Contacts of the helix formed by residues 4 - 25 (chain D) in PDB entry 4LLL
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 THR 4 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C PHE* 5.7 2.7 - - + +
112C GLU* 3.1 39.5 - - + +
3D PHE* 1.3 82.1 - - - +
5D TYR* 1.3 65.4 + - - +
6D SER* 3.5 17.7 - - - +
7D TYR* 2.9 26.0 + - - +
8D LEU* 3.0 12.3 + - - +
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Residues in contact with TYR 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C MET* 4.9 0.4 - - - -
112C GLU* 2.9 18.5 + - - +
115C LEU* 3.6 35.4 - - + -
116C VAL* 4.2 24.5 - - + -
119C LEU* 4.2 5.1 - - + +
124C ASN* 3.3 37.0 + - + +
127C MET* 4.5 6.1 - - + +
128C LYS* 4.4 22.2 - - + -
131C LEU* 4.9 9.0 - - + -
3D PHE 4.1 9.2 - - - -
4D THR* 1.3 73.2 - - - +
6D SER* 1.3 64.4 + - - +
8D LEU* 4.5 9.0 - - + +
9D PHE* 3.1 38.1 + + + +
134D MET* 3.8 27.4 - - + -
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Residues in contact with SER 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C MET* 4.0 27.6 - - - +
35C HIS* 3.2 19.4 + - - -
108C PHE* 6.1 3.8 - - - -
111C MET* 5.1 5.9 - - - +
112C GLU* 3.6 3.4 + - - -
4D THR* 3.0 16.5 - - - +
5D TYR* 1.3 79.9 - - - +
7D TYR* 1.3 56.6 + - - +
9D PHE* 4.1 1.2 - - - +
10D ARG* 2.7 58.1 + - - +
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Residues in contact with TYR 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ALA 4.9 7.3 + - - -
58C GLN* 5.4 5.4 + - - +
135C LEU* 5.1 5.9 - - + +
3D PHE* 3.7 47.2 - + + -
4D THR* 2.9 19.4 + - - +
6D SER* 1.3 78.7 - - - +
8D LEU* 1.3 77.0 + - + +
10D ARG* 3.5 19.9 + - - +
11D MET* 3.0 65.5 + - + +
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Residues in contact with LEU 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C LYS* 4.4 17.7 - - + +
131C LEU* 4.1 27.8 - - + +
132C THR* 3.9 36.3 - - + +
135C LEU* 4.2 14.8 - - + -
3D PHE* 3.8 40.8 - - + +
4D THR 3.0 11.1 + - - +
5D TYR* 4.2 8.5 - - + +
7D TYR* 1.3 87.3 - - + +
9D PHE* 1.3 62.2 + - - +
11D MET* 3.4 1.4 + - - +
12D ILE* 3.0 30.3 + - - +
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Residues in contact with PHE 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C PHE* 4.0 31.0 - + - +
12C ILE* 3.4 40.8 - - + -
13C SER* 3.2 20.2 + - - +
16C MET* 3.9 13.9 - - - -
115C LEU* 4.3 17.5 - - + -
127C MET* 4.2 15.9 - - + -
131C LEU* 3.5 29.2 - - + -
5D TYR* 3.1 25.3 + + + +
6D SER 4.1 1.3 - - - +
8D LEU* 1.3 76.4 - - - +
10D ARG* 1.3 65.2 + - - +
12D ILE* 3.9 4.0 - - + +
13D SER* 3.0 21.8 + - - -
131D LEU* 5.1 0.7 - - + -
134D MET* 4.3 11.9 - - + -
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Residues in contact with ARG 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C SER* 3.9 7.8 + - - -
31C ASN* 4.8 9.2 - - - +
32C GLU* 5.6 5.8 - - - -
35C HIS* 3.1 40.5 + - - +
57C LEU* 5.9 4.4 - - - +
59C ARG* 4.0 18.7 + - - +
6D SER* 2.7 50.3 + - - +
7D TYR* 3.9 28.7 - - - +
9D PHE* 1.3 78.3 - - - +
11D MET* 1.3 72.9 + - - +
13D SER* 4.5 1.1 - - - -
14D HIS* 3.4 22.9 + - - +
14F T 6.1 0.4 - - - -
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Residues in contact with MET 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ALA 4.3 0.4 - - - +
57C LEU* 3.2 36.1 - - + +
58C GLN* 3.5 28.5 - - + -
59C ARG* 4.1 7.9 - - - +
135C LEU* 3.5 25.1 - - + +
7D TYR* 3.0 59.9 + - + +
10D ARG* 1.3 93.1 - - - +
12D ILE* 1.3 61.3 + - - +
14D HIS* 4.2 2.4 - - - +
15D GLU* 3.3 33.1 + - + +
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Residues in contact with ILE 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C PHE* 3.5 40.8 - - + -
131C LEU* 3.9 42.8 - - + +
134C MET* 5.0 2.5 - - + -
135C LEU* 3.7 26.2 - - + +
138C LEU* 4.1 15.4 - - + +
8D LEU* 3.0 28.3 + - + +
9D PHE* 3.9 4.7 - - + +
11D MET* 1.3 77.1 - - - +
13D SER* 1.3 68.8 + - - +
15D GLU* 3.1 4.5 + - - +
16D MET* 2.9 26.0 + - + +
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Residues in contact with SER 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C PHE* 4.0 13.9 - - - +
10C ARG* 4.9 8.7 - - - +
13C SER* 3.4 32.5 - - - -
9D PHE 3.0 7.2 + - - -
10D ARG* 4.5 2.2 - - - -
12D ILE* 1.3 80.7 - - - +
14D HIS* 1.3 57.0 + - - +
16D MET* 3.1 12.9 + - - +
17D LYS* 2.9 29.0 + - - +
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Residues in contact with HIS 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLN* 3.6 9.0 + - + -
59C ARG* 3.5 34.3 + - - +
10D ARG 3.4 18.4 + - - +
11D MET* 4.2 3.6 - - - +
12D ILE 3.2 0.2 - - - -
13D SER* 1.3 80.1 - - - +
15D GLU* 1.3 75.5 + - + +
17D LYS* 3.1 9.2 + - - +
18D GLN* 2.8 48.4 + - + +
14F T 3.1 19.9 - - - -
15F C 2.7 30.0 + - - -
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Residues in contact with GLU 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLN* 4.0 23.7 + - + +
135C LEU* 5.4 7.2 - - + -
138C LEU* 3.6 25.2 - - + +
139C GLN 4.3 11.6 - - - +
11D MET* 3.3 19.4 + - + +
12D ILE 3.1 4.1 + - - +
14D HIS* 1.3 96.3 - - + +
16D MET* 1.3 57.3 + - - +
18D GLN* 4.2 9.3 - - - +
19D LYS* 3.0 60.0 + - - +
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Residues in contact with MET 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C SER* 3.5 37.0 - - - +
9C PHE* 3.9 29.4 - - + -
10C ARG* 5.2 4.5 - - + +
138C LEU* 3.5 28.3 - - + -
12D ILE* 2.9 12.7 + - - +
13D SER* 3.5 9.4 - - - +
15D GLU* 1.3 75.6 - - - +
17D LYS* 1.3 58.9 + - - +
19D LYS* 3.9 3.3 - - - -
20D ALA* 2.8 33.5 + - - +
31D ASN* 4.8 0.4 - - - -
111D MET* 4.0 20.5 - - + +
115D LEU* 3.9 26.0 - - - -
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Residues in contact with LYS 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D SER 2.9 12.9 + - - +
14D HIS* 3.3 13.5 - - - +
16D MET* 1.3 75.3 - - - +
18D GLN* 1.3 64.7 + - - +
20D ALA* 3.3 0.9 + - - +
21D ASP* 2.8 39.8 + - - +
31D ASN* 3.3 23.5 - - - +
32D GLU* 5.0 6.5 - - - +
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Residues in contact with GLN 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D HIS* 2.8 45.9 + - + +
15D GLU* 3.7 17.3 - - - +
17D LYS* 1.3 80.1 - - - +
19D LYS* 1.3 64.8 + - + +
21D ASP* 3.3 15.5 + - - +
22D GLN* 3.0 37.8 + - - +
15F C 3.3 46.0 - - - +
16F T 4.2 5.0 + - - -
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Residues in contact with LYS 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C LEU* 2.8 38.8 + - + +
139C GLN* 3.0 23.3 - - - +
15D GLU* 3.0 31.9 + - - +
16D MET* 4.0 3.4 - - - +
18D GLN* 1.3 73.0 - - + +
20D ALA* 1.3 68.0 + - - +
22D GLN* 3.4 21.5 + - - +
23D LYS* 3.1 39.7 + - - +
111D MET* 4.3 12.3 - - + -
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Residues in contact with ALA 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D MET 2.8 19.8 + - - +
17D LYS 3.6 3.6 - - - +
19D LYS* 1.3 75.0 - - - +
21D ASP* 1.3 51.3 + - - +
23D LYS* 3.0 7.9 + - - +
24D LEU* 2.5 45.5 + - + +
31D ASN* 3.8 24.0 - - + +
107D ILE* 4.8 3.6 - - + -
108D PHE* 4.2 5.4 - - + -
111D MET* 4.0 22.0 - - + -
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Residues in contact with ASP 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D LYS* 2.8 28.9 + - - +
18D GLN* 3.7 16.9 + - - +
20D ALA* 1.3 71.3 - - - +
22D GLN* 1.3 59.9 + - + +
24D LEU* 3.4 6.5 - - - -
25D GLU* 2.7 31.0 + - - +
29D ILE 4.9 2.2 - - - +
30D THR* 4.0 10.7 - - - +
31D ASN* 3.1 34.5 + - - +
32D GLU* 5.1 2.3 - - - +
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Residues in contact with GLN 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D GLN* 3.0 30.9 + - - +
19D LYS* 3.8 25.2 - - - +
20D ALA 3.2 0.2 - - - -
21D ASP* 1.3 76.7 - - + +
23D LYS* 1.3 64.5 + - + +
25D GLU* 3.1 28.8 - - - +
26D GLN 4.7 0.2 + - - -
16F T 4.7 15.3 + - - +
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Residues in contact with LYS 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LYS* 3.1 27.5 + - + +
20D ALA* 3.0 7.1 + - - +
22D GLN* 1.3 80.7 - - + +
24D LEU* 1.3 61.1 + - - +
25D GLU 3.1 1.5 + - - -
26D GLN* 3.7 20.8 + - - +
107D ILE* 3.5 42.8 - - + +
111D MET* 5.4 7.2 - - + -
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Residues in contact with LEU 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ALA* 2.5 22.9 + - + +
21D ASP* 3.6 6.3 - - - +
23D LYS* 1.3 70.5 - - - +
25D GLU* 1.3 65.9 + - - +
26D GLN 2.9 5.0 + - - -
27D PHE* 3.0 18.1 + - + +
28D ASP 3.5 5.4 + - - -
29D ILE* 3.6 42.5 + - + +
30D THR 4.1 2.9 - - - +
31D ASN* 3.5 38.4 - - + +
104D PHE* 3.8 19.3 - - + -
107D ILE* 3.7 20.6 - - + -
108D PHE* 3.7 20.0 - - + -
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Residues in contact with GLU 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ASP 2.7 13.0 + - - +
22D GLN* 3.1 23.0 - - - +
23D LYS 3.1 2.2 - - - -
24D LEU* 1.3 73.5 - - - +
26D GLN* 1.3 61.0 + - + +
28D ASP* 3.1 19.6 + - - +
29D ILE 4.8 3.1 - - - -
17F A 5.3 4.5 + - - -
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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
------------------------------------------------------------
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