Contacts of the helix formed by residues 44 - 64 (chain A) in PDB entry 3H90
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 VAL 44 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU 5.5 0.7 - - - +
41A ALA* 3.1 13.0 + - - +
43A LEU* 1.3 97.4 - - + +
45A ASP* 1.3 55.2 + - - +
46A SER 3.1 1.3 - - - -
47A LEU* 3.4 14.4 - - + -
48A VAL* 2.7 44.0 + - + +
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Residues in contact with ASP 45 (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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4A ZN 2.8 32.8 - - - -
41A ALA 3.7 3.9 + - - +
42A ALA* 4.4 17.6 - - + +
44A VAL* 1.3 78.6 - - - +
46A SER* 1.3 56.7 + - - +
48A VAL* 3.5 10.6 - - - +
49A ASP* 3.0 26.3 + - - +
153A HIS* 3.8 8.8 - - - -
157A ASP* 3.9 6.9 - - - +
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Residues in contact with SER 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 3.2 31.9 - - - +
27A LYS* 4.2 21.0 + - - +
28A ILE* 3.7 19.5 + - - +
42A ALA 3.6 17.7 + - - -
43A LEU* 3.7 9.1 + - - -
44A VAL 3.1 1.4 - - - +
45A ASP* 1.3 76.7 - - - +
47A LEU* 1.3 61.1 + - - +
49A ASP* 3.8 12.1 - - - -
50A ILE* 3.6 13.0 + - - +
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Residues in contact with LEU 47 (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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28A ILE* 4.1 20.9 - - + -
43A LEU* 3.4 20.9 + - + +
44A VAL* 2.9 19.0 + - + +
46A SER* 1.3 76.7 - - - +
48A VAL* 1.3 66.6 + - - +
49A ASP 3.3 0.2 - - - -
50A ILE* 3.5 15.5 + - + +
51A GLY* 3.5 14.2 + - - -
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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
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44A VAL* 2.7 32.4 + - + +
45A ASP* 3.5 11.7 - - - +
47A LEU* 1.3 73.0 - - - +
49A ASP* 1.3 61.0 + - - +
51A GLY* 3.1 3.7 + - - -
52A ALA* 2.8 36.8 + - + +
153A HIS* 6.4 0.9 - - + -
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Residues in contact with ASP 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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4A ZN 2.6 24.6 - - - -
24A LEU* 3.7 27.6 - - + +
45A ASP* 3.0 19.4 + - - +
46A SER* 3.8 5.9 - - - +
47A LEU 3.3 0.2 - - - -
48A VAL* 1.3 78.2 - - - +
50A ILE* 1.3 62.9 + - - +
52A ALA* 4.5 4.5 - - - +
53A SER* 2.6 32.3 + - - -
153A HIS* 2.8 26.0 + - - -
154A TYR* 3.3 18.5 - - - +
157A ASP* 3.1 7.1 - - - +
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Residues in contact with ILE 50 (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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22A LEU* 4.3 3.1 - - + +
24A LEU* 3.7 19.1 - - + -
25A LEU* 3.8 41.5 - - + -
28A ILE* 3.7 38.1 - - + -
46A SER 3.6 8.9 + - - +
47A LEU* 3.5 18.3 + - + +
48A VAL 3.3 0.4 - - - -
49A ASP* 1.3 76.4 - - - +
51A GLY* 1.3 59.7 + - - +
54A LEU* 2.8 45.4 + - + +
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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 LEU 3.5 5.8 + - - -
48A VAL* 3.1 5.6 + - - -
50A ILE* 1.3 77.4 - - - +
52A ALA* 1.3 65.6 + - - +
54A LEU* 3.0 8.9 + - - +
55A THR* 2.8 29.0 + - - -
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Residues in contact with ALA 52 (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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48A VAL* 2.8 30.3 + - + +
49A ASP* 4.0 4.7 - - - +
51A GLY* 1.3 70.4 - - - +
53A SER* 1.3 59.8 + - - +
55A THR* 3.1 9.5 - - - -
56A ASN* 2.9 23.8 + - - +
86A GLN* 5.6 7.0 - - + +
150A ASP* 6.0 0.2 - - - +
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Residues in contact with SER 53 (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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18A ALA* 4.1 3.5 - - - +
21A SER* 2.7 22.7 + - - -
22A LEU* 3.7 10.4 - - - +
49A ASP* 2.6 22.3 + - - -
52A ALA* 1.3 71.9 - - - +
54A LEU* 1.3 60.1 + - - +
56A ASN* 3.6 9.8 + - - +
57A LEU* 3.1 19.9 + - - +
86A GLN* 5.6 0.4 - - - -
150A ASP* 3.3 26.8 + - - +
153A HIS* 5.9 0.9 - - - -
154A TYR* 2.8 17.3 + - - -
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Residues in contact with LEU 54 (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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22A LEU* 3.7 28.0 - - + +
50A ILE* 2.8 33.6 + - + +
51A GLY* 3.4 6.5 - - - +
53A SER* 1.3 75.0 - - - +
55A THR* 1.3 65.5 + - - +
57A LEU* 3.1 24.9 + - + +
58A LEU* 3.1 25.4 + - + +
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Residues in contact with THR 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 2.8 17.3 + - - -
52A ALA* 3.1 10.8 + - - -
54A LEU* 1.3 74.4 - - - +
56A ASN* 1.3 63.9 - - - +
58A LEU* 2.9 21.1 + - + +
59A VAL* 2.9 36.3 + - + +
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Residues in contact with ASN 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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18A ALA* 5.2 5.0 - - - +
52A ALA 2.9 13.7 + - - +
53A SER* 3.6 13.9 + - - +
54A LEU 3.2 0.4 - - - -
55A THR* 1.3 76.4 - - - +
57A LEU* 1.3 55.8 + - - +
59A VAL* 3.3 5.4 + - - -
60A VAL* 3.0 48.2 + - - +
82A ALA* 3.9 16.0 - - - +
86A GLN* 3.4 22.1 + - - +
146A ALA* 3.9 9.3 + - - +
147A VAL* 5.0 2.4 - - - +
150A ASP* 3.2 36.6 + - - +
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Residues in contact with LEU 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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15A ALA* 4.4 2.7 - - + +
18A ALA* 3.5 35.4 - - + +
19A MET* 4.2 17.0 - - + -
22A LEU* 3.8 26.0 - - + -
53A SER 3.1 12.2 + - - +
54A LEU* 3.1 20.9 + - + +
56A ASN* 1.3 74.8 - - - +
58A LEU* 1.3 66.1 + - + +
60A VAL* 3.3 8.2 - - + +
61A ARG* 3.0 58.7 + - - +
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Residues in contact with LEU 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 LEU* 3.1 29.6 + - + +
55A THR* 2.9 19.3 + - + +
57A LEU* 1.3 81.6 - - + +
59A VAL* 1.3 58.3 + - + +
61A ARG* 3.2 14.0 + - - +
62A TYR* 2.9 26.7 + - - +
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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 THR* 2.9 33.3 + - + +
56A ASN* 3.3 8.0 + - - +
58A LEU* 1.3 77.1 - - + +
60A VAL* 1.3 57.6 + - + +
62A TYR* 3.2 10.0 + - + +
63A SER* 2.8 24.8 + - - -
78A ALA* 3.7 21.1 - - + +
79A GLU* 5.3 0.4 - - - -
81A LEU* 5.9 0.7 - - + -
82A ALA* 3.6 31.2 - - + +
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Residues in contact with VAL 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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14A ILE* 3.7 29.6 - - + +
15A ALA* 4.5 7.4 - - + -
18A ALA* 4.5 13.7 - - + -
56A ASN* 3.0 32.5 + - - +
57A LEU* 3.3 17.5 - - + +
59A VAL* 1.3 75.6 - - + +
61A ARG* 1.3 61.4 + - + +
63A SER* 2.8 26.6 + - - -
64A LEU* 2.8 24.4 + - + +
79A GLU* 5.1 0.7 - - + +
146A ALA* 4.0 19.7 - - + -
147A VAL* 5.3 4.3 - - + -
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Residues in contact with ARG 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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15A ALA* 5.2 8.3 - - - +
19A MET* 3.4 29.3 - - - +
57A LEU* 3.0 42.9 + - + +
58A LEU* 3.2 14.3 + - - +
60A VAL* 1.3 79.7 - - + +
62A TYR* 1.3 60.6 + - - +
64A LEU* 3.6 14.2 + - - +
65A GLN* 3.7 13.3 + - - +
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Residues in contact with TYR 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 LEU 2.9 13.3 + - - +
59A VAL* 3.3 11.7 - - + +
61A ARG* 1.3 75.0 - - - +
63A SER* 1.3 65.8 + - - +
64A LEU 3.1 1.0 + - - -
65A GLN* 3.1 52.0 + - - +
71A HIS* 3.0 34.3 + - - -
75A HIS* 3.2 33.8 - + + +
78A ALA* 4.0 13.9 - - + -
292A ZN 3.7 0.3 - - - -
203C GLN* 4.7 0.9 + - - -
206C LEU* 4.2 23.1 - - + +
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Residues in contact with SER 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 2.8 16.8 + - - -
60A VAL* 2.8 21.4 + - - -
62A TYR* 1.3 72.2 - - - +
64A LEU* 1.3 62.9 + - - +
65A GLN 3.5 2.4 + - - +
75A HIS* 3.6 28.3 + - - +
76A GLY* 3.7 10.2 + - - -
78A ALA* 3.8 13.2 - - - -
79A GLU* 3.3 31.7 + - - +
241A PRO* 5.4 0.7 - - - +
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Residues in contact with LEU 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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11A ARG* 4.7 26.7 - - + +
12A ALA* 5.7 1.8 - - - +
14A ILE* 4.0 27.1 - - + -
15A ALA* 5.1 9.4 - - + -
60A VAL* 2.8 35.3 + - + +
61A ARG* 4.1 9.9 - - - +
62A TYR 3.1 1.0 + - - -
63A SER* 1.3 83.2 - - - +
65A GLN* 1.3 66.4 + - - +
66A PRO* 3.6 4.7 - - - +
79A GLU* 5.1 3.1 - - - +
241A PRO* 5.3 8.7 - - + -
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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