Contacts of the helix formed by residues 954 - 965 (chain A) in PDB entry 5LUQ
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 GLY 954 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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886A TRP* 2.7 38.0 - - - -
950A GLU 3.0 19.1 + - - -
951A GLY 3.2 4.0 - - - -
952A GLY 2.9 2.2 - - - -
953A GLN* 1.3 77.4 - - - +
955A ALA* 1.3 66.4 + - - +
956A PRO* 3.2 3.4 - - - -
957A PRO* 3.0 7.7 - - - +
958A MSE 3.2 5.8 - - - +
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Residues in contact with ALA 955 (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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945A ALA* 5.8 2.2 - - + -
951A GLY 2.9 10.2 + - - +
952A GLY 3.8 10.8 - - - +
954A GLY* 1.3 74.6 - - - +
956A PRO* 1.3 62.8 - - + +
958A MSE 4.1 7.6 - - + +
959A TYR* 2.8 44.0 + - + +
960A GLN 3.7 0.3 + - - -
1001A PHE* 4.7 4.5 - - + +
1002A GLU* 3.7 37.7 - - + +
1005A ASP* 4.4 2.0 - - - +
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Residues in contact with PRO 956 (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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952A GLY 4.5 0.2 - - - +
953A GLN* 3.3 27.1 - - + +
954A GLY 3.0 6.4 - - - -
955A ALA* 1.3 93.9 - - + +
957A PRO* 1.4 65.6 - - + +
960A GLN* 3.3 30.3 - - - +
1001A PHE* 4.8 17.5 - - + +
1004A GLN* 6.0 7.5 - - + +
1005A ASP* 4.8 7.2 - - - +
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Residues in contact with PRO 957 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885A ALA* 4.4 3.4 - - - -
886A TRP* 3.6 42.0 - - + +
953A GLN 4.7 1.6 - - - +
954A GLY* 3.0 22.0 - - - +
956A PRO* 1.4 87.0 - - + +
958A MSE 1.3 70.6 + - - +
959A TYR 3.1 0.5 + - - -
961A LEU* 3.0 36.0 + - + +
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Residues in contact with MSE 958 (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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885A ALA* 3.9 10.3 - - - +
886A TRP* 3.8 7.8 - - + -
892A LEU* 3.3 56.4 - - + +
910A PHE* 5.7 0.7 - - - -
941A MSE 2.9 54.0 - - + +
944A LYS 4.3 3.8 - - - +
945A ALA* 4.2 14.8 - - + -
951A GLY* 4.7 14.1 - - - +
954A GLY 3.2 17.0 + - - +
955A ALA* 4.0 3.8 - - - +
957A PRO* 1.3 78.5 - - - +
959A TYR* 1.3 75.5 + - + +
961A LEU* 4.0 1.6 - - - +
962A TYR* 3.1 22.5 + - - +
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Residues in contact with TYR 959 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941A MSE 3.8 20.1 - - + +
942A LEU* 5.7 13.9 - - + -
955A ALA* 2.8 29.7 + - + +
958A MSE 1.3 81.9 - - + +
960A GLN* 1.3 53.0 + - - +
962A TYR* 4.2 0.5 - - - +
963A LYS* 2.6 73.2 + - + +
991A LEU* 3.2 30.7 + - + +
994A TRP* 6.2 0.2 - - - -
995A PHE* 3.3 11.9 - + - -
1002A GLU* 4.4 20.2 - - + -
1005A ASP* 2.8 39.7 - - + +
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Residues in contact with GLN 960 (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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955A ALA 3.7 2.4 + - - -
956A PRO 3.3 20.9 - - - +
957A PRO 3.4 1.0 + - - -
959A TYR* 1.3 78.5 - - - +
961A LEU* 1.3 82.8 + - + +
963A LYS* 2.9 17.5 + - - +
964A ARG 3.0 12.5 + - - -
1004A GLN* 5.3 8.0 - - + +
1005A ASP* 4.4 16.5 - - + +
1008A ALA* 5.4 10.2 - - - +
1009A LEU* 3.4 31.3 - - + +
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Residues in contact with LEU 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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883A TYR* 3.4 62.7 - - + +
885A ALA* 6.3 1.8 - - + -
957A PRO* 3.0 27.2 + - + +
958A MSE 4.1 1.6 - - - +
960A GLN* 1.3 105.0 - - + +
962A TYR* 1.3 62.2 + - - +
964A ARG* 4.4 5.9 + - + +
965A THR* 4.0 13.2 - - - +
1009A LEU* 5.3 1.1 - - + -
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Residues in contact with TYR 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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910A PHE* 4.1 27.8 - + + -
914A VAL* 5.7 5.2 - - + -
934A LEU* 2.9 45.8 - - + +
938A VAL* 3.4 19.7 - - + +
941A MSE 4.1 23.3 - - + -
958A MSE 3.1 16.7 + - - +
961A LEU* 1.3 77.7 - - - +
963A LYS* 1.3 74.6 + - + +
965A THR* 2.8 40.2 + - - -
966A PHE* 3.0 53.5 + + + -
969A LEU* 3.5 2.3 - - + +
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Residues in contact with LYS 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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959A TYR* 2.6 64.7 + - + +
960A GLN* 2.9 5.5 + - - +
962A TYR* 1.3 80.4 - - + +
964A ARG* 1.3 54.2 + - - +
966A PHE* 2.6 42.0 + - + +
967A PRO* 3.0 18.8 - - + +
988A VAL* 5.2 1.8 - - - -
991A LEU* 4.3 18.9 + - - -
992A ILE* 4.4 4.9 - - - +
995A PHE* 3.8 0.8 - - - -
1006A THR* 1.9 41.1 + - + +
1009A LEU* 3.3 16.4 - - + -
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Residues in contact with ARG 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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960A GLN 3.0 8.4 + - - +
961A LEU* 4.4 7.0 - - + +
963A LYS* 1.3 75.7 - - - +
965A THR* 1.3 67.8 + - + +
966A PHE 3.0 5.0 + - - -
967A PRO* 3.4 11.3 - - - +
968A VAL* 3.5 48.9 + - - +
1009A LEU* 3.1 37.6 - - + +
1012A ALA* 5.8 4.9 + - - +
1013A ILE* 4.0 28.7 - - - +
1016A GLY* 6.4 0.4 - - - -
1019A ASP* 6.0 0.2 + - - -
1021A VAL* 5.7 7.5 - - - +
1024A THR* 5.3 0.4 - - - +
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Residues in contact with THR 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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883A TYR* 6.1 3.4 - - + -
914A VAL* 4.4 29.6 - - + +
917A LEU* 3.9 13.6 - - - +
934A LEU* 5.2 0.2 - - - +
961A LEU 4.0 12.1 - - - +
962A TYR* 2.8 33.5 + - - +
964A ARG* 1.3 79.3 - - + +
966A PHE* 1.3 58.3 + - - +
968A VAL* 3.3 15.8 - - + +
969A LEU* 3.2 23.7 + - - +
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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