Contacts of the helix formed by residues 960 - 970 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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541A GLU* 3.4 28.0 - - - -
956A PHE* 3.8 19.9 - - - +
957A PRO* 2.8 26.2 + - - +
958A LEU 3.6 0.4 - - - -
959A GLY* 1.3 76.7 - - - +
961A TYR* 1.3 67.5 + - - +
962A THR* 3.3 4.1 + - - -
963A ILE* 3.3 6.5 + - - +
964A GLN* 3.1 21.2 + - - +
1137A 7O2 5.4 4.7 - - - -
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Residues in contact with TYR 961 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541A GLU 4.8 3.0 + - - -
544A PHE 3.7 25.0 + - - +
545A ASP* 4.9 2.2 - - - -
546A SER 5.7 0.9 - - - -
929A ARG* 6.0 0.4 - - - -
960A SER* 1.3 74.8 - - - +
962A THR* 1.3 64.5 + - - +
964A GLN* 3.3 27.6 + - - -
965A ASN* 2.8 55.1 + - + +
1137A 7O2 3.4 84.1 - + + -
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Residues in contact with THR 962 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A GLU* 3.1 39.9 + - - +
925A SER* 4.1 12.8 - - - +
956A PHE* 3.8 41.4 - - + -
960A SER* 3.3 3.5 + - - -
961A TYR* 1.3 87.3 - - - +
963A ILE* 1.3 56.6 + - - +
965A ASN* 3.2 7.1 + - - +
966A ILE* 2.9 35.4 + - + +
1137A 7O2 5.8 1.9 - - - -
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Residues in contact with ILE 963 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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949A TRP* 4.0 32.1 - - + -
952A LEU* 4.1 29.8 - - + +
953A VAL* 4.4 6.1 - - + -
956A PHE* 3.2 34.3 - - + +
957A PRO 4.1 6.1 - - - +
958A LEU* 4.9 8.1 - - + -
959A GLY* 5.0 6.7 - - - -
960A SER* 3.3 11.3 + - - +
962A THR* 1.3 74.7 - - - +
964A GLN* 1.3 63.8 + - + +
966A ILE* 3.1 13.8 + - + +
967A VAL* 2.8 33.4 + - + +
999A CYS* 5.4 5.2 - - + -
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Residues in contact with GLN 964 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A LYS* 3.8 18.4 - - - +
544A PHE 4.8 0.3 - - - +
545A ASP* 4.1 11.6 - - - +
960A SER 3.1 16.3 + - - +
961A TYR* 3.8 30.2 - - - +
963A ILE* 1.3 80.6 - - - +
965A ASN* 1.3 63.5 + - - +
967A VAL* 4.0 1.9 - - - +
968A ALA* 3.0 41.3 + - + +
998A ARG* 3.4 24.7 + - - +
999A CYS* 3.7 29.2 - - + -
1002A GLU* 5.9 0.2 - - - +
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Residues in contact with ASN 965 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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925A SER* 3.9 12.1 - - - +
929A ARG* 3.0 46.7 + - - +
961A TYR* 2.8 46.3 + - + +
962A THR* 3.3 11.4 - - - +
964A GLN* 1.3 84.9 - - - +
966A ILE* 1.3 56.8 + - - +
968A ALA* 4.0 3.0 - - - +
969A GLY* 3.0 26.5 + - - -
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Residues in contact with ILE 966 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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924A LEU* 5.1 0.9 - - + -
925A SER* 3.9 26.5 - - - +
928A ILE* 4.3 18.1 - - + +
945A VAL* 3.5 35.2 - - + -
949A TRP* 5.7 0.2 - - + -
952A LEU* 4.2 27.1 - - + -
956A PHE* 4.6 7.9 - - + -
962A THR* 2.9 35.7 + - + +
963A ILE* 3.1 11.9 + - + +
965A ASN* 1.3 77.1 - - - +
967A VAL* 1.3 63.0 + - + +
969A GLY* 4.1 0.7 - - - -
970A SER* 2.9 29.5 + - - -
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Residues in contact with VAL 967 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942A TRP* 5.3 0.9 - - + -
945A VAL* 5.1 3.6 - - + -
949A TRP* 3.8 33.7 - - + -
963A ILE* 2.8 24.3 + - + +
964A GLN* 4.0 5.4 - - - +
966A ILE* 1.3 80.8 - - + +
968A ALA* 1.3 55.6 + - - +
970A SER* 4.1 3.1 - - - -
971A THR* 2.6 41.4 + - + +
987A PHE* 3.9 24.0 - - + -
999A CYS* 4.4 15.9 - - + +
1000A VAL* 5.1 1.8 - - + +
1003A ALA* 4.0 22.2 - - + -
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Residues in contact with ALA 968 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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964A GLN* 3.0 28.2 + - + +
965A ASN* 4.0 4.0 - - - +
967A VAL* 1.3 78.7 - - - +
969A GLY* 1.3 61.9 + - - +
971A THR* 3.9 4.3 - - - -
972A TYR* 3.2 35.0 + - + +
1003A ALA* 5.4 4.5 - - - +
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Residues in contact with GLY 969 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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928A ILE* 5.1 1.3 - - - +
929A ARG* 4.7 30.2 - - - +
932A GLY* 4.8 10.4 - - - +
965A ASN 3.0 18.6 + - - -
966A ILE* 4.1 1.3 - - - -
967A VAL 3.3 0.2 - - - -
968A ALA* 1.3 77.5 - - - +
970A SER* 1.3 57.5 + - - +
971A THR 3.5 0.4 - - - -
972A TYR* 3.7 23.8 - - - -
973A LEU* 5.9 0.2 - - - +
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Residues in contact with SER 970 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928A ILE* 4.4 4.5 - - - -
932A GLY* 5.5 2.2 - - - -
938A HIS* 5.2 6.7 - - - +
941A ALA* 4.3 11.0 - - - -
942A TRP* 3.5 55.6 + - - +
945A VAL* 3.7 12.6 - - - +
966A ILE 2.9 19.9 + - - -
967A VAL* 3.6 3.8 + - - -
968A ALA 3.2 0.4 - - - -
969A GLY* 1.3 78.9 - - - +
971A THR* 1.3 58.3 + - - +
973A LEU 5.5 0.4 - - - -
974A PHE* 3.6 8.7 - - - -
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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