Contacts of the strand formed by residues 1342 - 1348 (chain C) in PDB entry 3B13
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 TYR1342 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1340C PRO* 4.0 18.4 - - + -
1341C ASP* 1.3 76.7 + - - +
1343C PHE* 1.3 58.6 + - - +
1362C ILE* 4.2 2.0 - - + -
1363C TYR 3.3 3.6 - - - +
1364C ARG* 3.4 50.5 + - + -
1410C THR* 3.2 8.3 - - - +
1411C VAL* 2.7 53.3 + - + +
1413C PRO* 3.9 29.4 - - + +
1436C SER 2.6 30.8 + - - -
1437C ASN* 3.9 1.9 - - - -
1439C VAL* 3.7 11.4 - - + +
1442C PHE* 3.6 20.0 - + + -
1475C LEU* 3.8 23.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1343 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1341C ASP* 3.8 25.4 - - + -
1342C TYR* 1.3 74.5 - - - +
1344C ALA* 1.3 59.6 + - - +
1345C VAL 4.0 0.3 + - - -
1361C PHE 3.6 0.5 - - - +
1362C ILE* 3.5 2.5 - - - -
1363C TYR* 2.9 41.6 + - + +
1365C GLY* 3.7 24.5 - - - -
1369C GLU* 3.9 7.4 - - - -
1370C ARG* 3.8 7.4 - - - -
1371C ARG* 3.3 44.2 - - + -
1374C PHE* 3.5 49.1 - + + -
1408C CYS* 4.3 6.3 - - - -
1409C PHE 3.5 5.4 - - - +
1410C THR* 3.6 20.4 - - - -
1411C VAL* 4.3 4.0 - - - -
26D ASN* 4.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1344 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1343C PHE* 1.3 71.8 - - - +
1345C VAL* 1.3 62.2 + - - +
1346C GLY 4.2 0.4 - - - -
1360C VAL* 4.3 9.0 - - + -
1361C PHE 3.4 5.6 - - - +
1362C ILE* 4.0 13.2 - - + -
1407C GLN 3.6 0.8 - - - +
1408C CYS* 3.1 7.6 - - - +
1409C PHE* 2.8 65.8 + - + +
1411C VAL* 3.9 13.2 - - + +
1469C PHE* 4.9 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1345 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1343C PHE 4.8 0.4 - - - +
1344C ALA* 1.3 78.3 - - - +
1346C GLY* 1.3 67.0 + - - +
1347C TYR* 3.5 37.4 + - + +
1359C LYS 3.8 0.9 - - - +
1360C VAL* 3.3 4.8 - - - +
1361C PHE* 2.9 38.2 + - - +
1363C TYR* 4.0 27.4 - - + -
1374C PHE* 4.0 21.1 - - + -
1378C LEU* 4.1 12.3 - - + -
1406C ILE* 3.9 10.5 - - + -
1407C GLN 3.3 2.9 - - - -
1408C CYS* 4.1 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1346 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1344C ALA 4.2 0.4 - - - -
1345C VAL* 1.3 73.0 - - - +
1347C TYR* 1.3 61.7 + - - -
1348C TYR* 3.5 25.1 - - - -
1359C LYS 3.6 6.3 - - - -
1360C VAL* 4.1 7.6 - - - +
1405C TYR 3.7 0.5 - - - +
1406C ILE* 3.3 12.1 - - - +
1407C GLN* 2.8 38.2 + - - +
1409C PHE* 5.8 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1347 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1345C VAL* 3.5 26.9 - - + +
1346C GLY* 1.3 72.9 - - - -
1348C TYR* 1.3 56.3 + - - +
1352C PHE* 3.4 36.1 - + + -
1356C LEU* 3.7 26.9 - - + +
1358C ASN* 2.6 37.4 + - - -
1359C LYS 3.1 6.6 + - - +
1361C PHE* 3.7 37.0 - + - -
1363C TYR* 3.0 26.1 + - - -
1378C LEU* 3.9 6.2 - - + +
1382C PHE* 3.7 33.5 - + - -
1405C TYR 4.0 0.2 - - - -
1406C ILE* 3.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1348 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1346C GLY* 3.5 25.6 - - - -
1347C TYR* 1.3 76.3 - - - +
1349C GLY* 1.3 62.1 + - - +
1352C PHE* 3.0 9.4 - - - -
1358C ASN* 3.0 36.1 - - - +
1360C VAL* 3.5 20.0 - - + +
1388C MET* 4.3 9.2 - - - -
1393C ALA* 5.0 3.1 - - - +
1394C PRO* 3.6 37.8 - - + +
1398C VAL* 4.7 11.9 - - + +
1399C LYS* 3.9 15.3 - - + -
1404C GLN* 3.6 0.5 - - - -
1405C TYR* 2.9 53.1 + - + +
1407C GLN* 3.5 25.6 + - + -
----------------------------------------------------------
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