Contacts of the helix formed by residues 1271 - 1280 (chain I) in PDB entry 6PSS
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 GLY1271 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1269I ARG* 3.5 13.3 + - - +
1270I PHE* 1.3 78.4 - - - +
1272I GLU* 1.3 65.6 + - - -
1273I MET 3.4 2.5 - - - -
1274I GLU* 2.6 17.1 + - - -
1275I VAL* 3.3 20.8 + - - +
343J LEU 4.3 1.3 - - - -
344J GLY* 3.6 19.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1272 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1269I ARG* 5.6 0.6 - - - +
1271I GLY* 1.3 71.8 - - - -
1273I MET* 1.3 62.9 + - + +
1275I VAL* 3.0 20.8 + - - +
1276I TRP* 3.1 48.9 + - + +
339J ARG* 5.0 18.2 - - - +
343J LEU* 4.5 28.0 - - + +
344J GLY* 4.6 3.4 - - - +
798J ARG* 4.8 14.5 - - - +
1324J SER 5.3 3.1 - - - +
1348J LYS* 5.3 7.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1273 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1271I GLY 3.4 0.4 - - - -
1272I GLU* 1.3 78.1 - - + +
1274I GLU* 1.3 64.1 + - - +
1275I VAL 3.3 0.2 - - - -
1276I TRP* 3.8 35.9 - - + +
1277I ALA* 3.4 22.9 + - - +
426J ALA 5.2 1.3 - - - +
427J PRO* 5.0 3.1 - - - -
428J THR* 3.3 40.6 - - - +
429J LEU* 3.8 29.4 - - + +
793J SER* 4.9 7.2 - - - -
794J GLY* 4.1 17.9 - - - +
797J THR* 4.7 4.7 - - - -
921J GLN* 4.7 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1274 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1269I ARG 4.2 11.4 - - - +
1270I PHE* 3.2 42.3 - - + -
1271I GLY* 2.6 37.4 + - - +
1272I GLU 3.2 0.8 - - - -
1273I MET* 1.3 80.4 + - - +
1275I VAL* 1.3 60.3 + - - +
1277I ALA 4.0 1.3 - - - -
1278I LEU* 3.5 5.0 + - - +
424J ASN* 3.4 27.9 + - - +
426J ALA* 3.5 14.7 - - - +
428J THR* 3.2 22.9 + - - +
434J ILE* 3.4 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1275 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1270I PHE* 3.9 17.5 - - + +
1271I GLY 3.3 15.7 + - - +
1272I GLU* 3.0 11.0 + - - +
1274I GLU* 1.3 77.6 - - - +
1276I TRP* 1.3 62.4 + - + +
1278I LEU* 2.9 5.6 + - - +
1279I GLU* 2.8 49.4 + - - +
1287I LEU* 3.8 28.4 - - + +
1291I LEU* 4.6 10.1 - - + -
343J LEU* 4.2 24.5 - - + +
1351J VAL* 4.3 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1276 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1272I GLU* 3.1 42.0 + - + +
1273I MET* 3.8 40.6 - - + +
1274I GLU 3.6 0.2 - - - -
1275I VAL* 1.3 80.0 - - + +
1277I ALA* 1.3 58.7 + - - +
1279I GLU* 3.3 18.0 + - - -
1280I ALA* 2.9 25.3 + - - +
343J LEU* 5.4 2.5 - - + +
428J THR 5.4 0.9 - - - -
429J LEU 6.0 0.2 - - - -
794J GLY 4.8 1.1 - - - -
797J THR* 4.3 7.4 - - + -
798J ARG* 3.6 43.7 - - + -
801J VAL* 3.5 36.6 - - + +
805J GLN* 4.6 4.7 - - - -
917J VAL* 3.6 16.9 - - + +
921J GLN* 3.2 17.6 + - - +
1348J LYS* 4.6 14.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1277 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1273I MET 3.4 17.6 + - - +
1275I VAL 3.2 0.8 - - - -
1276I TRP* 1.3 78.2 - - - +
1278I LEU* 1.3 56.9 + - - +
1280I ALA* 4.0 2.6 + - - -
1281I TYR* 3.1 28.1 - - - -
428J THR* 3.8 4.9 - - + +
430J HIS 3.4 25.8 - - - +
431J ARG* 3.8 10.6 - - - +
434J ILE* 3.7 19.9 - - + +
921J GLN* 3.2 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1278 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1270I PHE* 3.6 28.0 - - + -
1274I GLU 3.5 14.5 + - - +
1275I VAL* 2.9 9.6 + - - +
1277I ALA* 1.3 80.3 - - - +
1279I GLU* 1.3 63.0 + - - +
1280I ALA 3.1 1.7 + - - -
1281I TYR* 3.5 9.5 + - + +
1283I ALA* 3.6 33.9 + - + +
1286I THR* 4.3 2.5 - - - -
1287I LEU* 3.8 36.3 - - + +
1290I MET* 4.2 11.4 - - + -
422J LEU* 4.5 4.3 - - + -
434J ILE* 4.1 8.7 - - + -
484J MET* 3.6 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1279 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1275I VAL* 2.8 41.4 + - - +
1276I TRP* 3.7 8.6 - - - +
1278I LEU* 1.3 71.5 - - - +
1280I ALA* 1.3 58.5 + - - +
1281I TYR 2.8 14.1 - - - +
1287I LEU* 3.8 14.4 - - + -
343J LEU* 5.5 0.9 - - - +
805J GLN* 2.9 31.1 + - - -
914J ALA* 3.3 18.9 - - - +
917J VAL* 3.7 16.0 - - + +
1347J LEU* 3.5 26.3 - - + +
1348J LYS* 5.2 0.5 - - - -
1351J VAL* 3.8 13.4 - - - +
1357J ILE* 4.3 12.5 - - + +
1359J ALA* 4.8 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1280 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1276I TRP 2.9 11.6 + - - +
1277I ALA 4.2 0.9 - - - +
1278I LEU 3.1 0.4 - - - -
1279I GLU* 1.3 73.7 - - - +
1281I TYR* 1.3 64.8 + - - +
431J ARG* 3.7 27.8 + - + -
905J ARG* 5.5 0.2 + - - -
913J GLU* 4.9 2.6 - - - +
914J ALA* 5.0 0.8 + - - -
917J VAL* 4.8 1.6 - - + -
918J ILE* 3.3 42.9 - - + +
921J GLN* 3.3 27.6 - - - +
----------------------------------------------------------
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