Contacts of the strand formed by residues 1334 - 1339 (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 THR1334 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333A GLU* 4.2 2.1 + - - +
334A THR* 3.7 22.2 - - + -
377A ILE* 3.5 30.9 - - + +
1327B ILE* 6.0 0.7 - - - +
1332B CYS* 3.5 4.5 - - - +
1333B GLU* 1.3 88.0 - - + +
1335B GLN* 1.3 61.5 + - - +
1376B PRO* 4.2 4.3 - - - +
1377B ILE* 3.2 19.5 - - + +
1379B TRP* 3.1 23.2 + - + +
1400B MET 5.5 0.4 + - - -
1401B ILE* 3.6 12.0 - - - +
1402B PRO* 3.3 24.7 - - - +
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Residues in contact with GLN1335 (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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1323B GLY* 5.1 8.7 - - - -
1326B TYR* 5.8 0.2 - - - -
1334B THR* 1.3 76.2 - - - +
1336B ALA* 1.3 81.0 + - - +
1337B VAL* 3.9 8.0 + - + -
1355B ASP* 5.5 1.6 - - - +
1376B PRO* 4.1 20.6 - - + -
1377B ILE 2.9 5.7 + - - +
1378B VAL* 3.4 14.8 - - + +
1379B TRP* 3.1 25.7 + - - +
1402B PRO* 3.3 34.2 + - - +
1404B ASP* 3.7 21.0 + - - +
1496B LYS* 3.7 25.7 + - - +
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Residues in contact with ALA1336 (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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1334B THR 4.3 0.2 - - - -
1335B GLN* 1.3 78.5 + - - +
1337B VAL* 1.3 61.6 + - - +
1338B LEU* 4.0 13.5 - - + -
1379B TRP* 3.2 25.3 - - + +
1394B ILE* 5.3 0.2 - - + -
1401B ILE* 4.0 11.1 - - + +
1402B PRO 3.0 8.4 + - - +
1403B CYS* 3.7 26.0 - - - -
1404B ASP* 2.9 27.1 + - - +
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Residues in contact with VAL1337 (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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1335B GLN* 4.6 8.3 - - + +
1336B ALA* 1.3 75.5 - - - +
1338B LEU* 1.3 69.9 + - - +
1339B PRO* 3.4 11.7 - - + +
1347B PHE* 3.7 33.7 - - + -
1348B ALA* 3.9 20.0 - - + +
1351B PHE* 5.3 7.0 - - + -
1378B VAL* 4.0 23.8 - - + -
1379B TRP 2.9 8.2 + - - +
1380B GLY* 3.5 11.8 - - - -
1381B GLU 3.9 0.9 + - - -
1404B ASP* 3.8 9.6 - - + +
1406B LEU* 4.1 12.1 - - + -
1493B TYR* 5.3 7.2 - - + +
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Residues in contact with LEU1338 (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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1336B ALA* 4.3 8.1 - - + +
1337B VAL* 1.3 89.3 - - - +
1339B PRO* 1.3 63.1 - - - +
1340B TYR* 3.5 11.5 - - + -
1380B GLY* 4.0 14.8 - - - -
1381B GLU 3.6 17.5 - - - +
1390B PHE* 4.1 14.1 - - + -
1391B TYR* 3.4 34.1 - - + +
1394B ILE* 4.6 4.5 - - + -
1403B CYS* 4.1 17.0 - - + -
1404B ASP 2.8 17.6 + - - +
1405B PHE* 3.5 26.7 - - + -
1406B LEU* 3.2 17.9 + - - -
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Residues in contact with PRO1339 (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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1337B VAL* 3.4 18.6 - - + +
1338B LEU* 1.3 86.2 - - - +
1340B TYR* 1.3 59.0 + - - +
1341B ASP 3.0 9.2 + - - +
1344B LEU* 3.7 51.4 - - + +
1347B PHE* 4.5 9.4 - - + -
1348B ALA* 5.2 4.3 - - + +
1381B GLU 4.2 8.3 - - - +
1382B PRO* 3.2 9.5 - - + +
1383B GLY 3.0 16.1 + - - -
1406B LEU* 3.4 19.5 - - + +
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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