Contacts of the helix formed by residues 8 - 29 (chain B) in PDB entry 2LUC
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 8 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A THR 3.7 8.3 - - - +
46A GLU* 2.5 56.6 + - - +
48A ALA 5.6 0.2 - - - +
3B LYS* 4.9 11.9 - - - +
5B SER* 5.4 0.4 - - - -
7B PRO* 1.3 75.5 - - - +
9B GLU* 1.3 57.6 + - - +
10B THR* 3.2 9.7 - - - +
11B GLU* 2.8 19.9 + - - +
12B ARG* 2.7 34.7 + - - +
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Residues in contact with GLU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A SER* 3.3 26.6 + - - +
19A ALA* 3.5 24.0 - - - +
20A VAL* 3.3 18.4 - - + +
23A LYS* 4.4 9.1 + - - +
46A GLU* 4.8 3.9 + - - +
8B THR* 1.3 76.4 - - - +
10B THR* 1.3 58.0 + - - +
12B ARG* 3.1 37.9 + - - +
13B CYS* 3.1 23.6 + - - +
104B ARG* 3.5 20.2 + - - -
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Residues in contact with THR 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.1 9.0 - - - -
20A VAL* 3.9 18.3 - - + +
42A PHE* 3.7 25.5 - - + -
46A GLU* 3.8 14.8 - - + +
47A LEU* 3.7 8.8 - - + +
84A ILE* 3.1 22.8 - - - +
8B THR* 3.2 17.0 - - - +
9B GLU* 1.3 74.0 - - - +
11B GLU* 1.3 59.1 + - - +
13B CYS* 3.1 7.6 - - - +
14B ILE* 2.9 35.2 + - - +
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Residues in contact with GLU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLU 3.3 18.6 - - - +
47A LEU* 3.4 22.3 - - + +
49A ALA* 3.1 31.5 + - - +
50A PHE* 4.4 1.2 + - - +
6B SER 3.7 5.2 - - - +
7B PRO* 3.1 17.8 - - + +
8B THR* 2.8 40.3 + - - +
10B THR* 1.3 77.0 - - - +
12B ARG* 1.3 55.9 + - - +
14B ILE* 3.1 12.9 + - + +
15B GLU* 2.9 33.6 + - + +
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Residues in contact with ARG 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ARG* 3.8 27.5 + - - +
16A SER* 2.8 20.8 + - - -
7B PRO* 3.7 15.8 - - + +
8B THR 2.7 29.5 + - - +
9B GLU* 3.1 38.3 + - - +
11B GLU* 1.3 70.8 - - - +
13B CYS* 1.3 61.6 + - - +
15B GLU* 3.7 12.8 - - - +
16B SER* 2.6 41.3 + - - -
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Residues in contact with CYS 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A CYS* 3.3 43.8 - - - +
16A SER* 4.0 1.1 - - - -
17A LEU* 3.1 31.6 - - + -
84A ILE* 4.3 0.9 - - - -
9B GLU 3.1 13.1 + - - +
10B THR* 3.1 11.2 - - - +
12B ARG* 1.3 85.0 - - - +
14B ILE* 1.3 68.4 + - - +
16B SER* 3.1 5.4 - - - -
17B LEU* 3.0 35.2 + - - +
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Residues in contact with ILE 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 4.9 2.0 - - + -
84A ILE* 4.1 14.4 - - + -
87A LEU* 3.4 34.5 - - + +
88A ALA* 3.2 29.8 - - + +
91A CYS* 4.0 20.4 - - + -
10B THR* 2.9 32.3 + - - +
11B GLU* 3.1 13.2 + - + +
13B CYS* 1.3 88.3 - - - +
15B GLU* 1.3 56.7 + - - +
17B LEU* 3.2 11.1 + - - +
18B ILE* 3.0 25.0 + - + +
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Residues in contact with GLU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A CYS* 4.1 24.5 - - - -
95A PHE* 4.8 11.3 - - + -
104A ARG* 5.4 2.6 + - - +
7B PRO* 3.3 34.4 - - - +
11B GLU* 2.9 17.9 + - - +
12B ARG* 3.3 6.8 + - - +
14B ILE* 1.3 75.0 - - + +
16B SER* 1.3 60.9 + - - +
18B ILE* 3.2 14.3 - - + +
19B ALA* 2.8 28.1 + - - +
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Residues in contact with SER 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLU* 3.2 36.8 - - - -
12A ARG* 2.8 31.0 + - - -
13A CYS* 4.0 1.1 - - - -
12B ARG 2.6 20.0 + - - -
13B CYS 3.1 12.6 - - - -
15B GLU* 1.3 76.1 - - - +
17B LEU* 1.3 60.4 + - - +
19B ALA* 3.1 2.1 + - - +
20B VAL* 2.8 35.3 + - - +
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Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A THR* 4.1 9.0 - - - -
13A CYS* 3.1 33.2 - - + -
84A ILE* 4.6 8.1 - - + -
88A ALA* 4.7 2.0 - - + -
92A HIS* 4.0 4.0 - - - +
13B CYS* 3.0 16.8 + - - +
14B ILE* 3.2 14.8 + - - +
16B SER* 1.3 76.0 - - - +
18B ILE* 1.3 57.5 + - - +
20B VAL* 3.6 4.6 - - - +
21B PHE* 2.8 36.4 + - - +
80B PHE* 4.0 9.9 - - + -
81B LEU* 3.4 28.3 - - + -
84B ILE* 3.5 34.3 - - + -
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Residues in contact with ILE 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ALA 4.7 0.2 - - - +
91A CYS* 3.4 45.1 - - + -
92A HIS* 3.3 26.2 - - + +
95A PHE* 3.7 31.9 - - + -
102A GLN* 4.7 4.5 - - + +
14B ILE 3.0 15.1 + - - +
15B GLU* 3.2 16.4 - - - +
17B LEU* 1.3 76.7 - - - +
19B ALA* 1.3 58.1 - - - +
22B GLN* 2.9 62.3 + - - +
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLU* 3.4 12.6 - - - +
102A GLN* 3.9 15.5 - - - +
104A ARG* 3.3 38.3 - - - +
15B GLU 2.8 14.3 + - - +
16B SER 3.3 7.9 - - - +
18B ILE* 1.3 76.4 - - - +
20B VAL* 1.3 61.9 + - - +
23B LYS* 3.1 30.7 + - + +
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Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLU* 3.3 34.5 - - + +
10A THR* 3.9 13.9 - - + +
16B SER 2.8 16.8 + - - +
17B LEU* 3.6 9.4 - - - +
19B ALA* 1.3 69.4 - - - +
21B PHE* 1.3 71.8 + - - +
23B LYS* 3.1 28.2 - - - +
24B TYR* 3.3 12.1 + - - +
42B PHE* 3.5 20.0 - - + -
46B GLU* 4.1 8.3 - - - +
80B PHE* 3.4 27.6 - - + -
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Residues in contact with PHE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A HIS* 3.6 20.4 - + + -
17B LEU 2.8 22.0 + - - +
18B ILE 4.0 0.7 - - - +
20B VAL* 1.3 82.5 - - - +
22B GLN* 1.3 57.9 + - + +
24B TYR* 3.9 0.5 - - - +
25B ALA* 2.7 49.1 + - + +
32B TYR* 3.0 30.3 - - + -
34B LEU* 3.7 13.2 - - + +
75B LEU 3.0 27.4 - - - -
77B PHE* 3.3 34.3 - + - -
80B PHE* 3.4 42.2 - + + -
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Residues in contact with GLN 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A HIS* 2.7 25.7 + - - +
95A PHE* 4.1 6.3 - - - +
96A LEU* 3.9 11.1 - - - +
100A PRO* 2.9 42.9 + - - +
102A GLN* 3.5 23.9 - - + +
103A LYS* 4.1 6.8 - - - +
18B ILE* 2.9 30.1 + - - +
21B PHE* 1.3 91.8 - - + +
23B LYS* 1.3 57.5 + - - +
25B ALA* 4.5 1.3 - - - -
26B GLY* 3.1 25.8 + - - +
32B TYR* 4.4 13.1 - - + -
77B PHE* 4.6 3.1 - - + -
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Residues in contact with LYS 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLU* 4.4 8.3 + - - +
102A GLN 3.7 12.7 + - - +
103A LYS* 4.3 10.2 + - - +
104A ARG* 4.3 26.2 - - + +
19B ALA* 3.1 20.9 + - + +
20B VAL* 3.1 29.4 - - - +
22B GLN* 1.3 80.6 - - - +
24B TYR* 1.3 79.8 + - + +
26B GLY 4.1 1.6 - - - -
27B LYS* 3.3 25.8 + - - +
46B GLU* 2.7 30.6 + - - -
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Residues in contact with TYR 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B VAL 3.7 11.2 - - - +
21B PHE 3.3 1.6 + - - -
23B LYS* 1.3 96.6 - - + +
25B ALA* 1.3 60.9 + - - +
26B GLY 3.1 1.3 - - - -
27B LYS* 3.0 58.8 + - + +
34B LEU* 3.7 18.2 - - + -
38B GLU* 3.3 27.6 - - - +
41B SER* 3.9 9.0 - - - -
42B PHE* 3.3 32.5 - + + -
45B THR* 2.7 32.0 + - - +
46B GLU* 3.5 23.0 + - + +
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Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B PHE* 2.7 33.6 + - + +
22B GLN* 4.5 1.1 - - - -
24B TYR* 1.3 73.9 - - - +
26B GLY* 1.3 57.5 + - - +
27B LYS 3.0 4.0 + - - -
28B ASP 3.4 8.2 + - - +
29B GLY 3.6 6.6 + - - -
32B TYR* 3.7 11.8 - - - -
33B THR 3.4 50.4 + - - +
34B LEU* 3.5 11.1 - - + +
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Residues in contact with GLY 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LYS* 2.8 29.9 + - - +
22B GLN* 3.1 22.9 + - - +
23B LYS 4.1 1.1 - - - -
24B TYR 3.1 1.4 - - - -
25B ALA* 1.3 78.0 - - - +
27B LYS* 1.3 60.2 + - - +
28B ASP 3.5 0.2 - - - -
29B GLY* 4.0 10.8 + - - -
32B TYR* 4.3 17.2 - - - -
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Residues in contact with LYS 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LYS* 4.5 6.1 - - - +
23B LYS* 3.3 19.1 - - - +
24B TYR* 3.0 53.2 + - + +
26B GLY* 1.3 79.9 - - - +
28B ASP* 1.3 61.9 + - - +
29B GLY* 3.3 0.6 - - - -
38B GLU* 3.7 19.3 - - + +
41B SER* 5.3 4.2 - - - -
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Residues in contact with ASP 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B TYR 4.1 0.4 + - - -
25B ALA 3.4 2.4 + - - +
27B LYS* 1.3 78.3 - - - +
29B GLY* 1.3 65.1 + - - +
30B TYR* 3.1 17.5 + - - +
33B THR 4.0 12.6 - - - +
35B SER* 3.3 28.6 + - - -
38B GLU* 4.0 10.5 - - + +
74B GLN* 2.8 26.7 + - - -
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Residues in contact with GLY 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA 3.6 7.9 + - - -
26B GLY* 4.0 9.6 - - - -
27B LYS 3.3 2.6 - - - -
28B ASP* 1.3 79.2 - - - +
30B TYR* 1.3 66.7 + - - +
32B TYR* 4.9 3.8 - - - -
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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
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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