Contacts of the helix formed by residues 4 - 25 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C GLU 4.1 1.5 + - - +
3C PHE* 1.3 77.9 - - - +
5C TYR* 1.3 60.4 + - - +
6C SER* 3.5 20.4 + - - -
7C TYR* 3.5 9.0 + - - +
8C LEU* 3.0 24.6 + - - +
112D GLU* 3.2 27.8 - - + +
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Residues in contact with TYR 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C PHE 5.4 1.3 - - - -
4C THR* 1.3 72.0 - - - +
6C SER* 1.3 55.7 + - - +
8C LEU* 3.1 5.4 + - + -
9C PHE* 2.6 46.2 + + + +
134C MET* 4.1 23.1 - - + -
112D GLU* 2.8 19.2 + - - +
115D LEU* 3.9 34.5 - - + -
116D VAL* 3.9 33.9 - - + -
119D LEU* 4.7 3.4 - - + +
124D ASN* 3.7 33.1 + - + +
127D MET* 3.9 19.5 - - + +
128D LYS* 4.3 19.9 - - + +
131D LEU* 4.4 14.4 - - + -
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Residues in contact with SER 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C THR* 3.4 10.4 + - - -
5C TYR* 1.3 77.4 - - - +
7C TYR* 1.3 60.0 + - - +
9C PHE* 3.7 1.4 - - - +
10C ARG* 2.8 50.5 + - - +
16D MET* 3.5 23.9 - - - +
35D HIS* 3.7 20.4 + - - -
108D PHE* 5.8 1.1 - - - -
111D MET* 5.2 10.1 - - - -
112D GLU* 4.0 3.5 + - - -
115D LEU* 5.5 0.2 - - - +
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Residues in contact with TYR 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C PHE* 3.4 56.4 - + + -
4C THR* 3.5 18.3 + - - +
5C TYR 3.1 0.4 - - - -
6C SER* 1.3 79.1 + - - +
8C LEU* 1.3 72.1 + - - +
10C ARG* 3.1 19.5 + - - +
11C MET* 3.0 64.8 + - + +
56D ALA 4.4 14.9 + - - -
57D LEU* 5.7 2.2 - - + -
58D GLN* 4.2 9.2 + - - -
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Residues in contact with LEU 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C PHE* 5.1 5.8 - - + +
4C THR 3.0 14.9 + - - +
5C TYR* 3.6 9.4 - - + +
7C TYR* 1.3 88.0 - - + +
9C PHE* 1.3 62.7 + - - +
11C MET* 4.5 1.6 - - - +
12C ILE* 3.1 31.4 + - + +
128D LYS* 6.1 1.6 - - + +
131D LEU* 4.7 26.0 - - + -
132D THR* 5.7 3.1 - - - +
135D LEU* 5.4 1.1 - - - +
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Residues in contact with PHE 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C TYR* 2.6 32.4 + - + +
8C LEU* 1.3 74.5 - - - +
10C ARG* 1.3 64.5 + - - +
12C ILE* 4.1 5.4 - - + +
13C SER* 3.4 23.6 + - - -
131C LEU* 3.8 21.5 - - + -
134C MET* 3.4 35.0 - - + -
9D PHE* 4.0 25.0 - + - +
12D ILE* 3.5 33.4 - - + -
13D SER* 4.0 7.6 - - - +
16D MET* 3.9 24.9 - - + -
115D LEU* 4.8 4.0 - - + -
131D LEU* 3.7 25.6 - - + -
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Residues in contact with ARG 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C SER* 2.8 31.7 + - - +
7C TYR* 3.7 19.9 - - - +
9C PHE* 1.3 70.7 - - - +
11C MET* 1.3 97.0 + - + +
12C ILE 3.1 0.5 + - - -
13C SER* 3.2 5.7 + - - -
14C HIS* 3.0 24.8 + - - +
13D SER* 4.9 9.9 - - - +
16D MET* 5.5 4.7 - - + -
31D ASN* 5.4 6.5 - - - +
32D GLU* 6.1 5.8 - - - -
35D HIS* 3.2 53.3 + - - +
57D LEU* 4.8 11.1 - - - +
59D ARG* 4.5 14.7 + - - +
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Residues in contact with MET 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C TYR* 3.0 48.1 + - + +
8C LEU* 4.5 2.5 - - - +
10C ARG* 1.3 110.1 - - + +
12C ILE* 1.3 62.9 + - + +
14C HIS* 3.6 2.0 + - - +
15C GLU* 3.0 31.1 + - + +
57D LEU* 3.2 31.4 - - - +
58D GLN* 3.2 30.1 - - - +
59D ARG* 3.6 19.5 - - - +
135D LEU* 5.5 7.6 - - + -
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Residues in contact with ILE 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 3.1 22.5 + - - +
9C PHE* 4.1 5.8 - - + +
10C ARG 3.1 0.6 - - - -
11C MET* 1.3 76.2 - - - +
13C SER* 1.3 58.4 + - - +
15C GLU* 3.1 7.8 + - - +
16C MET* 2.9 38.5 + - + +
9D PHE* 3.4 49.1 - - + -
131D LEU* 3.5 31.0 - - + +
134D MET* 4.6 3.1 - - + -
135D LEU* 3.6 26.5 - - + +
138D LEU* 4.2 9.8 - - + +
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Residues in contact with SER 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C PHE 3.4 12.7 + - - -
10C ARG* 3.2 3.9 + - - -
12C ILE* 1.3 77.5 - - - +
14C HIS* 1.3 67.9 + - - +
16C MET* 3.2 7.8 + - - +
17C LYS* 2.9 25.7 + - - +
9D PHE* 3.2 34.0 + - - +
10D ARG* 3.9 5.0 + - - -
13D SER* 3.4 15.8 - - - -
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Residues in contact with HIS 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ARG 3.0 10.9 + - - +
11C MET* 3.7 4.3 - - - +
13C SER* 1.3 77.2 - - - +
15C GLU* 1.3 68.4 + - - +
17C LYS* 3.3 7.7 + - - +
18C GLN* 2.8 43.3 + - + +
58D GLN 3.7 10.3 - - - -
59D ARG* 3.2 52.8 + - - +
14E T 2.9 28.9 + - - -
15E C 2.3 30.0 + - - -
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Residues in contact with GLU 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C MET* 3.0 20.6 + - + +
12C ILE* 3.3 8.1 - - - +
14C HIS* 1.3 91.5 - - - +
16C MET* 1.3 55.2 + - - +
18C GLN* 2.9 13.8 + - - +
19C LYS* 2.5 38.5 + - - +
58D GLN* 5.1 13.3 + - - +
135D LEU* 5.4 2.2 - - + +
138D LEU* 3.8 36.5 - - + +
139D GLN* 4.5 15.0 - - + +
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Residues in contact with MET 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ILE* 2.9 28.2 + - + +
13C SER* 3.2 7.8 + - - +
15C GLU* 1.3 72.0 - - - +
17C LYS* 1.3 52.7 + - - +
19C LYS* 3.5 7.0 - - - +
20C ALA* 2.7 36.6 + - - +
31C ASN* 5.5 0.9 - - - -
111C MET* 3.7 35.5 - - + +
112C GLU* 5.8 1.3 - - - +
115C LEU* 4.2 20.2 - - + -
6D SER* 4.0 29.6 - - - +
9D PHE* 3.9 30.3 - - - -
138D LEU* 4.1 17.3 - - + -
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Residues in contact with LYS 17 (chain C).
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 2.9 12.8 + - - +
14C HIS* 3.3 13.2 - - - +
16C MET* 1.3 77.0 - - - +
18C GLN* 1.3 57.3 + - - +
20C ALA* 3.1 1.7 + - - +
21C ASP* 2.7 42.4 + - - +
31C ASN* 4.3 24.9 - - + +
32C GLU* 4.6 7.0 - - - +
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Residues in contact with GLN 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C HIS* 2.8 40.5 + - + +
15C GLU* 3.5 17.5 - - - +
17C LYS* 1.3 73.8 - - - +
19C LYS* 1.3 62.8 + - - +
21C ASP* 3.6 18.9 - - - +
22C GLN* 3.1 25.1 + - - +
60D THR* 5.7 0.4 - - - +
15E C 3.2 50.9 + - - +
16E T 4.0 6.9 + - - -
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Residues in contact with LYS 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C GLU* 2.5 20.4 + - - +
16C MET* 3.5 9.0 - - - +
18C GLN* 1.3 74.0 - - - +
20C ALA* 1.3 63.4 + - - +
22C GLN* 3.7 4.9 - - - +
23C LYS* 3.1 33.5 + - - +
111C MET* 4.2 13.5 - - + -
138D LEU* 4.9 12.6 - - + +
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Residues in contact with ALA 20 (chain C).
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 2.7 21.5 + - - +
17C LYS 3.7 2.0 - - - +
19C LYS* 1.3 71.5 - - - +
21C ASP* 1.3 55.3 + - - +
23C LYS* 3.3 4.7 + - - +
24C LEU* 2.8 43.7 + - + +
31C ASN* 3.6 25.4 - - + +
107C ILE* 4.9 2.7 - - + -
108C PHE* 4.2 14.8 - - + -
111C MET* 4.2 17.0 - - + -
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Residues in contact with ASP 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C LYS* 2.7 25.0 + - - +
18C GLN* 3.6 24.2 - - - +
20C ALA* 1.3 71.7 - - - +
22C GLN* 1.3 63.7 + - - +
24C LEU* 3.1 7.1 + - - +
25C GLU* 2.9 23.6 + - - +
29C ILE 4.8 2.6 - - - +
30C THR* 3.8 10.1 - - - -
31C ASN* 3.1 28.0 + - - +
32C GLU* 4.5 2.8 - - - +
15E C 5.8 0.7 - - - +
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Residues in contact with GLN 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C GLN 3.1 15.9 + - - +
19C LYS* 3.7 5.8 - - - +
21C ASP* 1.3 80.4 - - - +
23C LYS* 1.3 65.9 + - + +
25C GLU* 3.4 17.4 + - - +
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Residues in contact with LYS 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LYS* 3.1 27.3 + - - +
20C ALA 3.8 0.9 - - - +
22C GLN* 1.3 79.3 - - + +
24C LEU* 1.3 59.2 + - - +
25C GLU 3.0 5.8 + - - -
26C GLN* 3.3 26.9 + - - +
107C ILE* 3.6 38.8 - - + -
110C GLU* 4.5 20.3 + - - +
111C MET* 4.0 21.9 - - + +
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Residues in contact with LEU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ALA 2.8 25.7 + - - +
21C ASP* 3.5 3.1 - - - +
23C LYS* 1.3 68.4 - - - +
25C GLU* 1.3 58.2 + - - +
26C GLN 3.1 1.1 - - - -
27C PHE* 2.8 27.5 + - + +
28C ASP 3.4 6.8 + - - -
29C ILE* 3.5 31.5 - - + +
30C THR 3.8 8.5 - - - +
31C ASN* 3.7 28.5 - - - +
104C PHE* 3.5 35.4 - - + -
107C ILE* 3.8 17.3 - - + -
108C PHE* 4.0 21.1 - - + -
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Residues in contact with GLU 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ASP 2.9 10.4 + - - +
22C GLN* 3.4 17.5 - - - +
23C LYS 3.0 1.6 + - - -
24C LEU* 1.3 77.2 - - - +
26C GLN* 1.3 61.0 + - - +
27C PHE 3.2 1.2 + - - -
28C ASP* 3.2 14.3 + - - +
29C ILE 5.1 1.8 - - - -
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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