Contacts of the helix formed by residues 41 - 66 (chain A) in PDB entry 1DLB
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 TRP 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A ILE* 5.0 8.1 - - + -
32A GLN* 3.5 52.9 - - + +
38A ARG* 3.2 35.9 - - + +
39A GLY* 3.3 21.9 + - - +
40A GLY* 1.3 76.8 - - - +
42A MET* 1.3 65.5 + - - +
43A GLU 3.3 2.2 - - - -
44A TRP* 3.0 50.2 + + + -
45A ASP* 2.8 32.4 + - - +
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Residues in contact with MET 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLY 4.8 1.7 + - - +
40A GLY* 3.3 4.8 - - - -
41A TRP* 1.3 77.1 - - - +
43A GLU* 1.3 67.9 + - - +
45A ASP* 3.3 8.1 + - - +
46A ARG* 3.1 23.4 + - + +
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Residues in contact with GLU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLY 4.9 2.8 + - - +
41A TRP 3.3 0.8 - - - -
42A MET* 1.3 78.7 - - + +
44A TRP* 1.3 67.2 + - - +
46A ARG* 2.8 49.5 + - - +
47A GLU* 2.9 36.9 + - + +
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Residues in contact with TRP 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 4.5 7.2 - - + -
28A ILE* 3.6 41.7 - - + -
29A LYS* 3.9 19.1 - - + -
32A GLN* 3.7 15.7 - - - -
40A GLY 5.4 0.8 + - - +
41A TRP* 3.0 45.3 + + + +
43A GLU* 1.3 80.2 - - - +
45A ASP* 1.3 79.2 + - - +
47A GLU* 3.3 7.2 + - + +
48A ILE* 2.9 61.2 + - + +
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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
----------------------------------------------------------
29A LYS* 3.6 21.0 - - - +
32A GLN* 4.6 8.2 + - - -
41A TRP* 2.8 26.2 + - - +
42A MET* 3.5 10.4 + - - +
44A TRP* 1.3 91.7 - - - +
46A ARG* 1.3 57.6 + - - +
48A ILE* 3.4 3.8 + - - +
49A ASN* 2.9 44.5 + - - +
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Residues in contact with ARG 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A MET* 3.1 14.9 + - + +
43A GLU* 2.8 47.1 + - - +
45A ASP* 1.3 77.2 - - - +
47A GLU* 1.3 72.0 + - - +
49A ASN* 3.3 6.4 + - - +
50A ASN* 2.8 69.8 + - - +
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Residues in contact with GLU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLU* 2.9 39.9 + - + +
44A TRP* 3.6 7.9 - - + +
46A ARG* 1.3 88.1 + - - +
48A ILE* 1.3 66.5 + - + +
50A ASN* 3.8 7.0 + - - +
51A TYR* 3.0 53.3 + - + -
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Residues in contact with ILE 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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25A VAL* 3.8 39.3 - - + -
29A LYS* 4.5 6.3 - - - +
44A TRP* 2.9 60.4 + - + +
45A ASP* 3.7 6.3 - - - +
47A GLU* 1.3 75.5 - - + +
49A ASN* 1.3 61.9 - - - +
51A TYR* 3.8 2.4 - - - +
52A THR* 2.7 46.5 + - - +
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Residues in contact with ASN 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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29A LYS* 4.4 10.7 + - - +
45A ASP* 2.9 28.6 + - - +
46A ARG* 3.6 6.9 - - - +
48A ILE* 1.3 84.1 - - - +
50A ASN* 1.3 59.0 + - - +
52A THR* 3.8 5.1 - - - -
53A SER* 3.0 35.2 + - - +
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Residues in contact with ASN 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ARG* 2.8 58.7 + - - +
47A GLU* 3.8 9.6 + - - +
49A ASN* 1.3 76.0 - - - +
51A TYR* 1.3 62.9 + - + +
53A SER* 3.5 5.1 + - - -
54A LEU* 3.0 28.0 + - - +
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Residues in contact with TYR 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 GLU* 3.0 52.1 + - + +
48A ILE* 4.2 2.9 - - - +
50A ASN* 1.3 77.4 - - + +
52A THR* 1.3 61.0 + - - +
54A LEU* 3.4 27.2 - - + +
55A ILE* 2.8 45.7 + - + +
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Residues in contact with THR 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLN* 4.2 7.4 + - - +
22A GLN* 3.7 15.2 - - + +
25A VAL* 5.7 2.3 - - - +
48A ILE* 2.7 36.4 + - - +
49A ASN* 3.8 6.5 - - - -
51A TYR* 1.3 76.8 - - - +
53A SER* 1.3 57.5 + - - +
55A ILE* 3.2 6.9 + - - +
56A HIS* 2.9 60.6 + - + +
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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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49A ASN* 3.0 19.1 + - - +
50A ASN* 3.7 5.4 - - - -
52A THR* 1.3 76.8 - - - +
54A LEU* 1.3 62.1 + - - +
56A HIS* 3.4 10.6 + - - +
57A SER* 3.0 23.7 + - - -
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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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50A ASN 3.0 18.6 + - - +
51A TYR* 3.4 33.7 - - + +
52A THR 3.2 0.2 - - - -
53A SER* 1.3 74.5 - - - +
55A ILE* 1.3 68.3 + - + +
57A SER* 2.8 27.6 + - - +
58A LEU* 3.0 30.3 + - + +
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Residues in contact with ILE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 5.7 3.6 - - + -
18A GLN* 3.3 42.2 - - + +
21A LEU* 4.6 11.7 - - + -
51A TYR* 2.8 34.2 + - + +
52A THR* 3.7 4.0 - - - +
54A LEU* 1.3 76.6 - - + +
56A HIS* 1.3 63.4 + - - +
58A LEU* 3.2 12.5 + - + +
59A ILE* 2.9 39.8 + - + +
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Residues in contact with HIS 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLN* 4.0 18.2 + - + +
22A GLN* 2.7 34.8 + - - -
52A THR* 2.9 32.5 + - + +
53A SER* 3.5 8.9 - - - +
54A LEU 3.2 0.2 - - - -
55A ILE* 1.3 77.0 - - - +
57A SER* 1.3 57.8 + - - +
59A ILE* 3.4 8.1 + - + +
60A GLU* 3.0 45.3 + - + +
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Residues in contact with SER 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A SER 3.0 11.9 + - - -
54A LEU* 2.8 27.4 + - - +
56A HIS* 1.3 72.8 - - - +
58A LEU* 1.3 61.6 + - - +
60A GLU* 4.0 9.3 + - - +
61A GLU* 3.0 30.3 + - - +
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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* 3.0 40.7 + - + +
55A ILE* 3.7 11.4 - - + +
57A SER* 1.3 79.2 + - - +
59A ILE* 1.3 59.9 + - + +
61A GLU* 3.3 19.0 + - - +
62A SER* 2.9 33.3 + - - +
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Residues in contact with ILE 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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11A LEU* 4.5 4.7 - - + -
14A ILE* 4.5 14.8 - - + -
15A GLU* 3.8 39.7 - - + +
18A GLN* 4.1 21.5 - - + -
55A ILE* 2.9 39.7 + - + +
56A HIS* 3.7 9.9 - - + +
58A LEU* 1.3 74.5 - - + +
60A GLU* 1.3 62.6 + - + +
61A GLU 3.0 1.3 - - - -
62A SER* 3.0 8.0 + - - -
63A GLN* 2.8 40.5 + - + +
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Residues in contact with GLU 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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56A HIS* 3.0 33.8 + - - +
57A SER* 4.1 7.1 + - - +
59A ILE* 1.3 77.0 - - + +
61A GLU* 1.3 62.3 + - - +
63A GLN* 3.5 21.9 + - - +
64A ASN* 3.1 21.3 + - - +
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Residues in contact with GLU 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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57A SER 3.0 19.7 + - - +
58A LEU* 3.3 23.5 - - - +
60A GLU* 1.3 75.7 - - - +
62A SER* 1.3 65.9 + - - +
64A ASN* 2.9 18.2 + - + +
65A LEU* 2.9 37.6 + - + +
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Residues in contact with SER 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.4 31.7 - - - +
58A LEU* 2.9 18.0 + - - +
59A ILE* 3.0 3.5 + - - -
61A GLU* 1.3 76.1 - - - +
63A GLN* 1.3 58.0 + - - +
65A LEU* 2.9 30.2 + - - +
66A GLN* 3.0 16.5 + - - +
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Residues in contact with GLN 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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11A LEU* 4.1 2.0 - - + -
15A GLU* 2.7 30.7 + - - +
59A ILE* 2.8 26.0 + - + +
60A GLU* 3.5 25.0 - - - +
62A SER* 1.3 76.5 - - - +
64A ASN* 1.3 60.7 + - - +
66A GLN* 3.0 35.5 + - - +
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Residues in contact with ASN 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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60A GLU 3.1 12.1 + - - +
61A GLU* 2.9 13.2 + - - +
63A GLN* 1.3 76.5 - - - +
65A LEU* 1.3 64.7 + - - +
66A GLN 3.3 2.0 + - - -
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Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLU* 2.9 39.0 + - + +
62A SER* 2.9 18.0 + - - +
64A ASN* 1.3 83.6 - - - +
66A GLN* 1.3 65.8 + - - +
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Residues in contact with GLN 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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4A VAL* 5.5 5.9 - - - +
8A ASN* 3.6 41.4 + - - +
11A LEU* 3.1 23.8 - - + +
12A ARG* 6.0 1.0 - - - +
15A GLU* 5.0 1.2 + - - -
62A SER 3.0 11.4 + - - +
63A GLN* 3.0 38.6 + - - +
64A ASN 3.3 3.8 - - - -
65A LEU* 1.3 83.3 - - - +
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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