Contacts of the strand formed by residues 1236 - 1249 (chain D) in PDB entry 3CMT
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 ASN1236 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1232D LYS* 3.2 5.9 - - - +
1233D GLU* 2.7 50.1 + - + +
1235D GLU* 1.3 86.0 - - - +
1237D VAL* 1.3 65.8 + - - +
1238D VAL* 3.7 4.5 - - + +
2256D LYS* 6.3 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1237 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1227D ARG* 4.0 8.7 - - - +
1230D ALA* 4.0 10.5 - - + -
1231D VAL 3.7 3.6 - - - +
1232D LYS* 4.2 17.3 - - + -
1235D GLU 4.8 3.1 - - - +
1236D ASN* 1.3 75.7 - - - +
1238D VAL* 1.3 59.6 + - - +
1239D GLY 3.9 17.5 - - - +
1264D TYR* 3.7 13.1 - - + -
2253D ALA* 5.2 2.9 - - - +
2254D PRO 4.3 5.8 - - - +
2255D PHE* 3.7 46.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1238 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1231D VAL* 2.9 32.0 + - + +
1232D LYS 4.7 0.4 - - - -
1233D GLU* 3.9 31.6 - - + -
1236D ASN* 3.6 4.2 + - + -
1237D VAL* 1.3 73.4 - - - +
1239D GLY* 1.3 55.4 + - - +
1263D LEU* 3.8 12.9 - - + +
1264D TYR* 3.1 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1239 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1230D ALA* 3.7 4.3 - - - -
1231D VAL* 2.7 40.4 + - - +
1237D VAL* 3.9 4.0 - - - +
1238D VAL* 1.3 80.6 - - - +
1240D SER* 1.3 57.2 + - - -
1262D ILE 3.1 13.5 - - - -
1263D LEU* 4.1 2.9 - - - -
1264D TYR* 3.5 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1240 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1069D SER 4.9 2.0 + - - -
1070D SER 5.8 2.5 - - - -
1227D ARG* 3.0 28.6 + - - +
1229D GLY 3.7 4.0 - - - -
1231D VAL* 4.0 3.1 - - - -
1239D GLY* 1.3 71.6 - - - -
1241D GLU* 1.3 61.0 + - - +
1242D THR* 3.4 10.4 + - - -
1261D GLN* 3.6 0.9 - - - -
1262D ILE* 2.8 45.5 + - - -
1264D TYR* 2.7 25.8 + - - -
1502D ADP 3.5 13.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1241 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3232A LYS* 5.1 10.4 + - - +
3234A GLY* 4.9 15.8 - - - +
1227D ARG* 3.6 4.0 - - - -
1228D ILE* 2.8 42.5 + - + -
1229D GLY* 2.8 32.4 + - - +
1230D ALA 4.4 3.1 - - - +
1231D VAL* 3.4 14.4 - - + +
1240D SER* 1.3 71.0 - - - +
1242D THR* 1.3 59.3 + - - +
1259D GLU* 5.6 2.9 - - + +
1260D PHE* 3.8 10.1 + - - +
1261D GLN* 3.2 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1242 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1070D SER 4.2 5.7 + - - +
1225D ILE* 3.7 29.6 - - + -
1226D ARG 3.6 5.5 + - - +
1227D ARG* 4.8 1.0 - - - -
1228D ILE* 4.4 3.8 - - - +
1240D SER* 3.4 18.1 + - - -
1241D GLU* 1.3 74.9 + - - +
1243D ARG* 1.3 65.8 + - - +
1258D ALA 4.5 0.2 - - - -
1259D GLU* 3.2 6.8 - - - +
1260D PHE* 2.7 72.1 + - + +
1262D ILE* 3.6 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1243 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1224D ASP 3.6 1.7 - - - +
1225D ILE* 3.5 1.2 - - - -
1226D ARG* 2.9 39.6 + - + +
1228D ILE* 3.6 41.7 - - + +
1242D THR* 1.3 76.0 - - - +
1244D VAL* 1.3 66.7 + - - +
1245D LYS* 4.1 22.5 - - - +
1257D GLN* 3.3 29.8 + - - +
1258D ALA 3.3 4.3 - - - +
1259D GLU* 2.4 41.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047D LEU* 4.3 20.4 - - + +
1075D LEU* 4.3 6.5 - - + -
1223D LEU* 3.7 36.1 - - + -
1224D ASP 3.3 6.7 - - - +
1225D ILE* 3.8 22.2 - - + -
1242D THR* 4.4 0.2 - - + -
1243D ARG* 1.3 76.6 - - - +
1245D LYS* 1.3 65.6 + - - +
1246D VAL* 5.2 1.2 - - - +
1257D GLN* 3.3 5.0 - - - +
1258D ALA* 2.8 38.7 + - + +
1260D PHE* 3.7 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1223D LEU* 3.5 3.8 - - - -
1224D ASP* 2.8 51.4 + - + +
1226D ARG* 5.8 5.5 - - - +
1243D ARG* 4.1 18.8 - - - +
1244D VAL* 1.3 73.5 - - - +
1246D VAL* 1.3 63.3 + - - +
1247D VAL* 3.3 12.7 + - + -
1255D PHE* 6.1 4.9 - - + +
1256D LYS 4.0 3.1 - - - +
1257D GLN* 3.4 34.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047D LEU* 4.3 9.0 - - + -
1050D ALA* 4.1 29.4 - - + +
1051D LEU* 4.4 7.6 - - + +
1222D ARG 3.7 5.6 - - - +
1223D LEU* 4.0 17.7 - - + -
1244D VAL 5.2 0.7 - - - +
1245D LYS* 1.3 72.0 - - - +
1247D VAL* 1.3 59.9 + - - +
1248D LYS 3.7 19.3 - - - +
1249D ASN* 3.9 25.6 - - + +
1254D PRO* 4.5 2.9 - - + -
1255D PHE* 2.7 37.3 + - - +
1256D LYS 3.0 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D GLU* 6.1 0.7 - - - +
69D SER* 5.9 1.0 - - - -
1065D TYR* 3.5 28.0 - - + +
1222D ARG* 2.8 30.6 + - + +
1224D ASP* 3.6 24.2 - - + +
1245D LYS* 3.3 13.2 + - + +
1246D VAL* 1.3 73.9 - - - +
1248D LYS* 1.3 61.3 + - + +
1254D PRO* 4.5 1.4 - - - +
1255D PHE* 3.5 31.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D GLU* 3.8 8.7 - - + +
69D SER* 3.2 24.9 - - - +
501D ALF 2.7 40.0 - - - -
502D ADP 5.5 0.2 - - - -
1216D LYS 2.7 29.4 + - - +
1217D PHE 2.8 16.6 + - - -
1219D ALA 3.0 19.8 + - - +
1220D SER 4.9 0.9 - - - -
1221D VAL* 3.2 5.2 - - - -
1222D ARG* 2.9 47.3 + - + +
1246D VAL* 3.7 8.7 - - - +
1247D VAL* 1.3 82.3 - - + +
1249D ASN* 1.3 67.1 + - - +
1250D LYS* 4.5 6.3 - - - -
1254D PRO* 4.4 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D SER* 5.2 0.2 - - - -
502D ADP 3.0 29.2 + - - -
1051D LEU* 3.2 28.5 + - - +
1220D SER 3.5 2.0 - - - -
1221D VAL* 3.7 9.7 - - - +
1246D VAL* 3.9 12.1 - - + +
1248D LYS* 1.3 81.2 - - - +
1250D LYS* 1.3 59.5 + - - +
1251D ILE* 3.0 29.2 + - - +
1252D ALA 3.1 31.2 + - - +
1253D ALA 3.3 12.3 + - - -
1254D PRO* 3.8 18.7 - - + +
----------------------------------------------------------
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