Contacts of the strand formed by residues 1413 - 1420 (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 ALA1413 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1336B LYS* 3.3 5.6 - - + +
1338B MET* 3.6 39.7 - - + -
1409B MET 3.7 12.1 - - - +
1410B THR 4.7 4.3 + - - +
1411B GLN 3.6 2.6 - - - -
1412B ARG* 1.3 77.9 - - - +
1414B LEU* 1.3 59.3 + - - +
1415B TYR* 3.9 17.9 - - + -
1445B SER* 4.5 1.9 - - - -
1446B PRO* 3.6 9.9 - - - +
1511B PHE* 3.5 17.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1414 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1390A LEU* 5.5 0.7 - - + -
1335B MET* 6.2 3.1 - - + +
1336B LYS 2.8 11.3 + - - +
1337B LEU* 3.4 23.5 - - + +
1338B MET* 2.8 25.5 + - - +
1413B ALA* 1.3 73.0 - - - +
1415B TYR* 1.3 68.1 + - - +
1446B PRO* 3.6 35.4 - - + +
1448B ILE* 4.0 25.8 - - + -
1504B ILE* 4.0 6.5 - - + +
1507B GLU* 4.0 22.9 - - + -
1508B SER* 3.6 27.4 - - - +
1511B PHE* 4.3 7.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1401A PHE* 3.9 29.1 - + - -
1337B LEU* 4.6 1.8 - - - -
1338B MET* 3.3 33.8 - - + +
1340B VAL* 4.3 8.5 - - + -
1409B MET 4.5 6.8 + - - -
1410B THR 5.2 3.2 + - - -
1413B ALA* 3.9 22.0 - - + +
1414B LEU* 1.3 80.4 - - - +
1416B LEU* 1.3 58.9 + - - +
1417B ALA 4.0 0.2 - - - -
1438B ILE* 3.8 39.0 - - + -
1441B ARG* 4.1 16.3 + - - +
1445B SER* 3.8 20.9 - - - -
1446B PRO 3.0 19.8 + - - +
1447B VAL* 3.4 12.3 - - + -
1448B ILE* 2.8 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1337B LEU* 4.1 16.8 - - + +
1338B MET 2.7 12.0 + - - +
1339B ILE* 3.5 26.4 - - + -
1340B VAL* 2.9 32.5 + - - +
1350B LEU* 4.0 16.6 - - + -
1354B LEU* 4.0 27.4 - - + -
1414B LEU 4.2 0.2 + - - -
1415B TYR* 1.3 71.6 - - - +
1417B ALA* 1.3 59.1 + - - +
1418B VAL* 3.8 4.4 + - + +
1448B ILE* 3.4 36.6 - - + +
1450B VAL* 3.9 9.4 - - + -
1500B LEU* 4.3 0.9 - - + -
1504B ILE* 4.0 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1340B VAL* 3.6 15.3 - - + -
1415B TYR 4.0 1.4 + - - -
1416B LEU* 1.3 70.3 - - - +
1418B VAL* 1.3 59.7 + - - +
1431B MET* 4.0 11.9 - - + -
1434B TRP* 5.6 2.9 - - + -
1435B LEU* 5.1 5.2 - - + -
1438B ILE* 5.1 5.6 - - + -
1447B VAL* 3.8 21.8 - - + -
1448B ILE 2.9 8.7 + - - +
1449B LEU* 3.4 21.3 - - + +
1450B VAL 2.9 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1339B ILE* 3.8 28.9 - - + -
1340B VAL 2.9 11.7 + - - +
1341B GLY* 3.6 10.4 - - - -
1342B ASN 4.3 0.3 + - - -
1345B SER* 3.6 23.2 + - - +
1346B GLY 4.3 0.7 - - - -
1347B LYS* 3.8 14.6 - - + +
1350B LEU* 3.9 18.8 - - + -
1416B LEU* 4.0 6.3 - - + +
1417B ALA* 1.3 77.9 - - - +
1419B TYR* 1.3 63.9 + - - +
1431B MET* 3.2 16.4 - - - +
1450B VAL* 3.3 7.2 - - + +
1452B THR* 3.6 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1345B SER* 4.1 8.1 - - - -
1418B VAL* 1.3 76.4 - - - +
1420B ASP* 1.3 57.7 + - - +
1421B LEU* 3.6 26.9 - - + +
1427B GLU* 4.0 26.9 - - + +
1428B VAL* 4.0 19.7 - - + -
1431B MET* 3.9 18.2 - - + -
1449B LEU* 3.8 29.6 - - + -
1450B VAL 3.0 13.1 + - - -
1451B GLY* 3.3 26.9 + - - -
1452B THR* 2.7 34.9 + - - -
1465B CYS* 4.3 2.4 - - - +
1469B ILE* 3.4 17.3 - - + +
1486B HIS 4.6 0.3 + - - -
1487B PHE* 3.4 28.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1344B GLY 4.5 4.2 - - - +
1345B SER* 4.3 14.8 - - - -
1419B TYR* 1.3 73.1 - - - +
1421B LEU* 1.3 63.6 + - - +
1422B SER* 2.6 32.7 + - - -
1423B LYS* 3.1 36.6 + - + +
1424B GLY 4.0 0.2 + - - -
1427B GLU* 3.4 21.4 + - + +
1452B THR* 3.8 6.5 - - - +
1453B HIS* 3.1 32.6 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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