Contacts of the helix formed by residues 1033 - 1044 (chain M) in PDB entry 5D4D
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 GLY1033 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1031M ARG* 3.6 23.7 - - - +
1032M PHE* 1.3 72.9 - - - +
1034M GLU* 1.3 66.3 + - - -
1035M MET 3.2 2.9 - - - -
1036M GLU* 2.7 19.6 + - - -
1037M VAL* 2.9 25.8 + - - +
620N GLY* 4.1 8.3 - - - -
15R G 5.5 0.4 - - - -
16R T 4.3 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1034 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1031M ARG* 4.8 2.7 - - - +
1033M GLY* 1.3 72.8 - - - +
1035M MET* 1.3 62.0 + - + +
1037M VAL* 3.2 2.8 + - - +
1038M TRP* 2.9 53.7 + - + +
615N ARG* 3.1 47.1 + - - +
619N LEU* 3.7 36.1 + - + +
620N GLY* 4.4 1.0 - - - -
1096N ARG* 2.3 32.8 + - - -
15R G 4.9 6.6 + - - +
16R T 5.2 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1035 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1033M GLY 3.2 0.8 - - - -
1034M GLU* 1.3 79.5 - - + +
1036M GLU* 1.3 64.1 + - - +
1038M TRP* 3.2 39.1 - - + +
1039M ALA* 3.0 24.4 + - - +
706N PRO* 4.8 2.7 - - + -
707N THR* 3.1 51.5 - - - +
708N LEU* 4.1 18.8 - - + +
1092N GLY* 6.4 2.0 - - - -
1095N THR* 5.7 5.6 - - + -
1227N GLN* 4.6 0.9 + - - -
14R A 4.9 7.0 - - + -
15R G 3.5 43.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1036 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1031M ARG 4.3 7.7 - - - +
1032M PHE* 3.6 39.4 - - + -
1033M GLY* 2.7 38.4 + - - +
1035M MET* 1.3 78.3 + - - +
1037M VAL* 1.3 66.1 + - - +
1039M ALA* 2.9 18.6 + - - +
1040M LEU 3.0 10.7 + - - -
703N ASN* 3.8 24.9 - - - +
705N ALA* 4.9 7.6 - - - +
707N THR* 3.0 25.7 + - - +
713N ILE* 4.3 0.7 - - + -
15R G 4.9 5.2 - - - +
16R T 4.7 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1037 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032M PHE* 4.0 15.3 - - + -
1033M GLY 2.9 17.8 + - - +
1034M GLU 3.4 8.3 - - - +
1036M GLU* 1.3 77.2 - - - +
1038M TRP* 1.3 64.4 + - + +
1040M LEU* 3.2 2.8 + - - +
1041M GLU* 2.9 43.1 + - - +
1049M LEU* 3.7 30.3 - - + -
1053M LEU* 4.4 12.6 - - + -
619N LEU* 3.6 17.7 - - + +
620N GLY* 4.5 2.7 - - - -
1466N VAL* 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1038 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1034M GLU* 2.9 45.8 + - + +
1035M MET* 3.2 41.7 - - + +
1036M GLU 3.2 0.2 - - - -
1037M VAL* 1.3 76.6 - - + +
1039M ALA* 1.3 64.6 + - - +
1041M GLU* 3.3 23.0 + - - +
1042M ALA* 2.9 24.1 + - - +
707N THR 5.3 1.3 - - - -
708N LEU 5.9 1.1 - - - -
1095N THR* 4.1 16.4 - - + -
1096N ARG* 3.8 39.7 - - + -
1099N VAL* 3.5 45.2 - - + +
1223N ILE* 3.6 5.8 - - + +
1227N GLN* 3.4 20.1 + - + +
1463N LYS* 6.1 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1039 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1035M MET 3.0 11.9 + - - +
1036M GLU 2.9 11.3 + - - +
1038M TRP* 1.3 76.3 - - - +
1040M LEU* 1.3 63.3 + - - +
1042M ALA* 3.0 5.9 + - - +
1043M TYR* 3.0 27.5 + - - -
707N THR* 4.0 13.0 - - + -
710N ARG* 3.9 16.1 - - - +
713N ILE* 3.6 27.8 - - + -
1227N GLN* 3.7 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1040 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032M PHE* 3.4 35.4 - - + -
1036M GLU 3.0 7.2 + - - +
1037M VAL 3.2 6.2 + - - +
1039M ALA* 1.3 76.9 - - - +
1041M GLU* 1.3 62.0 + - - +
1043M TYR* 3.3 3.9 + - - +
1044M GLY 3.0 17.0 + - - -
1045M ALA* 3.0 18.2 + - + +
1048M THR* 3.7 20.2 - - + -
1049M LEU* 3.6 37.2 - - + -
1052M MET* 3.9 4.9 - - + -
701N LEU* 4.5 2.5 - - + -
713N ILE* 4.0 12.8 - - + -
763N MET* 3.5 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1041 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037M VAL* 2.9 24.3 + - - +
1038M TRP* 3.3 32.2 - - - +
1040M LEU* 1.3 75.1 - - - +
1042M ALA* 1.3 58.8 + - - +
1044M GLY* 2.9 19.8 + - - -
1049M LEU* 3.9 15.7 - - + -
1103N HIS* 6.2 0.2 - - - -
1220N ALA* 3.6 16.0 - - - +
1223N ILE* 3.6 12.9 - - + +
1462N LEU* 3.4 42.5 - - + +
1463N LYS* 4.6 4.2 + - - +
1466N VAL* 3.5 18.0 - - - +
1472N ILE* 4.1 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1042 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1038M TRP 2.9 10.6 + - - +
1039M ALA 3.0 8.9 + - - +
1041M GLU* 1.3 78.0 - - - +
1043M TYR* 1.3 60.3 + - - +
1044M GLY* 3.3 0.5 + - - -
710N ARG* 2.8 36.7 + - + -
1219N GLU* 4.1 5.5 - - - +
1220N ALA 4.6 4.6 + - - +
1223N ILE* 4.3 8.2 - - + +
1224N VAL* 4.0 18.7 - - + +
1227N GLN* 3.4 25.8 - - - +
17O TYR* 4.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1043 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1039M ALA 3.0 25.0 + - - -
1040M LEU* 3.7 7.4 - - - +
1041M GLU 3.3 0.2 - - - -
1042M ALA* 1.3 76.6 - - - +
1044M GLY* 1.3 57.3 + - - +
1045M ALA* 4.1 4.7 - - + +
710N ARG* 2.9 51.4 + - + +
711N LEU* 3.4 18.9 - - + +
713N ILE* 2.8 26.6 + - + -
714N GLN* 3.9 4.7 - - - +
762N GLN* 2.8 42.9 + - + +
763N MET* 3.5 46.2 - - + -
768N ASN* 3.9 15.4 + - - -
16O LYS* 5.7 2.3 + - - -
17O TYR* 3.1 14.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1044 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040M LEU 3.0 1.1 + - - -
1041M GLU 2.9 18.7 + - - -
1042M ALA 3.1 0.4 - - - -
1043M TYR* 1.3 80.8 - - - +
1045M ALA* 1.3 60.8 + - - +
1046M ALA* 3.2 3.4 + - - -
762N GLN* 3.5 5.2 + - - -
1218N GLY 5.2 0.7 - - - -
1220N ALA 5.5 1.8 - - - -
1472N ILE* 4.8 3.4 - - - -
1474N ALA* 4.0 3.3 - - - +
1475N GLY* 3.2 20.2 - - - -
1476N THR* 3.2 27.0 + - - -
17O TYR* 4.0 2.7 - - - -
----------------------------------------------------------
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