Contacts of the helix formed by residues 57 - 74 (chain A) in PDB entry 2B6V
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 ILE 57 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A PHE* 3.4 17.3 - - - -
53A SER* 3.1 8.5 + - - -
56A PHE* 1.3 90.3 - - + +
58A ILE* 1.3 63.4 + - - +
59A TYR* 3.6 24.9 - - + +
60A LEU* 3.2 47.4 - - + +
61A LYS 3.9 0.2 + - - -
115A ILE* 5.3 4.5 - - + -
228A LYS* 5.9 4.9 - - - -
231A SER* 4.2 13.9 - - - +
235A ILE* 6.2 2.0 - - + -
295A TYR* 2.9 46.4 - - + +
302A PHE* 5.6 3.9 - - + -
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Residues in contact with ILE 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PHE* 4.0 20.6 - - + -
54A LYS* 3.4 28.5 - - + +
56A PHE 3.3 16.8 + - - +
57A ILE* 1.3 69.6 - - - +
59A TYR* 1.4 57.3 + - + +
60A LEU 3.1 2.2 - - - -
61A LYS* 2.8 30.2 + - + +
62A ASN* 2.8 23.7 + - - +
135A VAL* 5.2 7.2 - - + -
138A SER* 3.5 41.5 - - - +
139A LYS* 5.2 7.2 - - + +
142A SER* 4.3 13.5 - - - +
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Residues in contact with TYR 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PHE 5.3 4.7 - - - -
57A ILE* 3.3 21.7 - - + -
58A ILE* 1.4 80.0 - - + +
60A LEU* 1.4 64.7 + - - +
62A ASN* 3.3 16.8 + - - +
63A ILE* 3.4 14.2 + - - +
111A PHE* 3.9 23.6 - - + -
114A LEU* 4.0 11.2 - - + -
115A ILE* 3.3 41.3 - - + -
118A ASP* 3.4 30.7 + - + +
138A SER* 4.6 16.4 - - - -
141A LEU* 3.3 43.4 - - + +
142A SER* 4.5 6.1 - - - -
228A LYS* 6.2 0.2 - - - -
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A SER* 4.3 12.6 - - - +
47A PHE* 5.5 1.6 - - + -
57A ILE* 3.2 30.5 - - + +
58A ILE 3.1 0.4 - - - -
59A TYR* 1.4 75.8 - - - +
61A LYS* 1.3 57.5 + - - +
63A ILE* 2.8 62.4 + - + +
64A VAL* 3.4 5.4 + - + +
291A ASP* 4.8 7.4 - - + +
292A PRO* 4.9 4.7 - - + -
295A TYR* 3.7 32.5 - - + -
302A PHE* 3.3 47.1 - - + -
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Residues in contact with LYS 61 (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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43A SER 5.9 0.2 - - - -
44A GLY* 4.9 9.0 + - - -
47A PHE* 3.2 63.5 - - + +
48A PHE* 5.1 4.6 - - - +
57A ILE 3.9 0.2 + - - -
58A ILE* 2.8 29.7 + - + +
60A LEU* 1.3 81.8 - - - +
62A ASN* 1.4 67.7 + - - +
64A VAL* 3.5 10.8 - - - +
65A ILE* 3.4 42.8 + - + +
146A TRP* 6.1 1.3 - - + -
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Residues in contact with ASN 62 (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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58A ILE* 2.8 27.0 + - - +
59A TYR* 3.3 11.0 + - - +
61A LYS* 1.4 81.6 - - - +
63A ILE* 1.4 67.0 + - - +
64A VAL 3.1 1.3 - - - -
65A ILE* 3.7 9.7 - - + +
66A ALA* 3.0 26.9 + - - +
107A VAL* 4.2 6.1 - - + +
111A PHE* 4.5 14.3 - - + -
142A SER* 2.8 29.3 + - - -
145A VAL* 6.3 0.2 - - - -
146A TRP* 2.9 38.1 + - + +
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Residues in contact with ILE 63 (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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40A ASN* 3.1 28.9 - - - +
59A TYR 3.4 9.2 - - - +
60A LEU* 2.8 32.5 + - + +
62A ASN* 1.4 76.9 - - - +
64A VAL* 1.3 62.5 + - + +
66A ALA* 3.7 2.3 - - - +
67A ASP* 2.7 56.2 + - - +
107A VAL* 4.7 0.9 - - - -
111A PHE* 3.1 37.0 - - + -
291A ASP* 3.7 34.5 - - + +
292A PRO* 3.7 7.0 - - + -
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Residues in contact with VAL 64 (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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40A ASN* 2.8 28.4 - - - +
41A GLY* 4.7 2.7 - - - -
43A SER* 3.0 36.1 - - - +
44A GLY* 3.6 20.2 - - - +
60A LEU* 3.4 10.5 + - + +
61A LYS* 3.5 11.4 - - - +
62A ASN 3.1 0.2 - - - -
63A ILE* 1.3 87.7 - - + +
65A ILE* 1.3 66.0 + - + +
67A ASP 3.3 0.3 + - - -
68A PHE* 2.8 36.7 + - + +
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Residues in contact with ILE 65 (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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61A LYS* 3.4 41.3 + - + +
62A ASN* 3.3 13.4 + - + +
63A ILE 3.3 0.4 - - - -
64A VAL* 1.3 81.2 - - + +
66A ALA* 1.3 60.9 + - - +
68A PHE* 3.2 7.3 + - - +
69A VAL* 2.9 39.9 + - + +
146A TRP* 5.8 6.3 - - + +
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Residues in contact with ALA 66 (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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62A ASN 3.0 15.1 + - - +
63A ILE 3.8 0.9 - - - +
65A ILE* 1.3 83.5 - - - +
67A ASP* 1.3 53.8 + - - +
69A VAL* 2.9 11.2 + - - +
70A MET 2.8 14.4 + - - -
103A VAL* 5.3 3.8 - - + -
104A ASN* 2.7 37.5 - - - +
107A VAL* 3.6 25.6 - - + -
149A MET* 5.1 4.7 - - - -
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Residues in contact with ASP 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASN* 3.4 13.4 + - - +
63A ILE* 2.7 45.0 + - - +
66A ALA* 1.3 69.8 - - - +
68A PHE* 1.3 59.7 + - - +
70A MET* 3.1 9.5 - - - +
71A SER* 3.0 22.7 + - - -
104A ASN* 2.8 22.7 + - - +
107A VAL* 4.9 3.0 - - - +
108A SER* 5.4 1.2 + - - -
287A ASN* 3.1 20.1 + - - +
288A VAL* 3.3 39.3 - - - +
291A ASP* 4.6 3.8 - - - +
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Residues in contact with PHE 68 (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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36A GLY 5.5 0.4 - - - -
37A ILE* 4.0 33.7 - - + -
40A ASN* 4.6 6.4 - - + +
41A GLY* 5.4 12.1 - - - -
64A VAL* 2.8 23.1 + - + +
65A ILE* 3.4 7.0 - - - +
67A ASP* 1.3 77.9 - - - +
69A VAL* 1.4 58.8 + - + +
71A SER* 2.8 29.9 + - - -
72A LEU* 3.1 45.1 + - + +
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Residues in contact with VAL 69 (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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65A ILE* 2.9 26.2 + - + +
66A ALA* 2.9 15.1 + - - +
68A PHE* 1.4 76.7 - - + +
70A MET* 1.3 63.5 + - - +
72A LEU* 4.6 5.4 - - + +
73A THR* 2.7 33.9 + - - +
74A PHE 3.7 1.2 + - - -
100A LEU* 3.5 32.8 - - + +
103A VAL* 4.8 6.7 - - + -
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Residues in contact with MET 70 (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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66A ALA 2.8 6.1 + - - -
67A ASP* 3.1 23.8 - - - +
69A VAL* 1.3 74.7 - - - +
71A SER* 1.4 62.8 + - - +
74A PHE* 2.9 59.4 + - + -
75A PRO* 2.9 13.2 - - + +
100A LEU* 3.8 3.4 - - - +
101A PHE* 4.5 6.7 - - + +
104A ASN* 3.1 36.7 + - + +
285A ALA* 3.3 31.9 - - - +
287A ASN* 3.2 22.7 - - - +
288A VAL* 3.5 16.4 - - + +
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Residues in contact with SER 71 (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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32A VAL* 5.4 0.7 - - - -
33A PHE* 3.5 13.2 - - - +
36A GLY* 5.0 0.4 - - - -
37A ILE* 3.2 39.3 - - - +
67A ASP 3.0 10.5 + - - -
68A PHE* 2.8 26.7 + - - -
70A MET* 1.4 78.8 - - - +
72A LEU* 1.4 63.7 + - - +
75A PRO* 3.5 22.9 - - - +
76A PHE* 3.4 13.7 - - - -
288A VAL* 4.5 7.4 - - - -
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Residues in contact with LEU 72 (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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33A PHE* 5.2 2.5 - - + -
37A ILE* 4.7 4.0 - - + -
68A PHE* 3.1 44.9 + - + +
69A VAL* 4.1 5.4 - - + +
71A SER* 1.4 91.1 + - - +
73A THR* 1.3 71.1 + - + +
75A PRO 2.6 20.8 - - - +
76A PHE* 3.1 34.9 - - + -
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Residues in contact with THR 73 (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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69A VAL* 2.7 26.2 + - - +
72A LEU* 1.3 86.4 - - + +
74A PHE* 1.4 60.8 + - - +
76A PHE* 6.0 1.6 - - + -
77A LYS* 3.3 27.2 - - - +
96A VAL* 3.3 21.6 - - + +
100A LEU* 3.2 24.9 - - - +
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Residues in contact with PHE 74 (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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29A TYR* 3.5 18.8 - + - -
69A VAL 3.7 2.0 + - - -
70A MET* 2.9 27.4 + - + +
73A THR* 1.4 73.2 + - - +
75A PRO* 1.4 83.1 - - + +
77A LYS* 3.4 9.9 - - - +
78A ILE* 3.2 37.9 + - + -
96A VAL 3.4 7.6 + - - +
97A SER* 3.2 33.8 + - - +
100A LEU* 3.7 6.0 - - + +
101A PHE* 3.4 40.4 - + - +
171A LYS* 3.0 29.2 - - - -
285A ALA* 3.7 5.4 - - + -
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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