +
1384B THR 3.3 12.6 - - - -
1385B ASN 2.9 6.9 + - - +
1387B GLN* 1.3 85.6 + - + +
1389B ALA* 1.3 58.9 + - - +
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Residues in contact with ALA1389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A GLY* 5.7 1.3 - - - -
161A LEU* 4.7 7.6 - - + -
349A ALA 5.7 0.4 - - - +
353A GLN* 3.1 44.3 - - + +
357A GLU* 3.2 18.8 + - - +
1385B ASN 3.2 11.8 + - - +
1386B GLY* 2.8 8.2 + - - +
1387B GLN 3.5 0.2 - - - -
1388B HIS* 1.3 80.7 - - - +
1390B PHE* 1.3 72.8 + - + +
1392B GLN 5.3 0.7 - - - -
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Residues in contact with PHE1390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A GLN* 3.5 33.7 - - + +
356A MET* 3.7 31.1 - - + +
357A GLU 4.8 1.3 - - - +
1338B LEU* 4.1 11.0 - - + -
1379B TRP* 3.6 28.9 - + - -
1381B GLU* 3.8 34.3 - - + -
1386B GLY* 3.0 18.3 + - - -
1389B ALA* 1.3 85.3 - - + +
1391B TYR* 1.3 88.2 + + - +
1392B GLN 2.9 6.5 - - - +
1393B LEU* 2.9 21.8 + - - +
1394B ILE* 3.6 11.2 + - + +
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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