Contacts of the strand formed by residues 1481 - 1492 (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 TRP1481 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1198C ASP* 4.1 44.0 - - + -
1201C MET* 4.1 27.8 - - + -
1202C SER* 4.2 15.1 + - - -
1361C PHE* 4.3 19.9 - + + -
1362C ILE 3.1 10.5 - - - +
1363C TYR* 3.3 50.1 + + + -
1475C LEU* 4.3 0.7 - - - -
1479C LEU* 3.1 36.9 + - + +
1480C ARG* 1.3 98.7 - - + +
1482C PHE* 1.3 74.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1482 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1361C PHE* 3.3 6.8 - - - -
1362C ILE 2.9 32.6 + - - +
1471C THR* 3.9 12.9 - - + +
1472C ALA* 4.6 3.1 - - + +
1473C TYR* 3.4 50.5 - + + +
1474C LYS 3.0 28.9 - - - -
1475C LEU* 3.5 25.8 - - + -
1477C GLY* 3.9 7.9 - - - -
1478C ILE* 3.7 28.0 - - + -
1479C LEU* 3.8 20.9 - - + -
1481C TRP* 1.3 81.3 - - - +
1483C GLU* 1.3 64.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1483 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1355C PHE 5.0 0.5 - - - +
1359C LYS* 2.8 47.7 + - + +
1360C VAL 4.0 5.4 - - - +
1361C PHE* 3.4 27.3 - - + -
1471C THR* 3.2 5.5 - - - -
1472C ALA* 3.0 31.4 + - + +
1482C PHE* 1.3 74.4 - - - +
1484C VAL* 1.3 74.5 + - - +
1485C VAL* 4.6 10.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1484 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1359C LYS* 5.8 0.2 - - - +
1360C VAL* 2.7 41.4 + - + +
1362C ILE* 3.6 36.1 - - + -
1469C PHE* 4.0 12.6 - - + -
1470C VAL 3.6 6.5 - - - +
1471C THR* 4.6 0.9 - - + -
1483C GLU* 1.3 85.2 - - - +
1485C VAL* 1.3 63.6 + - - +
1486C HIS 3.4 16.8 - - - +
1487C MET* 3.4 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1485 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1470C VAL* 2.8 26.4 + - + +
1471C THR 4.5 7.0 - - - +
1472C ALA* 4.2 23.6 - - + +
1483C GLU* 4.2 11.4 - - + +
1484C VAL* 1.3 79.0 - - - +
1486C HIS* 1.3 74.4 + - + +
1487C MET* 3.9 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1486 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1441C ARG* 5.0 9.9 - - - -
1468C SER* 5.5 1.8 - - - -
1470C VAL* 2.9 48.9 + - + -
1484C VAL* 3.4 5.4 - - - +
1485C VAL* 1.3 85.4 - - + +
1487C MET* 1.3 81.9 + - - +
1488C SER* 3.7 20.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1487 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1360C VAL* 4.4 16.2 - - + -
1467C THR* 3.8 16.2 - - + -
1468C SER 3.0 13.2 - - - +
1469C PHE* 3.4 24.2 - - + -
1484C VAL* 3.4 27.6 - - + -
1485C VAL 3.9 2.3 + - - +
1486C HIS* 1.3 87.1 + - - +
1488C SER* 1.3 64.3 + - - +
1489C GLN* 5.5 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1488 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1441C ARG* 5.6 0.5 + - - -
1466C ARG 4.8 0.2 - - - -
1467C THR* 3.4 10.0 - - - +
1468C SER* 2.9 44.2 + - - -
1486C HIS* 3.7 20.9 + - - -
1487C MET* 1.3 75.4 - - - +
1489C GLN* 1.3 66.9 + - - +
1490C THR* 4.6 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1489 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1446C ARG* 4.9 5.4 + - - -
1465C GLU* 3.2 33.2 - - - +
1466C ARG 3.6 2.7 + - - -
1467C THR* 2.4 46.4 + - - +
1487C MET* 5.5 2.2 - - - +
1488C SER* 1.3 77.8 + - - +
1490C THR* 1.3 66.2 + - - +
1491C THR* 5.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1490 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1464C ILE 3.9 0.2 - - - +
1465C GLU* 3.6 4.8 - - - +
1466C ARG* 2.9 42.5 + - - +
1468C SER* 5.6 1.7 + - - -
1488C SER* 4.6 5.9 + - - -
1489C GLN* 1.3 78.5 + - - +
1491C THR* 1.3 70.0 + - - +
1492C ILE* 4.2 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1491 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1448C VAL* 5.1 1.3 - - + -
1450C ARG* 3.6 34.1 + - - +
1463C TRP* 4.1 19.2 - - + -
1464C ILE 3.5 12.8 - - - +
1465C GLU* 3.6 21.6 + - + +
1489C GLN* 5.7 0.5 - - - +
1490C THR* 1.3 81.0 - - - +
1492C ILE* 1.3 68.1 + - - +
1493C SER 4.0 0.9 + - - -
1496C GLU* 3.9 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1492 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1463C TRP* 3.2 9.3 - - - -
1464C ILE* 2.8 57.3 + - + +
1466C ARG* 3.6 32.8 - - + +
1490C THR* 4.2 17.5 - - + -
1491C THR* 1.3 79.0 - - - +
1493C SER* 1.3 69.1 + - - +
1496C GLU* 3.3 30.7 - - + +
1497C ASN* 3.7 17.5 - - + +
1500C GLU* 4.2 11.7 - - - +
----------------------------------------------------------
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