Contacts of the strand formed by residues 1219 - 1233 (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 ALA1219 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061D ILE* 3.3 14.8 - - - +
1062D VAL* 4.6 0.2 - - - -
1063D GLU* 4.3 11.0 - - + +
1215D LEU* 2.9 21.5 + - + +
1216D LYS 4.2 0.7 - - - +
1217D PHE 3.4 1.1 - - - +
1218D TYR* 1.3 76.8 - - - +
1220D SER* 1.3 60.1 + - - +
1221D VAL 3.8 8.7 - - - +
1222D ARG* 3.7 29.2 - - + -
1248D LYS* 3.0 28.1 + - - -
1250D LYS* 4.1 1.7 - - - +
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Residues in contact with SER1220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ALA* 4.7 2.6 - - - +
1057D PRO* 4.4 9.4 - - - -
1060D ARG* 3.0 53.4 + - - +
1061D ILE 2.8 12.3 + - - -
1218D TYR 4.0 5.7 + - - -
1219D ALA* 1.3 74.9 - - - +
1221D VAL* 1.3 63.2 + - - +
1248D LYS* 4.5 2.4 - - - +
1249D ASN* 3.5 1.9 + - - -
1250D LYS* 2.8 43.1 + - - +
1251D ILE* 4.4 1.3 + - - -
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Residues in contact with VAL1221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1051D LEU* 3.6 20.6 - - + -
1056D LEU* 4.1 9.0 - - + -
1057D PRO* 4.1 25.1 - - + -
1061D ILE 3.8 1.6 + - - -
1062D VAL* 3.4 16.1 - - + +
1063D GLU 3.0 23.9 + - - -
1219D ALA* 3.8 1.0 - - - +
1220D SER* 1.3 86.2 - - - +
1222D ARG* 1.3 69.4 + - - +
1223D LEU* 3.6 26.9 - - + -
1246D VAL* 4.6 0.9 - - + -
1248D LYS 3.2 8.3 - - - +
1249D ASN* 3.7 17.7 - - - +
1251D ILE* 4.7 3.6 - - + -
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Residues in contact with ARG1222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D GLU* 4.3 11.7 + - - -
1063D GLU* 2.5 51.9 + - + +
1065D TYR* 3.7 31.2 + - + -
1209D THR* 4.4 8.1 + - - +
1216D LYS* 4.1 42.3 + - - +
1219D ALA* 3.7 19.3 - - + -
1221D VAL* 1.3 78.8 - - - +
1223D LEU* 1.3 66.6 - - - +
1246D VAL* 3.7 0.5 - - - -
1247D VAL* 2.8 41.3 + - + +
1248D LYS* 2.9 33.2 + - + +
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Residues in contact with LEU1223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047D LEU* 4.5 18.6 - - + -
1051D LEU* 4.3 4.0 - - + -
1056D LEU* 4.3 22.7 - - + -
1062D VAL* 4.6 2.0 - - + -
1063D GLU 2.7 12.2 + - - +
1064D ILE* 3.4 31.3 - - + -
1065D TYR* 2.9 35.4 + - - +
1075D LEU* 4.9 4.5 - - + -
1221D VAL* 3.6 20.4 - - + -
1222D ARG* 1.3 78.0 - - - +
1224D ASP* 1.3 59.3 + - - +
1225D ILE 3.8 0.6 + - - -
1244D VAL* 3.7 19.1 - - + -
1245D LYS 3.5 1.8 - - - +
1246D VAL* 4.0 24.7 - - + -
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Residues in contact with ASP1224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1065D TYR* 3.5 30.8 + - + +
1207D GLU* 4.9 0.3 - - - +
1222D ARG 4.2 0.4 + - - -
1223D LEU* 1.3 69.7 - - - +
1225D ILE* 1.3 62.1 + - - +
1226D ARG* 2.7 41.2 + - - +
1243D ARG 3.6 1.7 - - - +
1244D VAL* 3.3 3.5 - - - -
1245D LYS* 2.8 46.2 + - + +
1247D VAL* 3.6 23.8 - - + +
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Residues in contact with ILE1225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1064D ILE* 3.8 12.3 - - + -
1065D TYR 2.9 19.2 + - - +
1066D GLY* 3.4 2.6 - - - -
1067D PRO* 3.4 14.6 - - - +
1070D SER* 3.6 25.8 - - - +
1071D GLY* 3.8 18.2 - - - +
1072D LYS* 3.6 27.1 - - + +
1075D LEU* 4.0 15.7 - - + -
1223D LEU 3.8 0.4 - - - -
1224D ASP* 1.3 73.3 - - - +
1226D ARG* 1.3 72.7 + - - +
1242D THR* 3.7 22.0 - - + -
1243D ARG 3.5 2.9 - - - -
1244D VAL* 3.8 19.3 - - + +
1260D PHE* 4.6 0.9 - - + -
1262D ILE* 4.8 2.0 - - + -
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Residues in contact with ARG1226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1065D TYR* 4.7 1.6 - - - -
1067D PRO* 3.4 25.7 - - + +
1070D SER* 4.2 9.6 - - - -
1195D ILE* 3.2 18.2 - - - +
1207D GLU* 2.6 40.7 + - - -
1224D ASP* 2.7 34.5 + - - +
1225D ILE* 1.3 80.7 - - - +
1227D ARG* 1.3 65.7 + - - +
1228D ILE* 3.6 8.8 + - + +
1242D THR* 3.6 2.9 - - - +
1243D ARG* 2.9 39.1 + - + +
1245D LYS* 5.8 5.8 - - - +
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Residues in contact with ARG1227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067D PRO* 5.5 1.4 - - - +
1068D GLU 6.1 0.2 - - - +
1069D SER 4.6 7.2 - - - +
1070D SER* 4.2 20.0 - - - +
1226D ARG* 1.3 74.3 - - - +
1228D ILE* 1.3 62.7 + - - +
1229D GLY* 3.5 26.5 + - - +
1230D ALA* 3.5 27.9 - - - +
1237D VAL* 4.0 0.8 - - - +
1239D GLY 4.0 1.6 + - - -
1240D SER* 3.0 23.6 + - - +
1241D GLU 3.6 6.7 - - - +
1242D THR* 4.7 3.4 - - - +
1264D TYR* 3.6 8.9 + - - -
1502D ADP 5.2 0.8 + - - -
2255D PHE* 3.3 42.5 - - - -
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Residues in contact with ILE1228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1226D ARG* 3.9 9.4 - - + +
1227D ARG* 1.3 78.1 - - - +
1229D GLY* 1.3 58.6 + - - +
1241D GLU* 2.8 37.3 + - + +
1242D THR 4.2 4.5 - - - +
1243D ARG* 3.6 55.6 - - + +
1259D GLU* 4.0 21.1 - - + +
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Residues in contact with GLY1229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3232A LYS* 5.3 7.2 - - - -
1227D ARG* 3.5 23.0 - - - +
1228D ILE* 1.3 78.8 - - - +
1230D ALA* 1.3 57.5 + - - -
1240D SER* 3.7 0.3 - - - -
1241D GLU* 2.8 37.1 + - - +
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Residues in contact with ALA1230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3232A LYS* 4.3 16.1 + - - +
1227D ARG* 3.5 23.7 - - - +
1229D GLY* 1.3 72.7 - - - -
1231D VAL* 1.3 62.3 + - - +
1232D LYS* 3.6 22.5 + - + +
1237D VAL* 4.0 17.3 - - + -
1239D GLY 3.7 0.2 - - - -
1241D GLU* 4.8 2.6 - - - +
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Residues in contact with VAL1231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1229D GLY 4.2 0.2 + - - -
1230D ALA* 1.3 69.0 - - - +
1232D LYS* 1.3 62.4 + - - +
1237D VAL* 3.7 2.3 - - - -
1238D VAL* 2.9 42.9 + - + +
1239D GLY* 2.7 30.5 + - - +
1240D SER 4.0 1.6 - - - -
1241D GLU* 3.4 31.9 - - - +
1261D GLN* 3.5 30.5 - - + +
1263D LEU* 4.0 12.8 - - + -
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Residues in contact with LYS1232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3228A ILE 5.5 0.8 + - - -
3229A GLY* 4.6 14.8 - - - -
3230A ALA 4.5 16.2 + - - +
3232A LYS* 6.5 0.7 - - - +
3241A GLU* 5.4 7.3 + - - +
1230D ALA* 3.6 17.7 + - + +
1231D VAL* 1.3 80.0 - - - +
1233D GLU* 1.3 64.3 + - - +
1234D GLY* 3.5 20.8 + - - +
1235D GLU 4.7 3.6 - - - +
1236D ASN 3.2 10.8 - - - +
1237D VAL* 4.2 18.4 - - + -
1238D VAL* 4.7 1.3 - - - +
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Residues in contact with GLU1233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3291A TYR* 5.1 2.4 + - - -
3301A GLY* 5.4 2.4 - - - -
3302A LYS* 4.0 38.4 + - - +
1231D VAL 4.2 0.2 + - - -
1232D LYS* 1.3 71.4 - - - +
1234D GLY* 1.3 52.5 + - - +
1235D GLU* 2.7 16.9 + - - +
1236D ASN* 2.7 36.1 + - + +
1238D VAL* 3.9 27.1 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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