Contacts of the helix formed by residues 6 - 28 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A VAL* 1.3 86.8 - - - +
7A PRO* 1.3 77.5 - - + +
8A ARG* 3.1 34.6 + - + +
9A LEU* 4.1 25.5 - - + +
10A MET* 3.3 10.9 + - - +
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Residues in contact with PRO 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A VAL 3.5 4.9 - - - +
6A GLN* 1.3 94.5 - - + +
8A ARG* 1.3 71.7 + - - +
10A MET* 3.2 6.6 + - + +
11A LEU* 2.9 35.6 + - + +
272A ILE* 4.4 12.1 - - + -
278A TRP* 3.6 55.2 - - + +
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Residues in contact with ARG 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A GLN* 3.1 33.3 + - + +
7A PRO* 1.3 91.0 - - + +
9A LEU* 1.3 59.3 + - + +
11A LEU* 3.5 8.6 + - + +
12A GLY* 2.9 26.5 + - - -
278A TRP* 4.4 27.3 - - + -
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Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A VAL* 4.5 10.5 - - + -
6A GLN* 3.6 27.4 + - + +
7A PRO 3.3 0.4 - - - -
8A ARG* 1.3 79.8 - - + +
10A MET* 1.3 55.6 + - - +
12A GLY* 3.4 1.3 + - - -
13A PHE* 2.9 31.6 + - - +
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Residues in contact with MET 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL* 3.6 26.4 - - + +
6A GLN 3.3 10.3 + - - +
7A PRO 3.2 8.6 + - - +
9A LEU* 1.3 75.0 - - - +
11A LEU* 1.3 62.5 + - + +
13A PHE* 3.8 16.5 - - - +
14A LEU* 2.9 52.7 + - + +
268A ILE* 5.3 4.9 - - + -
271A ARG* 3.7 53.6 - - + +
272A ILE* 4.2 24.9 - - + -
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Residues in contact with LEU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PRO* 2.9 21.9 + - + +
8A ARG* 3.8 7.2 - - + +
9A LEU 3.3 0.2 - - - -
10A MET* 1.3 75.7 - - + +
12A GLY* 1.3 60.1 + - - +
14A LEU* 3.3 4.5 + - + -
15A LEU* 2.9 30.8 + - - +
272A ILE* 4.9 5.6 - - + -
278A TRP* 4.3 29.4 - - + +
281A PRO* 4.3 17.7 - - + +
282A GLY* 3.5 35.4 - - - +
285A LEU* 3.7 13.5 - - + +
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Residues in contact with GLY 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG 2.9 16.9 + - - -
9A LEU* 3.8 1.6 - - - -
11A LEU* 1.3 75.5 - - - +
13A PHE* 1.3 56.4 + - - +
15A LEU* 3.1 7.1 + - - +
16A ILE* 2.9 37.3 + - - +
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Residues in contact with PHE 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU 2.9 18.6 + - - +
10A MET* 3.8 14.8 - - - +
12A GLY* 1.3 76.1 - - - +
14A LEU* 1.3 71.6 + - + +
16A ILE* 3.6 16.2 - - + +
17A LEU* 2.9 58.2 + - + +
271A ARG* 5.2 10.3 - - - -
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Residues in contact with LEU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A MET* 2.9 35.0 + - + +
11A LEU* 3.9 4.0 - - - +
13A PHE* 1.3 89.0 - - + +
15A LEU* 1.3 57.8 + - - +
17A LEU* 3.6 13.4 - - + +
18A LEU* 2.9 26.5 + - - +
268A ILE* 3.9 21.5 - - + -
282A GLY* 3.5 29.2 - - - +
285A LEU* 4.0 16.4 - - + +
286A GLY* 4.3 15.5 - - - +
289A CYS* 3.7 16.3 - - + -
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Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU 2.9 17.5 + - - +
12A GLY* 3.5 7.6 - - - +
14A LEU* 1.3 74.0 - - - +
16A ILE* 1.3 63.0 + - + +
17A LEU 3.1 1.1 - - - -
18A LEU* 3.1 17.4 + - + +
19A VAL* 3.0 38.2 + - + +
285A LEU* 3.8 24.9 - - + +
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Residues in contact with ILE 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLY* 2.9 16.0 + - - +
13A PHE* 3.6 21.8 - - + +
15A LEU* 1.3 77.8 - - + +
17A LEU* 1.3 60.1 + - + +
19A VAL* 3.8 8.7 - - - +
20A ILE* 2.9 42.3 + - + +
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Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A PHE* 2.9 47.1 + - + +
14A LEU* 3.6 13.0 - - + +
15A LEU 3.1 0.2 - - - -
16A ILE* 1.3 77.6 - - + +
18A LEU* 1.3 60.3 + - - +
20A ILE* 3.5 10.7 + - + -
21A LEU* 2.9 52.7 + - + +
289A CYS* 3.8 19.5 - - + -
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Residues in contact with LEU 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU 2.9 15.3 + - - +
15A LEU* 3.4 24.7 - - + +
17A LEU* 1.3 77.2 - - - +
19A VAL* 1.3 59.1 + - + +
21A LEU* 3.3 2.3 + - - +
22A ALA* 2.9 30.3 + - + +
63A VAL* 3.6 42.6 - - + -
285A LEU* 4.9 11.2 - - + +
288A ALA* 3.7 29.6 - - + +
289A CYS* 3.8 11.2 - - - +
292A LEU* 4.5 4.0 - - + -
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Residues in contact with VAL 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 3.0 28.4 + - + +
16A ILE* 3.8 9.4 - - - +
18A LEU* 1.3 78.2 - - + +
20A ILE* 1.3 67.9 + - + +
22A ALA* 3.2 5.1 + - - +
23A LEU* 3.0 46.3 + - + +
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Residues in contact with ILE 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE* 2.9 30.1 + - + +
17A LEU* 3.9 13.9 - - + +
19A VAL* 1.3 80.1 - - + +
21A LEU* 1.3 61.4 + - + +
23A LEU* 4.3 6.5 - - + +
24A GLY* 2.9 28.6 + - - +
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Residues in contact with LEU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 2.9 47.7 + - + +
18A LEU* 3.7 4.3 - - - +
19A VAL 3.2 0.2 - - - -
20A ILE* 1.3 77.2 - - + +
22A ALA* 1.3 60.6 + - - +
24A GLY* 5.0 0.4 - - - -
25A SER* 2.8 38.6 + - - +
289A CYS* 3.8 24.7 - - + +
292A LEU* 3.9 13.1 - - + +
293A THR* 3.5 30.7 - - + +
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Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 2.9 18.8 + - + +
19A VAL* 3.2 5.6 + - - +
21A LEU* 1.3 74.3 - - - +
23A LEU* 1.3 64.2 + - + +
25A SER* 3.2 2.9 + - - -
26A ALA* 2.9 29.2 + - - +
59A VAL* 3.8 24.5 - - + +
60A LEU* 5.7 4.7 - - + -
63A VAL* 5.3 4.5 - - + -
292A LEU* 3.8 13.2 - - + +
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A VAL* 3.0 37.2 + - + +
20A ILE* 4.3 6.7 - - + +
22A ALA* 1.3 80.2 - - + +
24A GLY* 1.3 58.7 + - - +
26A ALA* 3.0 27.3 + - + +
27A ASN* 3.5 11.8 + - - -
51A TRP* 6.6 0.2 - - + -
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Residues in contact with GLY 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ILE* 2.9 20.0 + - - -
21A LEU 3.9 0.4 - - - -
23A LEU* 1.3 78.8 - - - +
25A SER* 1.3 58.3 + - - +
27A ASN* 3.5 13.5 + - - +
28A MET* 3.3 22.9 + - - +
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Residues in contact with SER 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 2.8 29.6 + - - +
22A ALA 3.8 3.1 - - - -
24A GLY* 1.3 72.8 - - - +
26A ALA* 1.3 64.4 + - - +
27A ASN 3.2 1.1 - - - -
28A MET* 3.2 9.4 + - - -
55A ARG* 4.7 0.9 - - - -
59A VAL* 4.1 15.7 - - - +
292A LEU* 4.3 5.6 + - - +
293A THR* 5.9 0.3 - - - -
296A THR* 2.8 43.7 + - - +
299A ARG* 3.0 25.5 + - - -
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Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ALA 2.9 13.3 + - - +
23A LEU* 3.0 18.6 + - + +
25A SER* 1.3 79.7 - - - +
27A ASN* 1.3 62.2 + - - +
28A MET 3.4 0.2 - - - -
51A TRP* 3.9 36.4 - - + +
55A ARG* 3.7 20.7 + - + +
56A LEU* 5.9 6.5 - - + +
59A VAL* 4.6 7.6 - - + +
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Residues in contact with ASN 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU 3.5 11.6 + - - -
24A GLY* 3.5 11.7 + - - +
25A SER 3.2 0.6 - - - -
26A ALA* 1.3 81.0 - - - +
28A MET* 1.3 63.1 + - + +
51A TRP* 5.8 1.0 + - - -
55A ARG* 3.6 8.3 + - - -
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Residues in contact with MET 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLY 3.3 20.2 - - - +
25A SER* 3.2 10.1 + - - +
27A ASN* 1.3 81.7 - - + +
55A ARG* 3.4 21.8 + - - -
296A THR* 4.3 20.2 - - + -
299A ARG* 2.9 41.4 + - - +
300A THR* 4.3 29.6 + - + +
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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
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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