Contacts of the helix formed by residues 960 - 972 (chain B) in PDB entry 5MJ6
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 SER 960 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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541B GLU* 3.6 24.4 - - - +
956B PHE* 3.6 21.4 - - - +
957B PRO* 2.6 36.8 + - - -
958B LEU 3.5 0.4 - - - -
959B GLY* 1.3 79.0 - - - +
961B TYR* 1.3 67.0 + - - +
962B THR* 3.2 5.2 + - - -
963B ILE* 3.4 6.3 + - - +
964B GLN* 3.1 18.9 + - - +
1127B 7O2 5.6 2.9 - - - -
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Residues in contact with TYR 961 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B GLU* 4.8 4.4 + - - -
544B PHE* 3.7 24.4 + - - +
545B ASP* 4.7 1.8 - - - -
546B SER* 5.5 2.7 - - - -
929B ARG* 5.9 1.3 - - - -
960B SER* 1.3 73.0 - - - +
962B THR* 1.3 62.1 + - - +
964B GLN* 3.6 24.8 - - - +
965B ASN* 2.8 62.0 + - + +
1127B 7O2 3.5 78.9 - + + -
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Residues in contact with THR 962 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B GLU* 3.3 36.1 + - - +
925B SER* 4.0 14.6 - - - +
956B PHE* 3.8 37.7 - - + -
960B SER* 3.1 4.3 + - - -
961B TYR* 1.3 83.0 - - - +
963B ILE* 1.3 57.9 + - - +
965B ASN* 3.2 7.6 + - - +
966B ILE* 2.8 38.3 + - + +
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Residues in contact with ILE 963 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
949B TRP* 3.8 30.5 - - + -
952B LEU* 4.1 26.0 - - + +
953B VAL* 4.5 7.6 - - + +
956B PHE* 3.2 39.7 - - + +
957B PRO 3.8 5.6 - - - +
958B LEU* 4.9 7.9 - - + +
959B GLY* 4.9 4.7 - - - -
960B SER* 3.4 16.5 + - - +
962B THR* 1.3 73.8 - - - +
964B GLN* 1.3 66.3 + - - +
966B ILE* 3.2 9.1 + - + +
967B VAL* 2.8 27.7 + - + +
997B LEU* 6.2 1.6 - - + -
999B CYS* 5.3 4.9 - - + -
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Residues in contact with GLN 964 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521B LYS* 2.3 33.2 + - - +
542B GLU* 5.3 2.8 + - - +
544B PHE 4.6 0.8 + - - -
545B ASP* 3.8 23.1 - - - +
959B GLY 5.4 0.2 - - - +
960B SER 3.1 13.9 + - - +
961B TYR* 3.3 28.3 + - + +
963B ILE* 1.3 76.4 - - - +
965B ASN* 1.3 57.0 + - - +
967B VAL* 3.9 1.7 - - - +
968B ALA* 2.9 33.4 + - + +
999B CYS* 3.9 34.8 - - + +
1002B GLU* 3.8 7.5 - - - +
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Residues in contact with ASN 965 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925B SER* 4.2 10.3 - - - +
929B ARG* 3.2 43.9 + - - +
961B TYR* 2.8 52.9 + - + +
962B THR* 3.3 7.2 - - - +
964B GLN* 1.3 75.6 - - - +
966B ILE* 1.3 60.6 + - - +
968B ALA* 3.4 4.8 + - - +
969B GLY* 2.9 29.8 + - - -
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Residues in contact with ILE 966 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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924B LEU* 5.1 1.1 - - + -
925B SER* 3.8 26.5 - - - +
928B ILE* 4.0 24.8 - - + +
945B VAL* 3.5 34.5 - - + +
949B TRP* 5.6 1.8 - - + -
952B LEU* 4.5 21.3 - - + -
956B PHE* 4.7 7.2 - - + -
962B THR* 2.8 40.8 + - + +
963B ILE* 3.7 10.5 - - + +
965B ASN* 1.3 73.5 - - - +
967B VAL* 1.3 61.1 + - + +
969B GLY* 4.1 0.7 - - - -
970B SER* 2.8 28.9 + - - -
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Residues in contact with VAL 967 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942B TRP* 5.4 0.9 - - + -
945B VAL* 5.0 4.5 - - + -
949B TRP* 3.6 37.2 - - + -
963B ILE* 2.8 26.4 + - + +
964B GLN* 4.0 4.3 - - - +
966B ILE* 1.3 73.0 - - - +
968B ALA* 1.3 60.9 + - - +
970B SER* 3.6 3.7 + - - -
971B THR* 2.9 32.9 + - + +
987B PHE* 4.0 22.4 - - + -
999B CYS* 4.4 16.4 - - + +
1000B VAL* 5.1 1.3 - - + -
1003B ALA* 4.0 22.7 - - + -
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Residues in contact with ALA 968 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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964B GLN* 2.9 24.2 + - + +
965B ASN* 3.8 4.7 - - - +
967B VAL* 1.3 79.2 - - - +
969B GLY* 1.3 59.0 + - - +
971B THR* 3.7 3.7 + - - -
972B TYR* 3.1 38.2 + - + +
1003B ALA* 5.3 4.7 - - + +
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Residues in contact with GLY 969 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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928B ILE* 5.7 1.1 - - - -
929B ARG* 4.8 28.3 - - - +
932B GLY* 4.9 9.5 - - - +
965B ASN 2.9 16.7 + - - -
966B ILE 4.1 0.7 - - - -
968B ALA* 1.3 77.7 - - - +
970B SER* 1.3 59.7 + - - +
971B THR 3.4 0.2 - - - -
972B TYR* 3.6 24.5 - - - -
973B LEU* 5.8 0.3 - - - +
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Residues in contact with SER 970 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928B ILE* 4.5 4.9 - - - -
932B GLY* 5.5 3.6 - - - -
938B HIS* 4.9 9.4 + - - +
941B ALA* 4.4 10.8 - - - -
942B TRP* 3.6 43.1 - - - +
945B VAL* 3.7 12.8 - - - +
966B ILE 2.8 18.5 + - - -
967B VAL* 3.6 4.9 + - - -
968B ALA 3.2 0.4 - - - -
969B GLY* 1.3 80.1 - - - +
971B THR* 1.3 58.9 + - - +
972B TYR 3.8 0.2 - - - -
973B LEU 5.4 0.4 - - - -
974B PHE* 3.7 16.6 - - - -
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Residues in contact with THR 971 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938B HIS* 6.0 0.2 - - - -
942B TRP* 3.7 34.5 - - + -
967B VAL* 2.9 26.2 + - + +
968B ALA* 3.7 2.8 + - - -
970B SER* 1.3 84.6 - - - +
972B TYR* 1.3 61.1 + - - +
973B LEU 3.0 10.5 + - - -
974B PHE* 3.0 33.8 + - + +
983B VAL* 4.3 11.2 - - + -
1003B ALA* 3.7 19.2 + - + +
1007B ILE* 3.8 16.4 - - - +
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Residues in contact with TYR 972 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774B LEU* 3.9 19.5 - - + +
777B ASN* 4.9 4.3 + - - -
778B LEU* 4.0 1.0 - - - +
929B ARG* 6.6 0.2 - - + -
933B ARG* 4.2 23.0 + - + +
968B ALA* 3.1 26.0 + - + +
969B GLY* 3.6 22.2 - - - -
970B SER 3.8 0.2 - - - -
971B THR* 1.3 77.7 + - - +
973B LEU* 1.3 95.8 + - + +
974B PHE 3.4 0.4 - - - -
1003B ALA 6.1 0.2 - - - -
1006B VAL* 4.1 22.5 - - + +
1010B ASN* 2.8 21.9 + - - +
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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