Contacts of the helix formed by residues 1385 - 1390 (chain C) in PDB entry 3FK2
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 ASN1385 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1415A LEU* 6.1 4.9 - - + -
1418A THR* 4.6 14.4 - - - +
1422A GLN* 5.1 1.2 - - - +
1277C LEU* 2.8 32.6 + - + +
1278C SER* 3.5 17.4 + - - -
1381C LYS 3.8 2.2 + - - +
1382C VAL 3.1 4.4 + - - +
1383C SER 3.0 1.0 - - - -
1384C HIS* 1.3 80.6 - - - +
1386C ASN* 1.3 55.8 + - - -
1387C LYS* 3.3 4.6 - - - +
1388C VAL* 3.0 29.1 + - - +
1389C ASN* 2.8 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1386 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1383C SER 2.8 24.0 + - - +
1384C HIS* 3.5 3.8 + - - +
1385C ASN* 1.3 72.4 - - - +
1387C LYS* 1.3 75.6 + - - +
1388C VAL 3.0 2.2 - - - -
1389C ASN* 3.2 10.3 + - - -
1390C LEU* 2.7 29.9 + - - +
1391C MET 3.6 23.6 - - - +
1392C THR* 3.7 24.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1387 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1384C HIS 5.9 1.8 - - - +
1385C ASN* 3.3 2.2 - - - +
1386C ASN* 1.3 88.2 + - - +
1388C VAL* 1.3 65.5 + - + +
1390C LEU* 4.0 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1388 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1394A GLU* 5.3 3.6 - - - +
1398A ILE* 3.7 36.1 - - + -
1422A GLN* 4.1 17.5 - - - +
1278C SER* 3.6 36.3 - - - +
1280C GLU* 3.9 10.9 - - - +
1385C ASN* 3.0 24.2 + - - +
1387C LYS* 1.3 84.2 - - + +
1389C ASN* 1.3 65.0 + - - +
1390C LEU* 3.2 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1389 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1277C LEU 2.9 28.7 + - - +
1278C SER 4.1 5.6 - - - -
1279C THR 3.4 19.7 - - - +
1280C GLU* 4.3 1.1 - - - +
1281C GLY 3.0 21.5 + - - -
1282C ILE* 4.7 3.1 - - + +
1382C VAL* 2.9 37.0 + - - +
1385C ASN* 2.8 20.9 + - - +
1386C ASN* 3.2 5.4 + - - -
1388C VAL* 1.3 71.9 - - - +
1390C LEU* 1.3 68.2 + - - +
1391C MET* 2.9 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1390 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1280C GLU* 3.6 36.1 - - + +
1281C GLY 4.5 2.0 - - - +
1284C ARG* 4.5 19.8 + - - +
1386C ASN* 2.7 31.2 + - - +
1387C LYS 4.0 8.7 - - - +
1388C VAL 3.7 13.2 - - - +
1389C ASN* 1.3 74.8 + - - +
1391C MET* 1.3 60.4 + - - +
1392C THR* 3.4 4.0 + - - +
1395C ASN* 2.9 22.3 + - - -
----------------------------------------------------------
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