Contacts of the helix formed by residues 1329 - 1343 (chain A) in PDB entry 3L8V
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 SER1329 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1262A THR* 6.1 1.8 - - - -
1263A LYS* 4.4 16.0 - - - +
1266A VAL* 4.7 1.6 - - - -
1327A ARG 3.6 1.4 + - - -
1328A PRO* 1.3 76.6 - - - +
1330A PHE* 1.3 59.2 + - - +
1331A SER* 3.6 11.2 + - - -
1332A GLU* 3.2 24.1 + - - +
1333A LEU* 2.9 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1189A ALA* 4.3 11.4 - - - +
1192A MET* 3.5 52.7 - - + -
1193A LYS* 3.7 22.7 - - - +
1196A ALA* 4.4 5.1 - - + +
1205A LEU* 4.3 0.4 - - + -
1262A THR* 4.0 18.0 - - + +
1265A ASP* 3.7 32.3 - - + -
1266A VAL* 3.6 17.0 - - + +
1269A PHE* 3.6 28.0 - + + -
1329A SER* 1.3 69.9 - - - +
1331A SER* 1.3 58.9 + - - +
1333A LEU* 3.7 16.3 - - + +
1334A VAL* 2.9 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1193A LYS* 3.8 36.8 + - - +
1329A SER* 3.8 9.1 - - - -
1330A PHE* 1.3 78.5 - - - +
1332A GLU* 1.3 60.2 + - - +
1334A VAL* 3.4 4.5 + - - +
1335A SER* 3.2 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1318A LYS* 4.7 4.5 - - - -
1328A PRO* 3.5 26.1 - - + +
1329A SER* 3.2 19.4 + - - +
1331A SER* 1.3 75.8 - - - +
1333A LEU* 1.4 59.9 + - - +
1335A SER* 3.2 8.8 + - - -
1336A ARG* 2.9 64.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1189A ALA* 4.6 4.0 - - + -
1266A VAL* 3.9 23.6 - - + -
1269A PHE* 3.8 26.7 - - + -
1315A VAL* 3.8 23.6 - - + -
1319A CYS* 3.7 14.1 - - - -
1328A PRO* 3.6 23.6 - - + +
1329A SER 2.9 18.6 + - - +
1330A PHE* 3.7 29.6 - - + +
1332A GLU* 1.4 73.0 - - - +
1334A VAL* 1.4 59.3 + - - +
1336A ARG* 4.6 4.7 - - - -
1337A ILE* 2.9 38.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1186A LEU* 3.5 7.7 - - + +
1189A ALA* 3.5 34.8 - - + +
1190A LYS* 3.7 34.3 - - + +
1193A LYS* 4.0 21.8 - - + +
1330A PHE 2.9 22.0 + - - +
1331A SER 3.6 6.3 - - - +
1332A GLU 3.3 0.2 - - - -
1333A LEU* 1.4 73.3 - - - +
1335A SER* 1.3 58.4 + - - +
1338A SER* 3.0 35.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1331A SER 3.2 11.4 + - - -
1332A GLU* 3.2 12.1 + - - -
1334A VAL* 1.3 78.8 - - - +
1336A ARG* 1.3 61.0 + - - +
1338A SER* 2.7 22.5 + - - -
1339A ALA* 3.3 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1315A VAL* 4.3 25.9 - - + +
1318A LYS* 3.5 34.6 - - - +
1328A PRO* 5.3 3.1 - - - -
1332A GLU* 2.9 52.4 + - + +
1333A LEU* 4.0 7.0 - - - +
1335A SER* 1.3 73.3 - - - +
1337A ILE* 1.3 63.1 + - + +
1339A ALA* 3.3 8.1 + - - +
1340A ILE* 3.3 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182A ILE* 3.8 25.6 - - + +
1185A GLY* 4.7 1.3 - - - +
1186A LEU* 3.9 25.8 - - + +
1189A ALA* 4.7 2.9 - - + -
1269A PHE* 3.5 38.4 - - + -
1273A LEU* 4.0 15.9 - - + -
1312A LEU* 4.2 14.6 - - + -
1315A VAL* 4.4 12.8 - - + -
1333A LEU* 2.9 28.8 + - + +
1336A ARG* 1.3 68.9 - - + +
1338A SER* 1.3 58.6 + - - +
1340A ILE* 3.3 7.3 + - + +
1341A PHE* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1186A LEU* 3.8 23.9 - - - +
1190A LYS* 5.8 2.0 - - - -
1334A VAL* 3.0 20.7 + - - -
1335A SER* 2.7 22.2 + - - -
1337A ILE* 1.3 75.2 - - - +
1339A ALA* 1.3 55.9 + - - +
1341A PHE* 3.7 5.1 + - - +
1342A SER* 3.2 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1335A SER 3.8 7.9 - - - +
1336A ARG* 3.3 11.8 + - - +
1338A SER* 1.3 80.2 + - - +
1340A ILE* 1.3 63.1 + - + +
1342A SER* 2.7 22.9 + - - -
1343A THR* 3.3 12.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182A ILE* 3.8 18.8 - - + -
1309A PRO* 4.7 1.3 - - + -
1311A PRO* 3.8 49.6 - - + +
1312A LEU* 4.0 18.6 - - + +
1315A VAL* 4.1 15.9 - - + -
1336A ARG* 3.3 18.1 + - + +
1337A ILE* 3.3 6.8 + - - +
1339A ALA* 1.3 75.4 - - + +
1341A PHE* 1.4 60.4 + - - +
1343A THR* 2.6 29.7 + - - +
1344A PHE* 3.1 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1179A LYS* 2.8 83.0 + - + -
1182A ILE* 3.8 13.9 - - + +
1183A GLY* 3.7 23.8 - - - -
1186A LEU* 4.2 21.8 - - + -
1337A ILE 2.9 18.8 + - - +
1338A SER 3.8 6.3 - - - +
1340A ILE* 1.4 76.1 - - - +
1342A SER* 1.4 59.9 + - - +
1343A THR 3.3 1.0 + - - -
1344A PHE* 3.3 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1179A LYS* 4.3 5.2 + - - +
1338A SER 3.2 13.0 + - - -
1339A ALA* 2.7 23.3 + - - -
1341A PHE* 1.4 81.1 - - - +
1343A THR* 1.3 61.3 + - - +
1344A PHE 3.4 5.1 - - - +
1345A ILE* 5.7 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1339A ALA 3.3 17.9 - - - +
1340A ILE* 2.6 21.0 + - - +
1342A SER* 1.3 78.2 - - - +
1344A PHE* 1.3 75.3 + - - +
1345A ILE* 4.2 6.1 + - - +
----------------------------------------------------------
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