Contacts of the helix formed by residues 6 - 28 (chain B) in PDB entry 4G1U
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 GLN 6 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B VAL* 1.3 88.2 - - - +
7B PRO* 1.3 75.0 - - + +
8B ARG* 3.1 35.7 + - + +
9B LEU* 4.1 26.1 - - + +
10B MET* 3.3 10.4 + - - +
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Residues in contact with PRO 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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5B VAL 4.0 4.9 - - - +
6B GLN* 1.3 95.2 - - + +
8B ARG* 1.3 74.2 + - - +
10B MET* 3.2 7.2 + - + +
11B LEU* 2.9 35.3 + - + +
272B ILE* 4.4 13.0 - - + -
278B TRP* 3.6 53.6 - - + +
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Residues in contact with ARG 8 (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 GLN* 3.1 33.4 + - + +
7B PRO* 1.3 92.7 - - + +
9B LEU* 1.3 58.6 + - + +
11B LEU* 3.8 8.3 - - + +
12B GLY* 2.9 26.0 + - - -
278B TRP* 4.4 25.6 - - + -
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Residues in contact with LEU 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 VAL* 4.5 9.9 - - + -
6B GLN* 3.6 26.0 + - + +
7B PRO 3.3 0.4 - - - -
8B ARG* 1.3 79.9 - - + +
10B MET* 1.3 57.3 + - - +
12B GLY* 3.4 1.2 + - - -
13B PHE* 2.9 31.9 + - - +
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Residues in contact with MET 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 3.6 26.4 - - + +
6B GLN 3.3 9.8 + - - +
7B PRO 3.2 8.4 + - - +
9B LEU* 1.3 77.9 - - - +
11B LEU* 1.3 59.0 + - + +
13B PHE* 3.8 16.7 - - - +
14B LEU* 2.9 50.7 + - + +
268B ILE* 5.3 4.9 - - + +
271B ARG* 3.6 51.4 - - + +
272B ILE* 4.2 25.4 - - + -
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Residues in contact with LEU 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 PRO* 2.9 21.9 + - + +
8B ARG* 3.8 6.5 - - + +
10B MET* 1.3 75.0 - - + +
12B GLY* 1.3 60.4 + - - +
14B LEU* 3.4 3.8 + - + -
15B LEU* 2.9 30.4 + - - +
272B ILE* 4.9 5.4 - - + -
278B TRP* 4.3 30.3 - - + +
281B PRO* 4.3 16.2 - - + +
282B GLY* 3.5 35.9 - - - +
285B LEU* 3.7 14.2 - - + +
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Residues in contact with GLY 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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8B ARG 2.9 17.1 + - - -
9B LEU* 3.8 1.6 - - - -
11B LEU* 1.3 75.6 - - - +
13B PHE* 1.3 57.1 + - - +
15B LEU* 3.1 7.8 + - - +
16B ILE* 2.9 37.9 + - - +
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Residues in contact with PHE 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 LEU 2.9 19.0 + - - +
10B MET* 3.8 14.4 - - - +
12B GLY* 1.3 75.9 - - - +
14B LEU* 1.3 70.1 + - + +
16B ILE* 3.6 16.8 - - + +
17B LEU* 2.9 57.2 + - + +
271B ARG* 5.2 10.3 - - - -
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Residues in contact with LEU 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 MET* 2.9 35.8 + - + +
11B LEU* 3.9 3.6 - - - +
13B PHE* 1.3 87.7 - - + +
15B LEU* 1.3 57.9 + - - +
17B LEU* 3.6 12.9 - - + +
18B LEU* 2.9 27.0 + - - +
268B ILE* 4.0 20.0 - - + -
282B GLY* 3.5 29.4 - - - +
285B LEU* 4.0 17.0 - - + +
286B GLY* 4.2 15.9 - - - +
289B CYS* 3.7 16.7 - - + -
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Residues in contact with LEU 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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11B LEU 2.9 18.3 + - - +
12B GLY* 3.1 7.6 + - - +
14B LEU* 1.3 74.7 - - - +
16B ILE* 1.3 63.0 + - + +
17B LEU 3.1 0.9 - - - -
18B LEU* 3.1 17.8 + - + +
19B VAL* 3.0 39.5 + - + +
285B LEU* 3.8 24.2 - - + +
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Residues in contact with ILE 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 GLY* 2.9 15.8 + - - +
13B PHE* 3.6 22.0 - - + +
15B LEU* 1.3 77.6 - - + +
17B LEU* 1.3 61.8 + - - +
19B VAL* 3.8 8.1 - - - +
20B ILE* 2.9 42.2 + - + +
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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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13B PHE* 2.9 47.1 + - + +
14B LEU* 3.6 13.5 - - + +
15B LEU 3.1 0.2 - - - -
16B ILE* 1.3 77.3 - - + +
18B LEU* 1.3 59.1 + - - +
20B ILE* 3.5 10.3 + - + -
21B LEU* 2.9 55.7 + - + +
289B CYS* 3.9 17.3 - - + -
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Residues in contact with LEU 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 LEU 2.9 15.5 + - - +
15B LEU* 3.1 24.9 + - + +
17B LEU* 1.3 76.1 - - - +
19B VAL* 1.3 59.4 + - + +
21B LEU* 3.3 2.2 + - - +
22B ALA* 2.9 29.9 + - + +
63B VAL* 3.6 42.6 - - + -
285B LEU* 4.6 11.4 - - + +
288B ALA* 3.7 28.9 - - + +
289B CYS* 3.8 10.7 - - - +
292B LEU* 4.5 4.0 - - + -
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Residues in contact with VAL 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 LEU* 3.0 26.9 + - + +
16B ILE* 3.8 9.9 - - + +
17B LEU 3.3 0.2 - - - -
18B LEU* 1.3 78.6 - - + +
20B ILE* 1.3 68.1 + - + +
22B ALA* 3.2 5.3 + - - +
23B LEU* 3.0 46.0 + - + +
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Residues in contact with ILE 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 ILE* 2.9 30.4 + - + +
17B LEU* 3.9 13.9 - - + +
19B VAL* 1.3 79.7 - - + +
21B LEU* 1.3 61.8 + - + +
23B LEU* 4.3 7.1 - - + +
24B GLY* 2.9 28.7 + - - +
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Residues in contact with LEU 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 LEU* 2.9 47.7 + - + +
18B LEU* 3.7 4.0 - - - +
20B ILE* 1.3 78.6 - - + +
22B ALA* 1.3 60.0 + - - +
24B GLY* 3.9 0.6 - - - -
25B SER* 2.8 39.1 + - - +
289B CYS* 3.8 24.5 - - + +
292B LEU* 3.9 13.6 - - + +
293B THR* 3.5 30.7 - - + +
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Residues in contact with ALA 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 LEU* 2.9 18.8 + - + +
19B VAL* 3.7 5.4 - - - +
21B LEU* 1.3 73.0 - - - +
23B LEU* 1.3 70.0 + - + +
25B SER* 3.2 3.1 + - - -
26B ALA* 2.9 23.7 + - - +
59B VAL* 3.8 23.8 - - + +
60B LEU* 5.8 3.8 - - + -
63B VAL* 5.3 4.9 - - + -
292B LEU* 3.8 12.7 - - + +
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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 VAL* 3.0 36.3 + - + +
20B ILE* 4.3 7.0 - - + +
22B ALA* 1.3 78.9 - - + +
24B GLY* 1.3 57.4 + - - +
26B ALA* 3.0 8.4 + - + +
27B ASN* 2.9 32.1 + - - +
51B TRP* 5.9 6.3 - - + -
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Residues in contact with GLY 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 ILE 2.9 20.2 + - - -
21B LEU* 3.9 0.7 - - - -
23B LEU* 1.3 77.1 - - - +
25B SER* 1.3 56.0 + - - +
27B ASN* 3.1 13.5 - - - +
28B MET* 3.0 32.5 + - - +
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Residues in contact with SER 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 LEU* 2.8 28.9 + - - +
22B ALA 3.8 3.4 - - - -
24B GLY* 1.3 75.9 - - - +
26B ALA* 1.3 64.2 + - - +
28B MET* 3.3 15.1 + - - -
55B ARG* 3.9 0.5 + - - +
59B VAL* 4.1 14.3 - - - +
292B LEU* 4.4 5.2 - - - +
293B THR* 5.9 0.2 - - - -
296B THR* 2.8 38.9 + - - +
299B ARG* 3.0 25.6 + - - -
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Residues in contact with ALA 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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22B ALA 2.9 13.1 + - - +
23B LEU* 3.3 13.9 - - + +
25B SER* 1.3 75.3 - - - +
27B ASN* 1.3 61.9 + - - +
51B TRP* 2.8 47.7 + - + +
55B ARG* 2.8 30.6 + - + +
56B LEU* 5.8 6.5 - - + -
59B VAL* 4.5 8.9 - - + +
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Residues in contact with ASN 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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23B LEU 2.9 15.1 + - - +
24B GLY* 3.1 17.9 - - - +
26B ALA* 1.3 77.9 - - - +
28B MET* 1.3 61.8 + - + +
51B TRP* 4.3 2.8 - - - +
55B ARG* 3.7 2.8 + - - -
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Residues in contact with MET 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 GLY 3.0 21.3 + - - +
25B SER* 3.3 15.4 + - - +
26B ALA 3.3 1.2 - - - -
27B ASN* 1.3 81.4 - - + +
55B ARG* 3.1 34.6 + - - -
296B THR* 4.1 19.3 - - + -
297B LEU* 6.4 0.2 - - - -
299B ARG* 4.1 8.6 + - - -
300B THR* 3.5 41.5 + - + +
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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