Contacts of the helix formed by residues 42 - 63 (chain A) in PDB entry 2EVT
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 PHE 42 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A PHE* 4.2 19.6 - - + +
37A LEU 4.3 7.9 - - - -
38A GLY* 3.8 16.2 - - - -
39A SER* 3.4 31.9 + - - +
40A PRO 3.3 0.4 - - - -
41A VAL* 1.3 74.8 - - + +
43A THR* 1.3 64.9 + - - +
44A PRO* 3.3 3.1 - - - -
45A ILE* 3.2 21.1 + - + +
46A LYS* 3.3 11.6 + - - +
151A ALA* 3.2 35.0 - - + -
154A ALA* 3.1 35.4 - - + -
155A ALA* 3.7 10.3 - - + -
156A PRO* 4.0 11.4 - - + -
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Residues in contact with THR 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A SER 4.4 1.9 + - - -
40A PRO* 3.4 27.1 + - - +
41A VAL 3.2 0.2 - - - -
42A PHE* 1.3 76.2 - - - +
44A PRO* 1.3 58.4 - - + +
46A LYS* 3.2 15.3 + - + +
47A ALA* 2.8 41.3 + - + +
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Residues in contact with PRO 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PRO 4.1 2.5 - - - +
41A VAL 3.0 19.7 - - - +
42A PHE 3.3 1.6 - - - -
43A THR* 1.3 93.9 - - + +
45A ILE* 1.3 62.2 + - + +
47A ALA* 3.5 5.4 + - + +
48A VAL* 3.2 26.5 + - - +
147A ILE* 3.6 28.3 - - + +
148A PHE* 3.7 31.5 - - + -
151A ALA* 5.1 0.2 - - + -
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Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PHE* 3.7 23.8 - - + -
42A PHE* 3.2 17.9 + - + +
44A PRO* 1.3 72.6 - - + +
46A LYS* 1.3 68.3 + - - +
47A ALA 3.2 0.9 + - - -
48A VAL* 3.2 14.8 + - + +
49A ILE* 3.6 15.1 + - + +
100A GLY* 5.4 1.6 - - - +
103A PHE* 3.8 38.8 - - + -
136A LEU* 5.2 4.5 - - + -
148A PHE* 3.8 26.2 - - + -
151A ALA* 3.7 30.3 - - + -
152A LEU* 4.5 13.2 - - + -
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Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PRO* 3.5 36.7 - - + +
34A PHE* 3.8 36.1 - - + -
35A ASP* 2.6 31.4 + - - +
42A PHE 3.3 8.8 + - - +
43A THR* 3.2 19.0 + - + +
45A ILE* 1.3 78.9 - - - +
47A ALA* 1.3 50.9 + - - +
49A ILE* 3.2 6.8 + - - +
50A SER* 2.8 41.0 + - - -
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A THR* 2.8 29.2 + - + +
44A PRO* 3.9 6.7 - - + +
46A LYS* 1.3 69.7 - - - +
48A VAL* 1.3 62.6 + - - +
49A ILE 3.1 1.6 - - - -
50A SER* 4.1 7.9 - - - +
51A GLY* 2.9 28.2 + - - +
52A ASN* 3.9 2.3 + - - -
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Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PRO 3.2 16.8 + - - +
45A ILE* 3.2 8.7 + - + +
47A ALA* 1.3 77.7 - - - +
49A ILE* 1.3 57.2 + - - +
52A ASN* 2.6 38.4 + - - +
96A TRP* 3.4 31.2 - - + +
97A LEU* 4.0 4.0 - - - -
100A GLY* 4.0 17.9 - - - +
136A LEU* 4.6 15.5 - - + -
140A HIS* 5.7 0.9 - - + +
148A PHE* 3.9 21.3 - - + -
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Residues in contact with ILE 49 (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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27A VAL 4.5 2.2 - - - +
30A LEU* 4.6 2.5 - - + -
31A PRO* 4.0 17.9 - - + -
34A PHE* 4.0 14.1 - - + -
45A ILE* 3.6 14.8 + - + +
46A LYS 3.2 5.9 + - - +
47A ALA 3.1 0.2 - - - -
48A VAL* 1.3 78.3 - - - +
50A SER* 1.3 59.6 + - - +
52A ASN 3.5 0.5 + - - -
53A ILE* 2.9 54.9 + - + +
97A LEU* 3.6 16.0 - - + +
100A GLY* 3.9 28.7 - - - +
101A LEU* 4.3 9.9 - - + +
104A ILE* 3.4 32.3 - - + -
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Residues in contact with SER 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PRO* 4.1 25.0 - - - +
46A LYS* 2.8 30.7 + - - -
47A ALA* 4.2 3.1 - - - -
49A ILE* 1.3 71.7 - - - +
51A GLY* 1.3 66.5 + - - +
53A ILE* 3.3 6.4 + - - +
54A THR* 3.1 27.1 + - - -
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Residues in contact with GLY 51 (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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47A ALA* 2.9 16.3 + - - +
50A SER* 1.3 77.4 - - - +
52A ASN* 1.3 63.9 + - - +
54A THR* 3.4 9.6 + - - -
55A LYS* 3.3 30.7 + - - +
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Residues in contact with ASN 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA 3.9 1.8 + - - -
48A VAL* 2.6 35.7 + - - +
49A ILE 3.5 1.0 + - - +
50A SER 3.3 0.4 - - - -
51A GLY* 1.3 75.9 - - - +
53A ILE* 1.3 64.3 + - - +
55A LYS* 3.3 16.3 + - - +
56A ILE* 3.1 29.1 + - - +
93A ALA* 3.3 36.9 - - - +
96A TRP* 3.4 25.5 - - - +
97A LEU* 3.9 8.2 - - + +
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Residues in contact with ILE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 4.3 23.3 - - + +
27A VAL* 3.6 37.5 - - + +
28A SER* 4.1 11.2 - - - +
31A PRO* 4.5 6.3 - - + -
49A ILE* 2.9 43.5 + - + +
50A SER* 3.3 5.6 + - - +
52A ASN* 1.3 75.1 - - - +
54A THR* 1.3 60.3 + - - +
56A ILE* 3.2 8.5 + - - +
57A LYS* 2.9 36.3 + - + +
97A LEU* 4.0 14.1 - - + +
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Residues in contact with THR 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A SER* 3.1 13.6 + - - -
51A GLY* 3.4 12.4 - - - -
53A ILE* 1.3 80.2 - - - +
55A LYS* 1.3 62.5 + - + +
57A LYS* 3.5 7.0 + - - +
58A ALA* 3.1 23.6 + - + +
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Residues in contact with LYS 55 (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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51A GLY* 3.3 18.4 + - - +
52A ASN* 3.3 24.0 + - - +
54A THR* 1.3 75.6 - - + +
56A ILE* 1.3 64.5 + - - +
58A ALA* 3.4 8.2 + - - +
59A VAL* 3.4 24.5 + - - +
89A GLY 5.4 3.1 - - - +
90A ALA* 5.0 1.1 - - - -
93A ALA* 3.7 15.3 - - + -
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Residues in contact with ILE 56 (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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20A THR* 4.5 2.0 - - + -
23A PHE* 5.3 0.4 - - + -
24A LEU* 3.8 25.6 - - + -
52A ASN 3.1 17.6 + - - +
53A ILE 3.8 3.8 - - - +
55A LYS* 1.3 73.2 - - - +
57A LYS* 1.3 67.5 + - - +
59A VAL* 3.1 4.3 + - - +
60A TYR* 2.9 20.8 + - - +
70A LEU* 5.4 2.9 - - + -
73A ILE* 4.0 27.0 - - + +
90A ALA* 3.9 18.6 - - + +
93A ALA* 3.8 13.7 - - + -
94A LEU* 3.8 25.8 - - + +
97A LEU* 3.6 29.8 - - + -
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Residues in contact with LYS 57 (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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21A GLY* 5.9 1.4 + - - -
24A LEU* 3.8 27.6 - - + +
53A ILE* 2.9 24.4 + - + +
54A THR* 3.8 7.6 - - - +
56A ILE* 1.3 76.3 - - - +
58A ALA* 1.3 57.0 + - - +
60A TYR* 3.8 16.5 - - - +
61A ASP* 2.9 69.2 + - - +
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Residues in contact with ALA 58 (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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54A THR 3.1 13.5 + - - +
55A LYS* 3.5 13.0 - - - +
56A ILE 3.1 0.4 - - - -
57A LYS* 1.3 78.3 - - - +
59A VAL* 1.3 62.9 + - + +
61A ASP* 4.0 5.6 - - - +
62A THR* 3.2 24.1 + - - +
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Residues in contact with VAL 59 (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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55A LYS 3.4 12.1 + - - +
56A ILE 3.1 6.3 + - - +
58A ALA* 1.3 75.7 - - + +
60A TYR* 1.3 63.4 + - - +
62A THR* 2.7 29.2 + - - +
67A PHE* 3.4 36.9 - - + -
73A ILE* 5.2 1.3 - - + -
77A GLU* 3.9 19.1 - - - +
81A TYR* 6.0 1.6 - - - +
89A GLY* 4.8 3.4 - - - -
90A ALA* 3.8 26.2 - - + +
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Residues in contact with TYR 60 (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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20A THR* 3.6 26.5 - - + -
21A GLY* 3.7 25.5 + - - -
22A PRO* 5.4 0.2 - - - +
24A LEU* 4.3 8.1 - - + -
56A ILE* 2.9 16.7 + - + +
57A LYS* 3.8 16.6 - - - +
59A VAL* 1.3 76.8 - - - +
61A ASP* 1.3 77.0 + - - +
63A ASN 3.2 3.8 + - - -
64A PRO* 3.0 62.7 + - + +
67A PHE* 3.3 36.6 - - + -
68A ARG* 4.6 3.4 - - + -
73A ILE* 5.4 1.7 - - + +
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Residues in contact with ASP 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LYS* 2.9 62.4 + - - +
58A ALA* 4.0 6.5 - - - +
59A VAL 3.3 0.2 - - - -
60A TYR* 1.3 83.0 - - - +
62A THR* 1.3 65.4 + - - +
63A ASN 3.3 0.9 + - - -
64A PRO* 3.5 13.6 - - - +
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Residues in contact with THR 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ALA 3.2 18.8 - - - +
59A VAL* 2.7 20.2 + - - +
61A ASP* 1.3 76.9 - - - +
63A ASN* 1.3 64.2 + - - +
64A PRO* 3.9 1.0 - - - +
67A PHE* 3.8 9.5 - - - -
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Residues in contact with ASN 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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59A VAL 3.9 0.2 + - - -
60A TYR 3.2 5.6 + - - -
61A ASP 3.1 0.2 - - - -
62A THR* 1.3 86.5 + - - +
64A PRO* 1.3 68.8 - - - +
65A ALA* 4.0 6.1 + - - +
66A LYS* 3.1 45.9 + - + +
67A PHE* 3.0 32.6 + - + -
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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