Contacts of the helix formed by residues 1124 - 1139 (chain C) in PDB entry 2X4Y
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 PRO1124 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1110C ARG* 4.1 3.4 - - - +
1122C VAL 3.5 8.5 - - - +
1123C PRO* 1.3 87.2 - - + +
1125C LEU* 1.3 65.5 + - - +
1126C GLU* 3.6 28.0 - - + +
1127C VAL* 2.9 27.1 + - + +
1128C LEU* 3.1 10.8 + - - +
1154C TRP* 3.6 23.8 - - + +
32D THR* 4.5 3.6 - - - +
33D GLY 4.6 7.6 - - - +
34D GLY* 5.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1110C ARG* 3.2 35.6 - - + +
1124C PRO* 1.3 71.6 - - - +
1126C GLU* 1.3 64.9 + - - +
1128C LEU* 3.3 13.2 + - + +
1129C LYS* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1124C PRO* 3.6 20.6 - - + +
1125C LEU* 1.3 86.8 + - - +
1127C VAL* 1.3 68.4 + - + +
1129C LYS* 3.1 12.3 + - + +
1130C LEU* 3.0 21.8 + - - +
35D VAL* 6.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1123C PRO* 4.6 1.6 - - + -
1124C PRO* 2.9 34.6 + - + +
1126C GLU* 1.3 79.9 - - + +
1128C LEU* 1.3 62.9 + - - +
1130C LEU* 3.2 7.6 + - - +
1131C GLY 3.0 6.8 + - - -
1144C LEU* 3.8 25.1 - - + -
1154C TRP* 3.9 26.5 - - + -
1156C TRP* 2.9 38.1 + - + +
34D GLY* 4.8 3.1 - - - -
35D VAL* 4.0 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1106C PRO* 3.9 32.3 - - + +
1110C ARG* 3.3 33.2 - - - +
1123C PRO* 3.8 19.5 - - + +
1124C PRO 3.1 10.8 + - - +
1125C LEU* 3.5 13.0 - - + +
1127C VAL* 1.3 76.8 - - - +
1129C LYS* 1.3 62.2 + - - +
1131C GLY* 3.0 10.6 + - - -
1132C GLU* 3.1 14.2 + - - +
1144C LEU* 4.3 0.4 - - + -
1156C TRP* 4.0 20.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1125C LEU 3.0 12.6 + - - +
1126C GLU* 3.4 13.7 - - + +
1128C LEU* 1.3 77.5 - - - +
1130C LEU* 1.3 62.7 + - - +
1131C GLY 3.4 0.2 + - - -
1132C GLU* 3.4 7.9 + - + +
1133C GLN* 3.3 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1126C GLU 3.0 12.0 + - - +
1127C VAL* 3.3 9.0 - - - +
1129C LYS* 1.3 76.6 - - - +
1131C GLY* 1.3 57.4 + - - +
1133C GLN* 3.2 21.9 + - - +
1134C MET* 2.8 65.7 + - + +
1155C GLN* 4.7 0.2 - - - +
1156C TRP* 4.3 7.4 - - + -
35D VAL* 3.5 41.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127C VAL 3.0 10.3 + - - -
1128C LEU 3.0 3.7 + - - -
1130C LEU* 1.3 76.7 - - - +
1132C GLU* 1.3 51.9 + - - +
1134C MET* 3.3 2.3 + - - +
1135C THR* 2.7 42.3 + - - -
1142C LEU* 4.5 0.2 - - - +
1156C TRP* 3.2 41.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1128C LEU 3.1 10.3 + - - +
1129C LYS* 3.6 11.4 - - - +
1131C GLY* 1.3 76.3 - - - +
1133C GLN* 1.3 57.2 + - + +
1135C THR* 3.3 5.1 + - - -
1136C GLN* 3.0 50.4 + - + +
1107E LYS* 2.9 33.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1129C LYS* 3.3 41.9 + - + +
1130C LEU* 3.2 21.1 + - - +
1132C GLU* 1.3 74.5 - - + +
1134C MET* 1.3 68.6 + - + +
1136C GLN* 3.5 7.8 + - - +
1137C GLU* 3.0 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1130C LEU* 2.8 53.1 + - + +
1131C GLY 3.9 1.6 - - - +
1133C GLN* 1.3 77.5 - - + +
1135C THR* 1.3 62.3 + - - +
1137C GLU* 3.5 21.0 - - - +
1138C ALA* 3.0 27.0 + - - +
1142C LEU* 3.6 15.0 - - + +
1155C GLN* 4.0 11.9 - - - +
1156C TRP* 3.9 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1131C GLY 2.7 24.4 + - - -
1132C GLU* 3.7 6.3 - - - -
1134C MET* 1.3 77.1 - - - +
1136C GLN* 1.3 55.4 + - + +
1139C ARG* 2.8 34.5 + - - -
1140C GLU 3.7 17.2 + - - +
1141C HIS* 5.1 1.8 - - - -
1142C LEU* 3.7 27.1 + - - +
1156C TRP* 5.1 2.4 - - - -
1141E HIS* 4.3 16.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1132C GLU* 3.0 30.5 + - + +
1133C GLN* 3.8 7.2 - - - +
1135C THR* 1.3 78.9 - - + +
1137C GLU* 1.3 57.0 + - - +
1139C ARG* 2.9 33.3 + - - +
1105E ASP* 5.7 2.8 + - - -
1107E LYS* 2.6 44.9 + - - +
1141E HIS* 5.4 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1133C GLN* 3.0 21.5 + - - +
1134C MET* 3.5 26.8 - - - +
1136C GLN* 1.3 77.5 - - - +
1138C ALA* 1.3 65.7 + - + +
1139C ARG* 3.4 20.0 + - - +
1082E PRO* 5.4 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1134C MET 3.0 18.2 + - - +
1135C THR 4.1 0.9 - - - +
1137C GLU* 1.3 79.9 - - + +
1139C ARG* 1.3 71.1 - - - +
1140C GLU* 3.3 34.2 + - + +
1142C LEU* 4.8 7.4 - - + -
1082E PRO* 4.3 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1135C THR 2.8 13.9 + - - -
1136C GLN* 2.9 27.3 + - - +
1137C GLU* 3.4 21.2 + - - +
1138C ALA* 1.3 78.0 - - - +
1140C GLU* 1.3 57.6 + - - +
1082E PRO* 3.5 29.5 - - + +
1083E LEU 3.0 24.2 + - - -
1084E ASP* 3.2 18.4 + - - +
1141E HIS* 3.4 38.1 - - - +
1143E TYR* 3.1 31.4 + - + +
1159E ARG* 5.9 1.7 - - - +
----------------------------------------------------------
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