Contacts of the strand formed by residues 1422 - 1429 (chain B) in PDB entry 6PUO
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 MET1422 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1421B GLY* 1.3 74.2 - - - +
1423B GLU* 1.3 63.1 + - - +
1445B VAL* 3.3 1.6 - - - +
1446B SER* 2.5 55.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1421B GLY 3.9 10.4 + - - +
1422B MET* 1.3 80.2 - - - +
1424B VAL* 1.3 67.0 + - - +
1426B LYS* 4.0 28.9 - - - +
1443B VAL* 3.8 15.6 - - - +
1444B ALA 3.4 4.5 - - - +
1445B VAL* 3.3 35.0 + - - +
1446B SER* 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1424 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1351B MET* 4.6 11.0 - - + -
1423B GLU* 1.3 79.9 - - - +
1425B TYR* 1.3 61.9 + - + +
1444B ALA* 2.7 20.9 + - + +
1446B SER* 3.7 29.6 - - - +
1491B LEU 4.9 1.8 - - - +
1494B LYS* 3.5 39.9 - - + +
1495B ALA* 4.2 8.3 - - + +
1498B GLU* 5.5 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1425 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1423B GLU* 5.0 0.2 - - - +
1424B VAL* 1.3 87.8 - - + +
1426B LYS* 1.3 88.3 + - - +
1427B GLY* 3.6 5.3 - - - -
1428B TYR* 2.6 36.3 + - - +
1429B MET* 5.4 3.6 - - + -
1442B THR* 4.1 13.0 - - + +
1443B VAL 3.8 0.7 - - - -
1444B ALA* 2.9 35.9 + - + +
1491B LEU* 5.5 12.6 - - + -
1494B LYS* 5.4 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1426 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1313B PHE* 4.3 29.1 - - + -
1423B GLU* 4.0 32.5 - - - +
1425B TYR* 1.3 98.1 - - - +
1427B GLY* 1.3 59.9 + - - +
1442B THR 3.4 7.0 - - - +
1443B VAL* 3.7 33.9 - - + -
1444B ALA 4.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1313B PHE* 4.2 19.9 - - - +
1314B HIS* 5.2 4.7 - - - -
1425B TYR* 3.6 4.7 + - - -
1426B LYS* 1.3 77.6 - - - +
1428B TYR* 1.3 65.8 + - - -
1429B MET 3.5 0.5 + - - -
1441B GLU* 3.3 9.0 - - - -
1442B THR* 3.2 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1239B HIS* 3.6 33.5 - - + +
1242B ALA* 4.4 1.2 - - - +
1314B HIS* 5.2 13.4 + - + +
1326B ASN* 3.7 15.5 + - - -
1327B PRO* 5.0 8.5 - - + -
1328B MET* 3.6 25.6 - - + -
1425B TYR* 2.6 26.3 + - - -
1427B GLY* 1.3 70.5 - - - -
1429B MET* 1.3 72.9 + - - +
1430B ASP* 4.5 2.5 + - + -
1434B ASN* 3.1 33.2 + - - +
1439B TRP* 3.6 26.0 - + + -
1440B ILE 3.6 7.0 - - - -
1441B GLU* 3.8 16.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1349B TYR* 3.6 33.9 - - + +
1425B TYR* 5.4 3.6 - - + -
1427B GLY 3.5 0.2 + - - -
1428B TYR* 1.3 79.6 - - - +
1430B ASP* 1.3 73.7 + - - +
1431B ASP* 5.0 5.8 - - + +
1434B ASN* 3.5 16.8 + - - -
1440B ILE* 2.9 45.9 + - + +
1442B THR* 3.8 29.8 - - + -
1487B ASN* 4.3 22.0 - - + +
1488B HIS* 5.9 0.9 - - - -
1490B THR* 5.9 0.7 - - - +
1491B LEU* 4.3 19.1 - - + -
----------------------------------------------------------
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