Contacts of the helix formed by residues 1300 - 1319 (chain D) in PDB entry 2F8N
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 PRO1300 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1298D LEU 4.1 4.7 - - - +
1299D LEU* 1.3 91.8 - - + +
1301D GLY* 1.3 54.6 + - - +
1302D GLU 3.4 1.8 - - - -
1303D LEU* 2.7 39.0 + - + -
1304D ALA 2.7 7.9 + - - -
92K GLU* 3.4 48.7 - - + +
95K LYS* 4.4 25.4 - - + +
96K LEU* 4.2 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1301 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1299D LEU 3.5 3.8 + - - -
1300D PRO* 1.3 67.7 - - - +
1302D GLU* 1.3 63.3 + - - -
1304D ALA* 3.2 7.9 + - - +
1305D LYS* 3.0 29.4 + - - +
92K GLU* 3.8 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1302 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1301D GLY* 1.3 68.4 - - - -
1303D LEU* 1.3 64.5 + - - -
1304D ALA 3.2 0.3 + - - -
1305D LYS* 3.2 42.9 + - - +
1306D HIS* 3.3 46.9 + - + -
92K GLU* 2.7 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1303 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1299D LEU* 4.1 3.9 - - + +
1300D PRO* 2.7 28.3 + - + +
1302D GLU* 1.3 71.6 - - - +
1304D ALA* 1.3 56.4 + - - +
1307D ALA* 2.9 30.6 + - - +
57K TYR* 3.4 28.6 - - + +
58K LEU* 3.8 26.5 - - + -
61K GLU* 4.1 18.6 - - + +
90K ASP* 5.5 0.4 - - - +
92K GLU* 3.0 31.6 + - + +
93K LEU* 3.5 35.4 - - + +
96K LEU* 4.5 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1304 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1295D VAL* 4.5 7.6 - - - +
1296D ARG* 4.9 9.0 - - + +
1299D LEU* 3.7 29.3 - - + +
1300D PRO 2.7 10.6 + - - +
1301D GLY* 3.2 12.8 - - - +
1302D GLU 3.0 0.2 - - - -
1303D LEU* 1.3 78.1 - - - +
1305D LYS* 1.3 52.7 + - + +
1307D ALA* 3.0 6.2 - - - +
1308D VAL* 2.7 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1305 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1301D GLY 3.0 23.9 + - - +
1302D GLU* 3.2 35.3 + - - +
1304D ALA* 1.3 73.7 - - + +
1306D HIS* 1.3 69.7 + - + +
1308D VAL* 2.9 18.3 + - - +
1309D SER* 3.0 14.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1306 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1302D GLU* 3.3 38.7 + - + +
1305D LYS* 1.3 81.5 - - + +
1307D ALA* 1.3 61.9 + - - +
1309D SER* 3.2 17.4 + - - -
1310D GLU* 3.0 24.9 + - + +
57K TYR* 2.8 35.8 + - + +
61K GLU* 5.3 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1307 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1295D VAL* 3.7 11.2 - - + -
1299D LEU* 3.6 22.7 - - + -
1303D LEU 2.9 21.2 + - - +
1304D ALA 3.0 9.6 + - - +
1306D HIS* 1.3 79.9 - - - +
1308D VAL* 1.3 54.6 + - - +
1310D GLU* 3.4 3.3 + - - +
1311D GLY* 3.0 23.9 + - - -
54K VAL* 4.1 14.9 - - + +
57K TYR* 3.2 19.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1308 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1292D GLN* 3.2 29.4 - - + +
1295D VAL* 4.5 13.0 - - + -
1296D ARG* 4.0 28.3 - - + +
1304D ALA* 2.7 22.3 + - + +
1305D LYS* 2.9 8.0 + - - +
1307D ALA* 1.3 71.0 - - - +
1309D SER* 1.3 63.1 + - - +
1311D GLY 3.8 0.7 - - - -
1312D THR* 2.9 23.0 + - - +
50K TYR* 3.1 22.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1309 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1305D LYS 3.0 14.0 + - - -
1306D HIS* 3.2 17.9 + - - -
1308D VAL* 1.3 75.1 - - - +
1310D GLU* 1.3 63.2 + - - +
1312D THR* 2.8 9.1 + - - -
1313D LYS* 2.7 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1310 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1306D HIS* 3.0 17.9 - - - +
1307D ALA 3.6 4.7 - - - +
1309D SER* 1.3 84.9 - - - +
1311D GLY* 1.3 65.4 + - - +
1313D LYS* 3.5 21.0 + - - +
1314D ALA* 2.7 26.5 + - - +
23K LEU* 6.4 0.7 - - + -
53K ALA* 3.9 13.4 - - + +
57K TYR* 3.8 38.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1311 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1307D ALA 3.0 9.4 + - - -
1309D SER 3.0 0.4 + - - -
1310D GLU* 1.3 80.8 - - - +
1312D THR* 1.3 62.7 + - - +
1314D ALA* 3.1 2.8 + - - +
1315D VAL 2.9 19.4 + - - -
50K TYR* 3.6 44.1 - - - -
53K ALA* 4.1 10.7 - - - +
54K VAL* 4.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1312 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1292D GLN* 3.6 17.5 + - - -
1308D VAL* 2.9 15.9 + - - +
1309D SER* 2.8 12.1 + - - -
1311D GLY* 1.3 67.9 - - - +
1313D LYS* 1.3 69.3 + - - +
1314D ALA 2.8 0.9 + - - -
1315D VAL* 3.0 12.7 + - + +
1316D THR* 2.7 39.3 + - - +
50K TYR* 3.6 3.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1313 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1309D SER* 2.7 21.1 + - - +
1310D GLU* 3.5 22.4 + - - +
1312D THR* 1.3 74.4 - - - +
1314D ALA* 1.3 58.2 + - - +
1316D THR* 3.9 7.1 - - - +
1317D LYS* 3.1 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1314 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1310D GLU 2.7 20.0 + - - +
1311D GLY 3.4 3.8 - - - +
1312D THR 2.8 0.6 + - - -
1313D LYS* 1.3 72.2 - - - +
1315D VAL* 1.3 66.4 + - - +
1317D LYS* 3.3 2.3 + - - +
1318D TYR* 2.8 25.5 + - - +
21K ALA* 3.9 19.7 - - - +
23K LEU* 4.1 8.1 - - + -
49K VAL* 3.8 16.3 - - + +
53K ALA* 3.6 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1315 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1288D SER* 4.2 15.3 - - - +
1311D GLY 2.9 13.8 + - - +
1312D THR* 3.2 26.2 - - + +
1314D ALA* 1.3 73.5 - - - +
1316D THR* 1.3 80.6 + - - +
1318D TYR* 3.3 4.8 + - + +
1319D THR* 2.9 33.6 + - - +
46K GLY* 4.0 27.6 - - - +
49K VAL* 3.9 10.9 - - + +
50K TYR* 4.6 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1316 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1312D THR* 2.7 35.7 + - - +
1313D LYS* 4.1 6.5 - - - +
1315D VAL* 1.3 76.8 - - - +
1317D LYS* 1.3 69.6 + - - +
1319D THR* 2.9 26.2 + - - +
1320D SER* 4.1 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1317 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1313D LYS* 3.1 16.9 + - + +
1314D ALA 3.7 3.4 - - - +
1316D THR* 1.3 82.3 - - + +
1318D TYR* 1.3 64.4 + - - +
1320D SER* 2.8 24.7 + - - +
1321D SER* 3.2 17.9 + - - +
19K SER 3.9 5.0 + - - -
20K ARG* 2.6 28.9 + - - +
21K ALA 3.6 15.5 - - - +
22K GLY* 4.0 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1318 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1314D ALA 2.8 17.6 + - - +
1315D VAL* 3.3 5.8 - - + +
1317D LYS* 1.3 75.9 - - - +
1319D THR* 1.3 61.7 + - - +
1320D SER 2.8 13.5 + - - -
1321D SER* 3.2 12.8 + - - -
1322D LYS 3.8 5.9 + - - +
17K ARG* 3.1 63.0 + - + +
20K ARG* 4.0 31.1 + - + -
21K ALA* 4.1 2.9 - - + -
45K ALA* 3.8 32.8 + - + +
46K GLY* 5.3 3.1 - - - -
49K VAL* 3.9 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1319 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1315D VAL* 2.9 25.9 + - - +
1316D THR* 2.9 11.7 + - - +
1318D TYR* 1.3 79.7 - - - +
1320D SER* 1.3 64.7 + - - +
1322D LYS 4.4 2.9 - - - -
----------------------------------------------------------
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