Contacts of the helix formed by residues 1397 - 1409 (chain N) in PDB entry 4G7Z
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 LYS1397 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1341N PRO* 5.7 7.7 - - - +
1345N GLU* 5.4 4.0 + - - -
1376N MET* 3.8 26.3 + - - +
1377N LYS* 2.9 17.0 + - - +
1379N VAL* 3.5 28.5 - - + +
1395N LEU 3.6 2.0 + - - -
1396N GLU* 1.3 70.3 - - - +
1398N TRP* 1.3 62.6 + - - +
1400N VAL* 3.1 20.4 - - + +
1401N GLU* 3.2 36.8 + - + +
1417N TRP* 4.9 6.7 - - - +
1419N PRO* 6.1 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1398 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1195N GLN* 3.5 30.3 - - + -
1197N ARG* 3.0 62.7 - - + +
1198N TYR* 5.4 4.0 - + + -
1396N GLU* 3.1 8.6 + - + +
1397N LYS* 1.3 80.6 - - - +
1399N ASP* 1.3 79.9 + - - +
1401N GLU* 3.3 16.7 + - + +
1402N ALA* 3.0 38.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1399 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1197N ARG* 4.8 5.5 + - - -
1198N TYR* 5.5 1.9 + - - -
1395N LEU* 4.7 6.6 - - + +
1396N GLU* 3.0 32.9 + - - +
1398N TRP* 1.3 94.2 - - - +
1400N VAL* 1.3 60.0 + - - +
1402N ALA* 3.2 4.4 + - - +
1403N LEU* 2.8 31.6 + - - +
1432N LYS* 5.5 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1400 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1379N VAL* 3.7 24.5 - - + -
1381N VAL* 5.6 0.2 - - + -
1389N LEU* 5.0 4.3 - - + -
1395N LEU* 3.4 20.1 - - + +
1396N GLU 3.4 1.6 + - - -
1397N LYS* 3.1 17.9 - - - +
1399N ASP* 1.3 78.4 - - - +
1401N GLU* 1.3 52.8 + - - +
1403N LEU* 3.8 7.5 - - + +
1404N ASN* 2.8 43.1 + - - +
1415N VAL* 3.9 24.2 - - + -
1417N TRP* 3.5 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1401 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1397N LYS* 3.2 39.3 + - - +
1398N TRP* 3.6 17.2 - - + +
1399N ASP 3.2 0.6 - - - -
1400N VAL* 1.3 82.3 - - - +
1402N ALA* 1.3 57.8 + - - +
1404N ASN* 3.9 5.2 - - - +
1405N GLU* 3.1 28.2 + - - +
1417N TRP* 3.5 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1402 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1398N TRP* 3.0 30.2 + - + +
1399N ASP* 3.2 6.3 + - - +
1401N GLU* 1.3 76.7 - - - +
1403N LEU* 1.3 64.0 + - - +
1405N GLU* 3.2 30.3 - - - +
1406N ARG* 3.4 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1403 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1387N SER* 4.2 5.8 - - - -
1388N ARG 6.2 0.4 - - - +
1389N LEU* 3.7 32.5 - - + -
1399N ASP 2.8 21.0 + - - +
1400N VAL* 3.8 6.5 - - - +
1402N ALA* 1.3 72.5 - - - +
1404N ASN* 1.3 59.0 + - - +
1406N ARG* 3.2 36.5 + - - +
1407N LEU* 3.0 43.7 + - + +
1415N VAL* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1404 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1400N VAL 2.8 17.3 + - - +
1401N GLU* 3.9 6.1 - - - +
1403N LEU* 1.3 74.7 - - - +
1405N GLU* 1.3 57.4 + - - +
1407N LEU* 3.1 9.8 + - - +
1408N ILE* 2.7 39.3 + - + +
1414N PRO* 3.7 11.1 - - + +
1415N VAL* 2.7 64.8 - - - +
1417N TRP* 3.1 21.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1405 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1401N GLU 3.1 14.7 + - - +
1402N ALA* 3.2 25.7 - - - +
1404N ASN* 1.3 75.2 - - - +
1406N ARG* 1.3 66.1 + - + +
1408N ILE* 3.6 10.9 - - + +
1409N ALA* 3.0 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1406 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1402N ALA 3.4 13.2 - - - +
1403N LEU* 3.2 34.4 + - - +
1404N ASN 3.1 0.2 - - - -
1405N GLU* 1.3 82.0 - - + +
1407N LEU* 1.3 60.0 + - - +
1409N ALA* 3.1 5.5 + - - +
1410N GLU* 2.6 59.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1407 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1386N ASP 5.2 2.7 - - - +
1387N SER* 3.8 33.9 - - - +
1403N LEU* 3.0 31.2 + - + +
1404N ASN* 3.1 26.4 + - - +
1406N ARG* 1.3 88.0 - - - +
1408N ILE* 1.3 56.4 + - - +
1410N GLU* 2.8 36.4 + - - +
1411N GLY 3.1 0.2 + - - -
1412N LYS* 2.8 35.9 + - + -
1413N THR 4.0 15.9 - - - +
1414N PRO* 4.9 0.2 - - + -
1415N VAL* 4.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1408 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1404N ASN* 2.7 25.4 + - + +
1405N GLU* 3.6 14.4 - - + +
1407N LEU* 1.3 73.6 - - - +
1409N ALA* 1.3 60.9 + - + +
1410N GLU 3.3 0.7 - - - -
1411N GLY* 3.9 8.6 + - - -
1412N LYS 3.5 12.8 + - - +
1414N PRO* 4.7 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1409 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1405N GLU 3.0 20.2 + - - +
1406N ARG* 3.1 5.0 + - - +
1407N LEU 3.1 0.4 - - - -
1408N ILE* 1.3 77.2 - - + +
1410N GLU* 1.3 57.1 + - - +
1411N GLY 3.3 5.2 - - - -
----------------------------------------------------------
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