Contacts of the helix formed by residues 1127 - 1139 (chain M) in PDB entry 3HOU
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 ASP1127 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1124M HIS* 3.6 28.6 - - + +
1125M ALA 2.9 4.4 - - - +
1126M ALA* 1.3 72.8 - - - +
1128M GLN* 1.3 67.4 + - - +
1129M GLU* 2.8 13.4 + - - +
1130M GLN* 2.6 54.6 + - + +
1131M ALA* 3.1 9.4 + - - +
1304M TRP* 4.5 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1128 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1126M ALA 2.7 13.9 + - - +
1127M ASP* 1.3 67.9 - - - +
1129M GLU* 1.3 59.8 + - + +
1131M ALA* 3.1 18.5 - - - +
1132M LYS* 3.8 24.1 + - - +
1284M MET* 3.8 22.2 - - - +
1304M TRP* 3.7 40.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1129 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127M ASP* 2.8 9.6 + - - +
1128M GLN* 1.3 74.5 - - + +
1130M GLN* 1.3 62.8 + - - +
1131M ALA 2.8 7.1 + - - -
1132M LYS* 3.1 43.2 + - - +
1133M LEU* 3.1 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1130 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1120M LEU* 5.4 2.2 - - + -
1124M HIS* 3.5 34.3 + - + +
1127M ASP* 2.6 41.5 + - + +
1129M GLU* 1.3 71.8 - - - +
1131M ALA* 1.3 57.8 + - - +
1133M LEU* 3.3 25.7 - - - +
1134M ILE* 3.0 58.9 + - + +
1321M GLY* 3.8 17.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1131 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1120M LEU* 6.5 0.9 - - - -
1127M ASP 3.1 7.8 + - - +
1128M GLN* 3.1 16.6 - - - +
1129M GLU 2.8 0.8 + - - -
1130M GLN* 1.3 73.5 - - - +
1132M LYS* 1.3 68.8 + - - +
1133M LEU 3.0 0.9 - - - -
1134M ILE* 2.7 21.9 + - - +
1135M ARG* 2.9 11.3 + - - +
1284M MET* 3.6 20.9 - - + -
1304M TRP* 4.4 20.4 - - + -
1306M LEU* 4.4 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1132 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1128M GLN* 3.8 37.0 - - - +
1129M GLU* 3.1 34.2 + - - +
1131M ALA* 1.3 76.0 - - - +
1133M LEU* 1.3 64.7 + - + +
1135M ARG* 3.0 20.9 + - - +
1136M SER* 2.9 31.8 + - - +
1284M MET* 3.8 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1133 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1129M GLU* 3.1 35.2 + - + +
1130M GLN* 3.3 35.4 - - - +
1131M ALA 3.0 0.2 - - - -
1132M LYS* 1.3 80.6 - - + +
1134M ILE* 1.3 62.9 + - + +
1136M SER* 3.7 6.5 + - - -
1137M ALA* 3.4 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1134 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1118M VAL* 6.3 0.4 - - + -
1120M LEU* 4.7 11.7 - - + -
1130M GLN* 3.0 37.7 - - + +
1131M ALA* 2.7 13.7 + - - +
1133M LEU* 1.3 72.1 - - + +
1135M ARG* 1.3 66.8 + - - +
1137M ALA* 2.7 20.3 + - + +
1138M ILE* 3.2 15.6 + - + +
1306M LEU* 4.1 14.4 - - + -
1319M VAL* 4.4 10.1 - - + -
1320M PRO 4.3 9.2 - - - +
1321M GLY* 3.1 29.4 - - - +
1322M ILE* 3.7 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1135 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706M HIS* 4.1 35.7 + - - +
1131M ALA 2.9 10.1 + - - +
1132M LYS* 3.2 18.4 - - - +
1134M ILE* 1.3 78.2 - - - +
1136M SER* 1.3 70.5 + - - +
1137M ALA 2.9 6.1 + - - -
1138M ILE* 3.2 5.5 - - - +
1139M GLU* 3.1 43.9 + - - +
1204M ASP 5.3 6.6 + - - -
1282M VAL* 4.2 15.5 + - + -
1283M VAL* 5.3 0.4 - - - +
1284M MET* 3.4 44.7 - - - +
1306M LEU* 3.7 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1136 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1132M LYS* 2.9 18.7 + - - +
1133M LEU* 3.8 6.3 - - - -
1135M ARG* 1.3 85.2 + - - +
1137M ALA* 1.3 56.7 + - - +
1138M ILE 3.6 0.7 - - - -
1139M GLU* 4.9 6.9 + - - -
1204M ASP 5.4 3.6 + - - -
1205M LYS* 5.9 0.5 - - - -
1206M ASP* 5.2 7.1 + - - -
1274M ARG* 4.1 46.2 + - - +
1275M GLY 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1137 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1133M LEU 3.4 12.6 - - - +
1134M ILE* 2.7 26.3 + - + +
1136M SER* 1.3 75.1 - - - +
1138M ILE* 1.3 63.8 + - + +
1274M ARG* 5.7 0.4 - - - -
1275M GLY* 3.9 14.9 + - - +
1276M VAL* 4.5 3.1 - - - +
1319M VAL* 4.9 10.8 - - + +
1320M PRO 5.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1138 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1118M VAL* 4.6 9.9 - - + -
1134M ILE* 3.3 10.8 - - + +
1135M ARG* 3.2 10.8 - - - +
1137M ALA* 1.3 83.1 - - - +
1139M GLU* 1.3 54.9 + - - +
1140M HIS 2.8 9.2 + - - -
1275M GLY* 3.2 6.1 - - - -
1276M VAL* 2.6 35.8 + - + +
1279M ILE* 3.7 12.7 - - + +
1282M VAL* 4.2 16.6 - - + -
1306M LEU* 3.9 26.9 - - + -
1308M THR* 5.8 2.0 - - - +
1316M VAL* 3.4 34.3 - - + -
1319M VAL* 4.2 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1139 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706M HIS* 2.7 39.0 + - - -
1135M ARG* 3.1 27.2 + - - +
1136M SER* 4.9 5.9 + - - -
1137M ALA 4.6 0.2 - - - +
1138M ILE* 1.3 72.1 - - - +
1140M HIS* 1.3 70.9 + - - +
1141M THR* 3.2 10.0 + - - -
1204M ASP 5.7 0.5 - - - +
1205M LYS* 4.4 21.5 - - - +
1274M ARG* 4.5 1.2 - - - +
1275M GLY* 3.9 4.4 + - - -
1279M ILE 3.8 3.1 - - - -
1280M GLU 3.9 14.6 - - - +
1281M ARG* 4.1 4.1 - - - -
1282M VAL* 3.3 33.3 + - + +
----------------------------------------------------------
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