Contacts of the helix formed by residues 959 - 971 (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 ASN 959 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879M GLU* 2.9 35.5 + - - +
880M LYS 5.2 3.4 + - - -
881M GLN* 3.5 15.9 - - - +
956M LEU 4.9 0.2 + - - -
957M PRO 4.0 0.2 - - - -
958M VAL* 1.3 70.1 - - - +
960M ILE* 1.3 60.3 + - - +
961M ARG* 3.0 13.9 + - - +
962M ARG* 3.0 58.1 + - - +
963M ILE* 3.4 20.4 + - - +
1052M GLN* 4.2 7.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 960 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881M GLN* 3.0 10.7 + - - +
958M VAL* 3.0 22.9 + - + +
959M ASN* 1.3 70.9 - - - +
961M ARG* 1.3 70.2 + - - +
962M ARG 3.3 0.2 - - - -
963M ILE* 2.9 26.3 - - + +
964M ILE* 3.4 18.4 + - + +
1018M PHE* 4.3 11.7 - - + -
1021M LEU* 4.3 11.2 - - + -
1022M LEU* 3.8 40.2 - - + -
1025M ARG* 4.3 27.8 - - + +
1026M LEU* 5.1 2.7 - - + -
1049M ILE* 3.9 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 961 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589M GLN* 5.0 14.1 + - - +
881M GLN* 4.2 1.7 + - - +
882M SER* 6.3 1.2 - - - -
959M ASN* 3.0 9.6 + - - +
960M ILE* 1.3 79.4 - - - +
962M ARG* 1.3 65.7 + - - +
964M ILE* 3.3 10.8 + - - +
965M GLN* 2.8 43.3 + - + +
1025M ARG* 3.8 27.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 962 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587M HIS* 4.3 11.9 - - + +
631M HIS 5.3 0.4 + - - -
632M VAL* 3.8 37.3 - - - +
635M ARG* 4.5 16.2 - - - +
636M GLU* 2.6 41.3 + - - +
879M GLU* 2.6 42.2 + - - -
959M ASN* 3.0 28.1 + - - +
961M ARG* 1.3 73.1 - - + +
963M ILE* 1.3 54.6 + - - +
964M ILE 2.4 18.9 + - - -
965M GLN* 2.6 35.6 + - - +
966M ASN* 3.0 17.9 + - - +
1052M GLN* 5.6 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 963 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958M VAL* 4.3 1.8 - - + -
959M ASN 3.4 8.5 + - - +
960M ILE* 2.9 43.3 - - + +
962M ARG* 1.3 77.4 - - - +
964M ILE* 1.3 57.2 + - - +
966M ASN* 4.1 11.6 - - - +
967M ALA* 3.7 14.6 + - - +
1044M TRP* 3.8 6.8 - - + -
1045M VAL* 4.1 11.5 - - + +
1048M ASN* 3.3 24.7 - - + +
1049M ILE* 3.1 49.8 - - + +
1052M GLN* 3.6 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 964 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
960M ILE* 3.4 15.1 + - + +
961M ARG* 3.3 10.9 + - - +
962M ARG 2.4 15.6 + - - -
963M ILE* 1.3 68.7 - - + +
965M GLN* 1.3 61.5 + - + +
966M ASN 3.1 2.0 - - - -
967M ALA* 2.9 5.6 - - - +
968M GLN* 2.8 45.2 + - + +
1025M ARG 4.9 0.2 - - - +
1026M LEU* 4.3 15.0 - - + -
1035M TYR* 3.3 55.2 - - + -
1037M LEU* 4.5 7.6 - - + -
1045M VAL* 3.6 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 965 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587M HIS* 3.1 53.1 + - + +
588M LEU* 5.5 0.3 - - - -
589M GLN* 6.1 0.2 - - - +
961M ARG* 2.8 55.7 + - + +
962M ARG* 2.6 26.2 + - - +
964M ILE* 1.3 74.8 - - + +
966M ASN* 1.3 64.2 + - - +
968M GLN* 3.2 19.5 + - - +
969M GLN* 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 966 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585M GLY 4.0 16.4 - - - +
587M HIS* 4.7 7.8 - - - +
636M GLU* 3.2 35.1 + - - +
962M ARG* 3.0 21.0 + - - +
963M ILE* 4.1 7.0 - - - +
965M GLN* 1.3 75.6 - - - +
967M ALA* 1.3 60.1 + - - +
968M GLN 3.1 0.3 + - - -
969M GLN* 3.2 3.7 + - - -
970M THR* 2.6 41.2 + - - +
1044M TRP* 3.6 20.3 - - + -
1052M GLN* 5.8 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 967 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963M ILE 3.7 0.9 - - - +
964M ILE* 2.9 18.9 - - + +
966M ASN* 1.3 76.9 - - - +
968M GLN* 1.3 59.6 + - + +
971M PHE* 2.8 29.8 + - - +
1037M LEU* 5.0 2.5 - - + -
1041M ALA* 4.3 11.6 - - + +
1044M TRP* 3.0 26.6 - - + -
1045M VAL* 3.3 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 968 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964M ILE* 2.8 30.2 + - + +
965M GLN* 3.3 21.7 - - - +
966M ASN 3.1 0.2 - - - -
967M ALA* 1.3 71.5 - - - +
969M GLN* 1.3 65.5 + - - +
971M PHE* 2.9 14.6 + - - +
972M HIS* 2.9 11.1 + - - -
973M ILE* 3.4 22.0 + - + +
975M HIS* 3.7 21.1 - - + -
1034M GLU 4.9 0.6 + - - -
1035M TYR* 3.0 31.5 + - - +
1037M LEU* 4.3 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 969 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585M GLY* 4.8 6.3 - - - -
587M HIS* 4.6 9.0 - - + +
608M ILE* 3.5 27.7 - - - +
609M ASP* 2.8 42.9 + - - +
965M GLN 3.0 13.6 + - - +
966M ASN* 4.1 3.6 - - - +
968M GLN* 1.3 78.7 - - - +
970M THR* 1.3 61.8 + - - +
971M PHE 3.2 0.7 + - - -
972M HIS* 3.3 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 970 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
966M ASN* 2.6 31.1 + - - +
969M GLN* 1.3 73.8 - - - +
971M PHE* 1.3 92.0 + - + +
972M HIS* 4.0 10.8 + - - -
1044M TRP* 3.8 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 971 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967M ALA 2.8 24.9 - - - +
968M GLN 2.9 3.6 + - - +
970M THR* 1.3 102.1 - - + +
972M HIS* 1.3 73.1 + - - +
973M ILE* 2.6 18.6 + - + +
1038M THR* 5.6 3.0 - - + +
1040M GLN* 3.2 42.4 - - + +
1041M ALA* 4.0 19.5 - - + -
1044M TRP* 3.9 38.6 - + + -
----------------------------------------------------------
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