Contacts of the strand formed by residues 1322 - 1328 (chain B) in PDB entry 5EIX
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 GLU1322 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1222B ILE* 3.2 21.0 - - + +
1240B ARG* 5.3 4.5 - - + -
1241B MET 3.2 15.9 - - - +
1242B ARG* 2.5 37.6 + - + +
1316B PHE* 3.3 33.4 + - + +
1317B ALA* 5.1 1.6 - - - -
1319B THR 4.2 5.9 - - - +
1320B ASP* 4.0 10.2 - - - +
1321B LEU* 1.3 78.8 - - - +
1323B LYS* 1.3 61.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1240B ARG* 3.3 4.5 - - - -
1241B MET 2.9 32.6 + - - +
1258B PRO* 4.3 11.0 - - + +
1259B HIS 3.7 10.1 - - - +
1260B GLN* 4.8 9.4 - - + +
1261B VAL* 5.4 2.2 - - + +
1320B ASP* 4.1 17.7 - - - +
1321B LEU 4.2 0.4 + - - -
1322B GLU* 1.3 76.7 - - - +
1324B SER* 1.3 71.4 + - - +
1325B TYR* 3.3 39.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1238B SER* 4.9 9.4 - - - -
1239B VAL 4.0 3.1 - - - -
1240B ARG* 4.4 7.2 - - - +
1323B LYS* 1.3 85.3 - - - +
1325B TYR* 1.3 67.5 + - - +
1326B ARG* 4.4 0.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1181B PRO* 6.5 0.4 - - + -
1215B PHE* 4.5 20.9 - + + -
1238B SER* 3.1 7.7 + - - -
1239B VAL* 2.9 55.7 + - + +
1241B MET* 3.6 27.8 - - + -
1258B PRO* 3.3 8.5 - - - +
1259B HIS* 2.4 62.7 + - + -
1260B GLN* 5.1 2.5 - - + -
1323B LYS* 3.3 34.5 - - + +
1324B SER* 1.3 78.4 - - - +
1326B ARG* 1.3 66.5 + - - +
1327B ILE* 4.1 3.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1172B ILE* 5.6 9.9 - - - +
1177B ALA* 4.4 14.8 - - - +
1179B ASP* 3.1 55.4 + - + +
1181B PRO* 5.2 1.7 - - - +
1237B GLY 4.1 0.9 - - - -
1238B SER* 3.9 9.0 - - - +
1324B SER 5.9 0.4 - - - +
1325B TYR* 1.3 76.4 - - - +
1327B ILE* 1.3 64.0 + - - +
1328B ASN* 5.8 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1179B ASP 3.5 2.7 - - - +
1181B PRO* 4.0 26.0 - - + -
1213B PRO* 4.6 7.4 - - + -
1231B ILE* 4.9 17.9 - - + +
1232B TYR* 5.4 8.3 - - + -
1235B GLY 4.4 6.7 - - - +
1236B ARG* 3.3 6.5 - - - +
1237B GLY* 2.9 47.3 + - - +
1238B SER 4.7 2.0 - - - -
1239B VAL* 4.0 25.4 - - + +
1325B TYR* 4.1 8.3 - - + +
1326B ARG* 1.3 80.3 - - - +
1328B ASN* 1.3 63.7 + - - +
1329B LEU* 3.7 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1177B ALA* 2.9 35.3 + - - +
1178B THR* 3.8 1.4 + - - -
1179B ASP* 2.7 44.1 + - + +
1235B GLY 3.7 5.1 - - - +
1236B ARG* 4.6 8.3 - - + +
1326B ARG* 5.8 2.8 - - + +
1327B ILE* 1.3 74.5 - - - +
1329B LEU* 1.3 53.7 + - - +
1330B ASN* 2.6 25.4 + - - +
1340B VAL* 4.8 8.1 - - - +
----------------------------------------------------------
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