Contacts of the helix formed by residues 876 - 893 (chain B) in PDB entry 3BYA
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 LYS 876 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLU* 5.6 0.7 - - - -
14A GLU* 4.7 18.3 + - + +
114A GLU* 4.8 6.8 + - - +
116A LEU* 3.4 36.8 - - + +
120A GLU* 4.2 22.7 - - - +
124A MET* 3.3 36.3 - - + +
127A GLU* 3.1 7.0 + - - -
875B LYS* 1.3 102.0 - - + +
877B LYS* 1.3 56.8 + - - +
878B ALA* 3.2 2.5 - - - +
879B THR* 3.1 22.9 + - - +
880B PHE 2.8 23.6 + - - -
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Residues in contact with LYS 877 (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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11A GLU* 4.8 1.1 - - - +
124A MET* 5.6 1.3 - - - +
127A GLU* 3.1 48.0 + - + +
128A ALA* 4.9 2.0 - - + +
144A MET* 3.9 36.9 + - + +
875B LYS 2.4 21.9 + - - +
876B LYS* 1.3 66.5 - - - +
878B ALA* 1.3 54.7 + - - +
880B PHE* 3.6 8.2 - - + +
881B ARG* 2.7 65.3 + - + +
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Residues in contact with ALA 878 (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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11A GLU* 3.5 43.3 + - + +
12A PHE* 4.0 27.1 - - + -
15A ALA* 4.4 1.8 - - - -
72A MET* 3.8 3.3 - - - +
875B LYS 3.5 2.6 + - - +
876B LYS* 4.9 0.4 - - - -
877B LYS* 1.3 78.6 - - - +
879B THR* 1.3 52.7 + - - +
881B ARG* 3.4 8.2 + - - +
882B ALA* 2.7 36.3 + - - +
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Residues in contact with THR 879 (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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11A GLU 4.5 2.3 + - - -
14A GLU* 4.2 7.3 - - - +
15A ALA* 3.8 27.2 + - - +
18A LEU* 3.6 27.8 - - + -
109A MET* 3.9 23.3 - - + -
114A GLU* 4.4 7.5 + - - +
124A MET* 4.4 1.1 - - + -
876B LYS* 3.1 29.1 + - + +
878B ALA* 1.3 74.5 - - - +
880B PHE* 1.3 67.2 + - - +
882B ALA* 3.3 1.4 + - - +
883B ILE* 3.1 24.3 + - - +
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Residues in contact with PHE 880 (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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92A PHE* 3.7 39.7 - + - -
100A ILE* 4.0 22.9 - - + -
105A LEU* 4.2 15.7 - - + -
124A MET* 3.4 34.7 - - + +
128A ALA* 3.9 22.9 - - + -
136A VAL* 4.2 12.8 - - + -
141A PHE* 4.0 11.7 - + - -
144A MET* 3.6 23.6 - - + -
876B LYS 2.8 13.9 + - - +
877B LYS* 3.6 8.3 - - - +
879B THR* 1.3 74.4 - - - +
881B ARG* 1.3 60.5 + - - +
883B ILE* 3.6 5.3 + - - +
884B THR* 3.0 27.9 + - - -
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Residues in contact with ARG 881 (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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12A PHE* 6.2 1.3 - - + -
72A MET* 5.0 11.5 + - + -
73A ALA 5.9 2.0 + - - -
143A GLN 4.9 0.8 + - - -
144A MET* 2.7 43.2 + - + +
145A MET* 3.1 48.0 + - - +
146A THR 4.7 7.1 + - - +
877B LYS* 2.7 50.0 + - + +
878B ALA* 3.6 7.0 - - - +
880B PHE* 1.3 71.9 - - - +
882B ALA* 1.3 53.1 + - - +
884B THR 3.1 0.9 + - - -
885B SER* 2.8 36.8 + - - -
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Residues in contact with ALA 882 (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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15A ALA* 3.9 14.8 - - + -
18A LEU* 6.2 0.7 - - + -
19A PHE* 4.6 9.2 - - + -
68A PHE* 4.3 7.0 - - + -
72A MET* 3.2 30.9 - - + +
878B ALA 2.7 22.2 + - - +
879B THR 3.3 4.9 + - - +
881B ARG* 1.3 71.3 - - - +
883B ILE* 1.3 61.9 + - + +
885B SER* 3.8 1.8 - - - -
886B THR* 2.6 35.6 + - - +
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Residues in contact with ILE 883 (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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18A LEU* 4.3 9.2 - - + -
19A PHE* 5.0 7.0 - - + -
35A VAL* 6.3 0.2 - - + -
39A LEU* 3.9 31.1 - - + +
92A PHE* 3.6 26.5 - - + -
109A MET* 3.2 37.7 - - + -
112A LEU* 3.6 23.1 - - + -
879B THR* 3.1 18.5 + - + +
880B PHE* 3.8 3.6 - - - +
882B ALA* 1.3 81.3 - - + +
884B THR* 1.3 63.1 + - - +
886B THR* 3.3 5.2 + - - -
887B LEU* 3.0 26.1 + - + +
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Residues in contact with THR 884 (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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85A ILE* 5.4 4.5 - - + -
88A ALA* 3.9 11.2 - - + +
92A PHE* 3.7 7.3 - - - -
141A PHE* 3.4 41.2 - - + -
144A MET* 4.1 1.4 - - - +
145A MET* 3.6 28.0 - - + -
880B PHE 3.0 16.2 + - - -
881B ARG 3.1 5.2 + - - -
883B ILE* 1.3 79.5 - - - +
885B SER* 1.3 58.1 + - - +
887B LEU* 3.2 10.7 + - - +
888B ALA* 2.8 29.3 + - + +
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Residues in contact with SER 885 (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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71A MET* 4.4 20.3 + - - +
72A MET* 4.9 11.0 - - - -
145A MET* 3.9 12.5 - - - +
881B ARG 2.8 16.9 + - - -
882B ALA* 3.8 6.3 - - - -
884B THR* 1.3 77.8 - - - +
886B THR* 1.3 57.7 + - - +
888B ALA* 3.3 8.9 + - - +
889B SER* 2.9 28.1 + - - -
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Residues in contact with THR 886 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 3.4 24.4 - - + -
32A LEU* 3.9 20.9 - - + -
35A VAL* 5.3 0.7 - - + -
36A MET* 3.6 23.7 - - - +
39A LEU* 5.7 2.2 - - - -
51A MET* 5.1 3.2 - - - +
68A PHE* 5.9 0.5 - - - -
71A MET* 4.3 17.0 - - + +
882B ALA 2.6 22.7 + - - -
883B ILE* 3.6 4.5 - - - -
885B SER* 1.3 73.2 + - - +
887B LEU* 1.3 67.2 + - - +
889B SER* 3.3 9.2 - - - -
890B SER* 3.2 20.5 + - - -
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Residues in contact with LEU 887 (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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36A MET* 4.8 2.5 - - + -
39A LEU* 4.1 18.4 - - + -
41A GLN* 3.6 41.5 - - + +
88A ALA* 4.0 15.3 - - + +
91A VAL* 3.8 28.9 - - + -
92A PHE* 4.5 2.9 - - + -
883B ILE* 3.0 31.7 + - + +
884B THR* 3.3 8.7 - - - +
886B THR* 1.3 75.6 - - - +
888B ALA* 1.3 63.1 + - - +
890B SER* 2.4 26.0 + - - +
891B PHE* 3.0 26.8 + - + -
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Residues in contact with ALA 888 (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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84A GLU* 3.9 29.7 - - + +
85A ILE* 5.9 3.8 - - + -
88A ALA* 5.0 0.4 - - - +
145A MET* 6.3 0.4 - - + -
884B THR* 2.8 18.9 + - + +
885B SER* 3.3 12.3 + - - +
887B LEU* 1.3 72.8 - - - +
889B SER* 1.3 62.4 + - - +
891B PHE* 3.3 13.6 + - - +
892B LYS* 3.0 29.5 + - - +
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Residues in contact with SER 889 (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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51A MET* 3.9 17.0 + - - +
54A GLU* 4.3 3.3 + - - -
71A MET* 4.9 11.7 - - - +
885B SER 2.9 12.9 + - - -
886B THR* 3.3 15.0 - - - -
887B LEU 3.2 0.2 - - - -
888B ALA* 1.3 75.9 - - - +
890B SER* 1.3 61.2 + - - +
892B LYS* 3.3 24.6 + - - +
893B ARG* 2.9 39.5 + - - -
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Residues in contact with SER 890 (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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36A MET* 3.2 35.6 - - - +
41A GLN* 4.7 3.8 - - - +
43A PRO* 5.5 1.3 - - - -
47A GLU* 5.9 0.9 - - - -
51A MET* 3.5 21.8 - - - +
886B THR 3.2 2.1 + - - -
887B LEU* 2.4 32.1 + - - +
889B SER* 1.3 76.9 - - - +
891B PHE* 1.3 70.4 + - - +
892B LYS 3.4 0.2 + - - -
893B ARG* 3.6 16.5 + - - +
894B ARG* 4.3 4.2 + - - +
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Residues in contact with PHE 891 (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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41A GLN* 3.3 29.6 - - - -
84A GLU* 3.7 22.7 - - + -
87A GLU* 3.5 58.3 - - + +
88A ALA 3.6 11.4 - - - -
91A VAL* 4.7 0.2 - - + -
887B LEU* 3.0 45.9 + - + -
888B ALA* 3.7 6.1 - - - +
890B SER* 1.3 79.0 - - - +
892B LYS* 1.3 66.5 + - - +
893B ARG 3.2 0.7 + - - -
894B ARG* 3.3 22.4 + - - +
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Residues in contact with LYS 892 (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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54A GLU* 5.1 7.2 - - - +
84A GLU* 3.6 30.0 + - - +
888B ALA* 3.0 12.9 + - - +
889B SER* 3.3 36.6 + - - +
890B SER 3.2 0.2 - - - -
891B PHE* 1.3 78.0 - - - +
893B ARG* 1.3 67.2 + - - +
894B ARG 3.3 8.0 + - - +
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Residues in contact with ARG 893 (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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47A GLU* 3.8 53.6 - - + +
50A ASP* 4.0 20.5 + - - +
51A MET* 3.5 18.1 - - + +
54A GLU* 2.9 40.0 + - - -
889B SER* 2.9 41.3 + - - +
890B SER 3.6 8.9 + - - +
891B PHE 3.2 1.2 + - - -
892B LYS* 1.3 84.7 - - + +
894B ARG* 1.3 59.7 + - - +
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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