Contacts of the strand formed by residues 1389 - 1395 (chain B) in PDB entry 6XAF
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 VAL1389 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1335A MET* 4.1 11.1 + - - +
1365A GLN* 6.5 1.6 - - + -
1375B ASP* 4.2 30.3 - - + +
1376B TRP 3.6 13.7 - - - +
1377B PRO* 3.9 23.1 - - + -
1387B ASP 5.5 0.2 - - - +
1388B LEU* 1.3 87.6 - - - +
1390B LEU* 1.3 65.8 + - - +
1391B ASN* 3.8 3.0 + - + +
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Residues in contact with LEU1390 (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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1335A MET* 3.7 24.0 - - + +
1336A LYS 5.0 1.1 - - - +
1337A LEU* 4.3 15.0 - - + +
1414A LEU* 6.5 0.2 - - + -
1504A ILE* 4.1 15.9 - - + +
1505A ILE* 5.5 0.9 - - + -
1508A SER* 3.6 34.3 - - - +
1375B ASP* 3.4 3.3 - - - -
1376B TRP* 2.7 54.5 + - + +
1378B ILE* 3.7 26.4 - - + +
1387B ASP* 5.3 6.3 - - - +
1389B VAL* 1.3 75.7 - - - +
1391B ASN* 1.3 60.9 + - - +
1392B VAL* 3.5 12.3 + - + -
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Residues in contact with ASN1391 (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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1335A MET 3.1 15.5 + - - +
1336A LYS* 3.2 18.9 + - + +
1337A LEU 3.0 19.4 + - - -
1371A ILE* 5.2 1.8 - - - +
1403A SER* 4.8 7.5 + - - -
1373B VAL* 3.9 17.2 - - - +
1374B LYS 4.0 2.6 + - - -
1375B ASP* 2.7 27.2 + - - +
1389B VAL* 3.8 2.9 + - + +
1390B LEU* 1.3 69.0 - - - +
1392B VAL* 1.3 59.6 + - - +
1393B TRP* 2.9 33.8 + - - -
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Residues in contact with VAL1392 (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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1337A LEU* 3.3 31.0 - - + +
1339A ILE* 3.7 20.4 - - + -
1351A LEU* 3.7 32.3 - - + -
1372B ASP 3.5 1.7 - - - +
1373B VAL* 3.2 7.8 - - - +
1374B LYS* 2.7 42.0 + - + +
1376B TRP* 3.9 22.0 - - + -
1390B LEU* 3.7 15.0 - - + +
1391B ASN* 1.3 71.7 - - - +
1393B TRP* 1.3 66.0 + - - +
1394B ASP 4.7 0.2 - - - +
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Residues in contact with TRP1393 (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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1336A LYS* 3.5 24.3 - - + +
1337A LEU 2.8 8.3 + - - +
1338A MET* 3.5 14.7 - - - -
1339A ILE* 2.7 32.2 + - - +
1371A ILE* 3.9 22.4 - - + -
1393A TRP* 3.6 40.4 - + - -
1403A SER* 5.1 0.2 - - - -
1404A THR* 4.1 7.0 - - + -
1409A MET* 3.7 29.8 - - + -
1371B ILE* 3.8 12.6 - - + -
1372B ASP 3.6 4.0 - - - -
1373B VAL* 3.7 22.6 - - + +
1391B ASN* 2.9 35.7 + - - -
1392B VAL* 1.3 76.1 - - - +
1394B ASP* 1.3 57.7 - - - +
1395B PHE* 3.6 28.8 - + + -
1404B THR* 4.9 1.8 - - + -
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Residues in contact with ASP1394 (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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1339A ILE* 4.1 8.7 - - + +
1347A LYS* 3.6 24.4 - - - +
1348A THR* 2.8 39.3 + - - +
1351A LEU* 4.4 21.6 - - + +
1601A MG 4.3 1.9 - - - -
1369B VAL 5.2 0.9 - - - +
1370B GLY 3.7 1.0 - - - +
1371B ILE* 3.5 5.6 - - - +
1372B ASP* 2.8 49.7 + - + +
1392B VAL 4.0 0.2 - - - -
1393B TRP* 1.3 70.9 - - - +
1395B PHE* 1.3 66.0 + - - +
1396B ALA 4.0 0.2 + - - -
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Residues in contact with PHE1395 (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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1338A MET* 3.7 27.4 - - + -
1339A ILE 3.0 21.7 + - - +
1340A VAL* 3.8 20.6 - - + -
1347A LYS* 2.9 30.0 + - - +
1409A MET* 6.0 0.4 - - + -
1434A TRP* 5.3 0.2 - - + -
1370B GLY 3.7 2.0 - - - -
1371B ILE* 3.9 15.9 - - + -
1393B TRP* 3.6 38.6 - + + -
1394B ASP* 1.3 74.6 + - - +
1396B ALA* 1.3 60.5 + - - +
1397B GLY 3.5 11.4 + - - +
1400B GLU 3.8 4.0 - - - -
1401B PHE* 3.6 36.3 - + + +
1404B THR* 3.7 29.4 - - + -
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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