Contacts of the helix formed by residues 59 - 77 (chain R) in PDB entry 2F4V
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 59 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835A U 5.3 1.9 + - - -
53R ARG* 3.2 10.7 - - - +
58R LEU* 1.3 79.6 - - - +
60R GLY* 1.3 55.2 + - - +
61R LYS* 2.6 20.5 + - - +
62R GLU* 2.6 33.2 + - - +
63R GLN* 2.5 33.4 + - - +
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Residues in contact with GLY 60 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A G 6.1 0.9 - - - -
834A C 4.8 6.8 + - - -
835A U 3.6 15.8 + - - -
53R ARG* 3.0 26.5 - - - +
59R SER* 1.3 73.2 + - - +
61R LYS* 1.3 55.5 + - - +
63R GLN* 4.5 2.3 - - - +
64R ARG* 3.2 32.2 + - - +
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Residues in contact with LYS 61 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A G 4.1 2.0 + - - -
663A A 3.6 27.5 + - - -
664A G 5.0 1.3 - - - +
835A U 3.5 16.0 + - - +
836A G 2.6 39.4 + - - +
97F PHE* 4.0 29.6 - - + -
59R SER* 2.6 13.8 + - - +
60R GLY* 1.3 72.1 - - - +
62R GLU* 1.3 60.6 + - + +
63R GLN 3.2 0.9 - - - -
64R ARG* 3.5 23.5 + - - +
65R ILE* 2.9 39.6 + - + +
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Residues in contact with GLU 62 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F PHE* 4.4 22.8 - - + -
99F ALA* 3.2 29.0 - - + +
23R LYS* 5.2 8.7 + - - +
31R LEU* 4.0 5.8 - - + +
58R LEU* 3.0 32.3 - - + +
59R SER* 2.6 41.9 + - - +
61R LYS* 1.3 76.7 - - + +
63R GLN* 1.3 53.2 + - - +
65R ILE* 3.1 11.2 + - - +
66R LEU* 2.8 32.9 + - - +
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Residues in contact with GLN 63 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720A C 3.5 26.2 + - - +
721A G 3.8 14.6 - - - +
50R ILE* 4.0 8.7 - - - +
51R LEU 3.1 25.5 + - - -
53R ARG* 3.6 20.0 - - + +
56R THR* 2.7 27.3 + - - +
58R LEU* 3.3 15.2 - - + +
59R SER 2.5 23.2 + - - +
60R GLY* 4.5 2.7 - - - +
62R GLU* 1.3 70.0 - - - +
64R ARG* 1.3 67.7 + - - +
65R ILE 2.9 2.0 + - - -
66R LEU* 3.5 9.7 - - - +
67R ALA* 3.1 23.2 + - - +
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Residues in contact with ARG 64 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663A A 3.6 4.4 + - - -
664A G 2.6 59.0 + - - +
665A A 4.1 14.6 - - - +
720A C 5.2 1.3 - - - -
721A G 5.5 1.3 + - - -
834A C 3.8 7.3 + - - -
835A U 2.6 32.9 + - - -
60R GLY* 3.2 21.0 + - - +
61R LYS* 3.5 31.8 + - - +
63R GLN* 1.3 79.7 - - - +
65R ILE* 1.3 61.0 + - + +
67R ALA* 3.4 6.6 - - - +
68R LYS* 3.3 20.4 + - - +
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Residues in contact with ILE 65 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A G 5.0 10.5 - - - +
97F PHE* 4.5 16.6 - - + -
31R LEU* 3.6 34.1 - - + +
32R ARG* 3.5 34.5 - - + +
61R LYS* 2.9 27.9 + - + +
62R GLU* 3.1 14.4 - - - +
63R GLN 2.9 0.2 - - - -
64R ARG* 1.3 76.1 - - + +
66R LEU* 1.3 68.5 + - - +
68R LYS* 3.3 13.7 - - + +
69R THR* 3.1 16.5 + - - -
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Residues in contact with LEU 66 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29R PHE* 5.9 0.7 - - + -
31R LEU* 3.8 18.6 - - + -
40R LEU* 5.1 7.6 - - + -
43R PHE* 3.4 50.0 - - + -
50R ILE* 5.8 2.0 - - + -
56R THR* 5.4 1.1 - - + -
58R LEU* 4.6 8.3 - - + -
62R GLU 2.8 15.9 + - - +
63R GLN* 3.1 19.3 + - - +
65R ILE* 1.3 71.5 - - - +
67R ALA* 1.3 57.5 + - - +
69R THR* 2.1 51.6 + - + -
70R ILE* 2.9 28.8 + - + -
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Residues in contact with ALA 67 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720A C 3.8 35.2 - - + +
721A G 6.1 0.2 - - - +
50R ILE* 4.2 16.9 - - - +
63R GLN* 3.1 7.7 + - - +
64R ARG* 3.4 13.9 - - - +
66R LEU* 1.3 76.7 - - - +
68R LYS* 1.3 66.4 + - - +
69R THR 2.8 1.7 + - - -
70R ILE* 3.3 1.5 + - - +
71R LYS* 2.9 34.4 + - - +
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Residues in contact with LYS 68 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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735A C 3.8 28.1 - - - +
736A C 2.7 43.0 + - - +
737A A 5.8 1.0 + - - -
64R ARG 3.3 9.2 + - - +
65R ILE* 3.3 18.8 - - + +
66R LEU 2.9 1.2 + - - -
67R ALA* 1.3 77.3 - - - +
69R THR* 1.3 64.3 + - - +
71R LYS* 3.9 9.9 + - - +
72R ARG* 3.4 28.2 + - - +
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Residues in contact with THR 69 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31R LEU 3.2 27.6 + - - +
32R ARG* 3.4 18.9 + - - +
33R ASP 4.6 1.1 - - - +
34R TYR* 4.1 22.6 - - - +
40R LEU* 4.3 13.7 - - + -
65R ILE 3.1 5.4 + - - -
66R LEU* 2.1 37.8 + - + +
68R LYS* 1.3 67.3 - - - +
70R ILE* 1.3 70.9 + - - +
71R LYS 3.0 0.9 - - - -
72R ARG* 2.6 30.1 + - - +
73R ALA* 3.3 3.3 + - - +
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Residues in contact with ILE 70 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40R LEU* 4.7 8.5 - - + -
43R PHE* 4.7 8.1 - - + +
44R LEU* 4.3 15.9 - - + -
50R ILE* 3.5 42.4 - - + -
66R LEU* 2.9 50.9 + - + -
67R ALA 4.0 0.4 - - - +
69R THR* 1.3 77.0 - - - +
71R LYS* 1.3 64.5 + - - +
73R ALA* 2.9 19.9 + - - +
74R ARG* 3.0 33.3 + - + +
79R LEU* 4.4 15.9 - - + -
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Residues in contact with LYS 71 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A C 4.4 12.6 - - - +
720A C 2.9 34.8 + - - -
721A G 3.8 9.9 + - - -
734A G 3.3 43.2 + - - +
735A C 3.6 24.8 + - - +
50R ILE* 4.6 5.2 - - + -
67R ALA* 2.9 35.2 + - - +
68R LYS 3.9 6.1 - - - +
69R THR 3.0 0.6 - - - -
70R ILE* 1.3 81.3 - - - +
72R ARG* 1.3 60.4 + - - +
74R ARG* 3.2 34.8 - - - +
75R ILE* 3.2 16.1 + - - +
81R PHE* 5.3 0.2 - - - -
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Residues in contact with ARG 72 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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735A C 4.1 14.1 - - - +
736A C 3.0 35.2 + - - -
737A A 3.9 7.5 + - - -
89F MET* 3.5 30.6 - - + +
91F VAL* 3.0 41.4 - - - +
92F LYS 5.0 0.2 + - - -
94F GLN* 4.3 16.5 + - - -
32R ARG* 4.9 9.5 + - - +
34R TYR* 3.9 26.3 - - + -
68R LYS* 3.4 22.4 - - - +
69R THR* 2.6 23.2 + - - +
71R LYS* 1.3 69.9 - - - +
73R ALA* 1.3 58.2 + - - +
75R ILE* 2.7 25.7 + - - +
76R LEU* 3.1 9.9 + - - +
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Residues in contact with ALA 73 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34R TYR 3.9 20.0 + - - +
35R ARG* 5.9 0.2 - - - -
37R VAL* 5.9 0.7 - - + -
40R LEU* 4.4 7.4 - - + -
69R THR 3.3 3.6 + - - +
70R ILE 2.9 9.1 + - - +
72R ARG* 1.3 74.9 - - - +
74R ARG* 1.3 56.4 + - - +
75R ILE 2.6 1.9 + - - -
76R LEU* 2.8 11.8 + - - -
77R GLY 2.5 32.0 + - - -
78R LEU* 3.5 11.9 + - + -
79R LEU* 3.8 28.7 - - + +
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Residues in contact with ARG 74 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718A G 3.1 20.0 + - - -
719A C 2.7 47.3 + - - +
50F TYR* 2.9 20.8 + - - -
44R LEU* 4.8 0.8 - - - +
48R GLY 3.5 12.3 + - - -
50R ILE* 3.5 14.7 - - - +
70R ILE* 3.0 26.4 + - + +
71R LYS* 3.2 25.8 - - - +
73R ALA* 1.3 76.2 - - - +
75R ILE* 1.3 57.4 + - - +
77R GLY* 3.0 7.0 + - - -
79R LEU* 3.3 18.8 - - + +
80R PRO 2.9 27.9 + - - +
81R PHE* 3.3 44.5 - - + +
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Residues in contact with ILE 75 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672A U 4.9 4.7 - - - +
673A G 3.6 32.5 + - - +
734A G 3.6 28.5 - - + +
735A C 4.2 18.2 - - - +
50F TYR* 2.9 8.1 + - - -
87F ARG* 2.6 40.1 + - - -
88F VAL 6.1 0.7 - - - +
89F MET* 3.7 22.9 - - - -
71R LYS 3.6 11.7 - - - +
72R ARG* 2.7 14.5 + - - +
73R ALA 2.6 4.9 + - - -
74R ARG* 1.3 71.1 - - - +
76R LEU* 1.3 51.9 + - - +
77R GLY 3.0 3.6 - - - -
81R PHE* 4.6 4.9 - - + -
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Residues in contact with LEU 76 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F ASN* 3.9 17.0 - - + +
9F VAL* 5.7 0.7 - - + -
50F TYR* 4.0 0.4 - - - -
52F ILE* 3.5 16.8 - - - +
60F PHE* 3.6 25.3 - - + -
87F ARG* 3.7 15.6 + - + +
89F MET* 3.6 38.8 - - + -
34R TYR* 3.9 33.2 - - + +
35R ARG* 5.1 3.6 - - + -
72R ARG 3.1 8.2 + - - +
73R ALA* 2.8 7.8 + - - -
75R ILE* 1.3 73.7 - - + +
77R GLY* 1.3 62.3 + - - +
78R LEU* 3.0 28.3 - - + -
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Residues in contact with GLY 77 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F LEU* 3.1 16.3 - - - +
49F ALA 3.1 20.5 + - - -
50F TYR* 2.9 33.9 - - - -
52F ILE* 4.8 0.2 - - - -
73R ALA 2.5 13.7 + - - -
74R ARG 3.2 4.7 - - - -
75R ILE 3.0 2.2 - - - -
76R LEU* 1.3 74.3 - - - +
78R LEU* 1.3 56.4 + - - +
79R LEU 3.2 4.9 - - - -
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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
------------------------------------------------------------
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) + - + + + + + -
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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