Contacts of the helix formed by residues 3 - 23 (chain B) in PDB entry 1XGS
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 3 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET 5.7 0.7 - - - -
2B ASP* 1.3 70.5 - - - +
4B GLU* 1.3 61.0 + - - +
5B LYS 3.4 0.2 - - - -
6B LEU* 3.2 11.7 + - + +
7B MET* 2.9 40.4 + - - +
284B ILE* 4.4 25.4 - - + -
286B GLU* 5.7 2.9 - - - +
291B ILE* 5.9 4.3 - - + -
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Residues in contact with GLU 4 (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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2B ASP* 3.2 6.1 - - + +
3B THR* 1.3 79.7 + - - +
5B LYS* 1.3 69.9 + - + +
7B MET* 3.4 6.5 + - - +
8B LYS* 2.9 46.4 + - - +
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Residues in contact with LYS 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ASP* 3.6 14.4 + - + +
3B THR 3.4 0.6 - - - -
4B GLU* 1.3 86.6 - - + +
6B LEU* 1.3 60.8 + - - +
8B LYS* 3.7 7.6 - - - +
9B ALA* 2.9 30.5 + - - +
87B ILE* 3.7 21.6 - - + +
88B ASP* 2.9 34.9 + - + +
90B PHE* 3.6 39.9 - - + +
157B ARG* 5.3 2.8 - - - +
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Residues in contact with LEU 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET 5.7 4.3 - - - +
2B ASP 3.8 10.3 + - - +
3B THR* 3.2 13.3 + - + +
5B LYS* 1.3 77.1 - - - +
7B MET* 1.3 58.3 + - - +
9B ALA* 3.9 4.1 - - - +
10B GLY* 3.1 23.7 + - - -
90B PHE* 3.7 32.8 - - + -
91B ILE 3.6 26.1 - - - +
92B ALA* 4.7 1.6 - - - +
155B ILE* 5.6 1.6 - - + -
183B VAL* 3.6 38.1 - - + -
282B THR* 5.8 0.7 - - + -
284B ILE* 4.1 22.9 - - + -
293B THR* 3.8 11.4 + - + +
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Residues in contact with MET 7 (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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3B THR* 2.9 27.1 + - - +
4B GLU* 3.7 6.7 - - - +
6B LEU* 1.3 77.0 - - - +
8B LYS* 1.3 58.3 + - - +
10B GLY* 3.3 1.1 + - - +
11B GLU* 2.9 29.7 + - - +
284B ILE* 4.5 6.1 - - + -
291B ILE* 3.5 42.0 - - + -
292B VAL 5.5 0.2 - - - +
293B THR* 4.1 21.3 - - - +
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Residues in contact with LYS 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLU* 2.9 32.7 + - - +
5B LYS* 3.3 8.3 + - - +
7B MET* 1.3 72.2 - - - +
9B ALA* 1.3 66.6 + - - +
11B GLU* 3.0 31.4 + - - +
12B ILE* 3.0 44.9 + - + +
44B LEU 5.9 1.3 - - - +
87B ILE* 4.0 18.8 - - + -
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Residues in contact with ALA 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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5B LYS 2.9 17.9 + - - +
6B LEU 3.9 3.4 - - - +
8B LYS* 1.3 76.2 - - - +
10B GLY* 1.3 57.8 + - - +
12B ILE* 3.3 3.3 + - - +
13B ALA* 2.8 29.1 + - - +
85B VAL* 3.7 23.4 - - - +
87B ILE* 3.8 14.3 - - + +
90B PHE 3.5 21.8 - - - +
91B ILE 4.4 0.4 - - - -
92B ALA* 3.4 9.9 - - + +
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Residues in contact with GLY 10 (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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6B LEU 3.1 14.3 + - - -
7B MET 3.7 2.0 - - - -
8B LYS 3.2 0.2 - - - -
9B ALA* 1.3 74.1 - - - +
11B GLU* 1.3 59.1 + - - +
13B ALA* 3.3 1.7 + - - +
14B LYS* 2.9 28.4 + - - +
92B ALA* 3.4 16.3 - - - +
293B THR* 3.2 28.7 - - - +
294B THR* 3.8 3.3 - - - -
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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
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7B MET 2.9 17.0 + - - +
8B LYS* 3.0 36.7 + - - +
10B GLY* 1.3 75.9 - - - +
12B ILE* 1.3 64.5 + - - +
14B LYS* 3.1 33.4 + - - +
15B LYS* 3.1 44.8 + - - +
293B THR 3.7 2.3 + - - -
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Residues in contact with ILE 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LYS* 3.0 28.4 + - + +
9B ALA 3.6 6.1 - - - +
11B GLU* 1.3 79.9 - - + +
13B ALA* 1.3 62.5 + - - +
15B LYS* 3.1 9.2 + - + +
16B VAL* 3.0 29.2 + - + +
41B ILE* 4.4 7.4 - - - +
44B LEU* 3.9 47.6 - - + +
45B GLY 4.2 0.4 - - - -
46B GLY* 3.9 17.5 - - - +
85B VAL* 4.0 20.0 - - + -
87B ILE* 4.0 17.9 - - + -
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Residues in contact with ALA 13 (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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9B ALA 2.8 17.9 + - - +
10B GLY 3.3 4.7 + - - +
12B ILE* 1.3 75.0 - - - +
14B LYS* 1.3 62.7 + - - +
16B VAL* 3.3 6.2 - - - +
17B ARG* 3.0 27.0 + - - +
83B VAL* 4.0 5.0 - - + +
85B VAL* 3.8 17.2 - - + +
92B ALA* 3.9 19.5 - - + +
94B THR* 3.9 21.3 - - + -
294B THR* 4.0 1.6 - - + -
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Residues in contact with LYS 14 (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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10B GLY 2.9 12.3 + - - +
11B GLU* 3.1 37.1 + - - +
12B ILE 3.2 0.2 - - - -
13B ALA* 1.3 77.5 - - - +
15B LYS* 1.3 73.4 + - - +
17B ARG* 3.7 28.2 - - - +
18B GLU* 3.0 36.0 + - + +
94B THR* 4.9 0.2 - - - +
293B THR 5.4 0.6 + - - +
294B THR 3.8 13.0 + - - +
295B GLU* 3.4 27.9 + - - +
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Residues in contact with LYS 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLU* 3.1 41.1 + - - +
12B ILE* 3.1 8.8 + - + +
14B LYS* 1.3 91.1 - - - +
16B VAL* 1.3 62.4 + - - +
18B GLU* 3.4 5.3 + - - +
19B LYS* 3.1 22.0 + - - +
40B MET* 4.0 8.5 - - + +
44B LEU* 4.1 29.8 - - + +
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Residues in contact with VAL 16 (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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12B ILE* 3.0 15.6 + - + +
13B ALA* 3.3 17.0 - - - +
15B LYS* 1.3 72.4 - - - +
17B ARG* 1.3 63.4 + - - +
19B LYS* 3.2 2.6 + - - +
20B ALA* 2.8 30.9 + - - +
37B ILE* 4.1 18.6 - - + +
40B MET* 3.6 35.1 - - + +
41B ILE* 3.9 32.8 - - + +
44B LEU* 4.0 11.2 - - + -
83B VAL* 4.3 13.2 - - + -
85B VAL* 4.7 0.7 - - + -
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Residues in contact with ARG 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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13B ALA 3.0 19.0 + - - +
14B LYS* 3.7 23.8 - - - +
16B VAL* 1.3 77.5 - - - +
18B GLU* 1.3 98.9 + - - +
20B ALA* 3.3 8.5 + - - +
21B ILE* 3.1 30.0 + - - +
81B ILE* 5.3 5.4 - - + +
83B VAL* 3.9 18.6 - - + -
94B THR* 3.0 27.6 + - + +
95B ALA* 5.0 3.1 + - - -
96B VAL* 4.2 28.9 - - + +
281B HIS* 3.3 13.5 - - - -
294B THR* 2.4 29.9 + - - -
295B GLU 4.4 5.5 + - - -
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Residues in contact with GLU 18 (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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14B LYS* 3.0 28.4 + - + +
15B LYS* 3.9 5.4 - - - +
17B ARG* 1.3 111.0 + - - +
19B LYS* 1.3 61.9 + - - +
21B ILE* 3.6 26.6 + - - +
22B LYS* 3.6 30.0 + - - +
96B VAL* 5.8 0.2 - - - +
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Residues in contact with LYS 19 (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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15B LYS 3.1 12.8 + - - +
16B VAL 3.2 7.4 + - - +
18B GLU* 1.3 73.9 - - - +
20B ALA* 1.3 65.9 + - - +
22B LYS* 2.9 31.5 + - + +
23B LEU* 3.1 45.5 + - + +
25B ARG* 6.0 1.1 - - - +
37B ILE* 6.5 0.4 - - + -
40B MET* 3.7 29.9 - - + -
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Residues in contact with ALA 20 (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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16B VAL 2.8 15.8 + - - +
17B ARG* 3.3 7.8 + - - +
19B LYS* 1.3 77.4 - - - +
21B ILE* 1.3 61.3 + - - +
23B LEU* 3.3 12.0 + - - +
24B ALA* 3.1 23.4 + - - +
33B LEU* 4.1 3.7 - - + +
37B ILE* 3.4 34.7 - - + +
81B ILE* 3.9 23.5 - - + +
83B VAL* 5.4 0.2 - - + -
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Residues in contact with ILE 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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17B ARG* 3.1 13.9 + - - +
18B GLU* 3.6 36.8 - - - +
19B LYS 3.1 0.2 - - - -
20B ALA* 1.3 77.5 - - - +
22B LYS* 1.3 63.6 + - + +
24B ALA* 3.3 17.7 + - - +
81B ILE* 4.3 5.8 - - + -
96B VAL* 3.8 37.7 - - + -
98B VAL* 4.0 23.4 - - + +
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Residues in contact with LYS 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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18B GLU* 3.6 24.9 + - - +
19B LYS* 2.9 26.3 + - + +
21B ILE* 1.3 80.1 - - + +
23B LEU* 1.3 59.4 + - - +
24B ALA 3.6 0.3 + - - -
25B ARG* 3.3 32.4 + - - +
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Residues in contact with LEU 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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19B LYS* 3.1 43.2 + - + +
20B ALA* 3.3 5.6 + - - +
22B LYS* 1.3 75.6 - - - +
24B ALA* 1.3 59.0 + - - +
25B ARG* 2.8 26.4 + - - +
28B MET* 2.9 42.4 - - + +
33B LEU* 3.6 28.9 - - + -
36B SER* 4.3 21.8 - - - +
37B ILE* 5.1 3.6 - - + +
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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