Contacts of the strand formed by residues 1514 - 1519 (chain C) in PDB entry 5ZCJ
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 LYS1514 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1509C ASP* 3.7 1.7 - - - +
1510C VAL* 3.2 35.1 + - + -
1511C GLY 3.0 24.1 + - - +
1512C ALA* 3.1 5.4 - - - +
1513C GLY* 1.3 76.1 - - - +
1515C TYR* 1.3 71.6 + - - +
1526C ASP* 4.3 25.8 - - + +
1527C VAL 3.8 5.6 - - - +
1528C LEU* 3.6 27.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1515 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1486C PHE* 3.7 37.0 - + + -
1506C ILE* 4.3 24.7 - - + -
1508C ARG 3.4 7.9 - - - +
1509C ASP* 3.9 26.1 + - + -
1510C VAL* 3.8 5.8 - - - -
1513C GLY* 3.6 27.4 - - - -
1514C LYS* 1.3 78.2 - - - +
1516C LYS* 1.3 61.2 + - - +
1517C LEU* 3.8 0.8 + - + -
1526C ASP* 3.2 2.0 - - - -
1527C VAL* 2.6 41.9 + - - +
1529C GLY* 3.9 8.3 - - - -
1532C ILE* 3.8 26.2 - - + -
1602C LEU* 3.8 18.1 - - + +
1603C GLY 4.6 5.1 + - - -
1604C PRO* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1516 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1506C ILE* 3.7 4.2 - - - +
1507C THR* 2.8 40.5 + - - +
1508C ARG* 2.9 61.9 + - + +
1510C VAL* 3.5 5.8 - - + +
1515C TYR* 1.3 72.2 - - - +
1517C LEU* 1.3 62.2 + - - +
1524C GLU* 3.7 28.8 - - + +
1525C CYS* 3.5 9.1 - - - +
1526C ASP* 2.9 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1517 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1491C VAL* 3.5 24.5 - - + -
1493C ALA* 3.6 20.2 - - + -
1504C GLY* 4.1 8.1 - - - -
1505C LYS 3.4 12.6 - - - +
1506C ILE* 4.6 4.0 - - + +
1507C THR* 4.4 0.2 - - - -
1515C TYR 4.8 0.7 - - - +
1516C LYS* 1.3 74.9 - - - +
1518C LEU* 1.3 63.0 + - - +
1519C PHE* 3.3 51.6 + - + +
1523C TYR 3.6 2.4 - - - +
1524C GLU* 3.2 8.8 - - - -
1525C CYS 2.8 35.5 + - - +
1527C VAL* 4.1 14.4 - - + -
1532C ILE* 4.3 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1518 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1504C GLY* 3.4 0.2 - - - -
1505C LYS* 2.9 34.9 + - + +
1507C THR* 3.5 24.6 - - + +
1517C LEU* 1.3 72.5 - - - +
1519C PHE* 1.3 72.8 + - - +
1520C ASP* 4.8 0.9 - - - +
1522C GLY* 3.8 25.4 - - - +
1523C TYR 3.7 0.4 - - - -
1524C GLU* 4.0 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1519 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1493C ALA* 3.2 29.6 - - + -
1495C TRP* 3.4 41.1 - + + -
1502C TYR* 3.6 17.9 - - + -
1503C SER 3.6 15.0 - - - +
1504C GLY* 3.8 0.7 - - - -
1517C LEU* 3.3 32.3 - - + -
1518C LEU* 1.3 81.8 - - - +
1520C ASP* 1.3 59.5 - - - +
1521C ASP* 3.0 24.9 - - - +
1522C GLY* 2.9 22.0 + - - -
1523C TYR* 2.8 38.0 + + - +
1525C CYS* 4.2 9.4 - - - -
1527C VAL* 4.4 4.3 - - + -
----------------------------------------------------------
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