Contacts of the helix formed by residues 11 - 25 (chain D) in PDB entry 4GCK
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 ARG 11 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D ASN* 1.3 80.6 - - - +
12D ARG* 1.3 64.2 + - - +
14D GLU* 2.9 28.5 + - - +
15D ILE* 2.9 34.1 + - + +
41D VAL* 5.6 1.1 - - + -
43D VAL* 3.6 30.4 - - + +
51D HIS* 3.1 36.2 + - + +
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Residues in contact with ARG 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ASN 3.7 8.9 - - - +
11D ARG* 1.3 79.2 - - - +
13D GLU* 1.3 70.5 + - - +
15D ILE* 3.6 2.1 + - - +
16D LEU* 3.2 37.2 + - + +
51D HIS* 3.5 34.6 + - + +
52D PHE* 3.4 40.4 - - + -
57D ARG* 5.4 3.2 + - - +
61D SER* 3.6 19.6 + - - -
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Residues in contact with GLU 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ASN* 3.2 22.6 + - - +
11D ARG 3.1 0.6 - - - -
12D ARG* 1.3 87.5 + - - +
14D GLU* 1.3 58.6 + - + +
16D LEU* 3.5 16.3 + - - +
17D GLN* 2.9 39.7 + - - +
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Residues in contact with GLU 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ASN* 3.1 25.8 + - - +
11D ARG* 2.9 44.5 + - - +
13D GLU* 1.3 77.5 - - - +
15D ILE* 1.3 54.4 + - - +
17D GLN* 3.4 6.1 + - - +
18D SER* 2.8 38.4 + - - +
41D VAL* 4.7 15.3 - - + +
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Residues in contact with ILE 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ARG* 2.9 23.6 + - + +
12D ARG 3.8 4.3 - - - +
14D GLU* 1.3 75.9 - - - +
16D LEU* 1.3 53.3 + - + +
18D SER* 3.0 3.8 + - - -
19D LEU* 2.7 34.8 + - + +
37D LEU* 4.0 14.4 - - + +
41D VAL* 4.0 19.7 - - + -
43D VAL* 5.5 1.6 - - + -
48D LEU* 3.5 34.3 - - + -
51D HIS* 4.1 22.0 - - + +
52D PHE* 4.0 20.6 - - + -
58D MET* 4.0 26.9 - - - -
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Residues in contact with LEU 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ARG* 3.2 28.8 + - - +
13D GLU* 3.9 16.4 - - - +
15D ILE* 1.3 74.9 - - - +
17D GLN* 1.3 61.0 + - - +
19D LEU* 3.3 7.0 + - + +
20D ALA* 2.9 29.6 + - - +
52D PHE* 3.6 23.6 - - + -
58D MET* 3.4 34.5 - - + +
61D SER* 3.7 22.2 - - - +
62D LEU* 3.9 20.5 - - + +
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Residues in contact with GLN 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D GLU* 2.9 25.4 + - - +
14D GLU* 3.6 6.5 - - - +
16D LEU* 1.3 78.5 - - - +
18D SER* 1.3 56.9 + - - +
20D ALA* 3.4 10.6 + - - +
21D LEU* 2.9 41.0 + - + +
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Residues in contact with SER 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D GLU* 2.8 22.8 + - - +
15D ILE 3.5 4.0 - - - -
17D GLN* 1.3 73.4 - - - +
19D LEU* 1.3 67.3 + - - +
21D LEU* 3.2 11.8 + - - +
22D MET* 2.8 30.3 + - - +
37D LEU* 4.2 2.7 - - - -
40D SER* 4.3 17.5 + - - -
41D VAL* 4.0 25.8 + - - +
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Residues in contact with LEU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ILE* 2.7 20.3 + - + +
16D LEU* 3.5 7.4 - - + +
18D SER* 1.3 72.7 - - - +
20D ALA* 1.3 51.1 + - - +
22D MET* 3.0 4.0 + - - +
23D LEU* 2.7 44.4 + - + +
32D ILE* 3.9 29.4 - - + -
37D LEU* 3.7 16.9 - - + +
55D LYS* 6.1 1.6 - - + -
58D MET* 3.8 34.3 - - + -
59D PHE* 4.1 22.7 - - + -
62D LEU* 3.5 27.1 - - + -
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Residues in contact with ALA 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU 2.9 17.0 + - - +
17D GLN* 3.5 11.2 - - - +
19D LEU* 1.3 76.5 - - - +
21D LEU* 1.3 56.5 + - - +
23D LEU* 3.2 13.2 + - - +
24D GLU* 2.8 29.4 + - - +
62D LEU* 4.7 4.7 - - + -
104D GLY* 3.9 3.9 - - - -
105D LEU* 4.4 23.1 - - + +
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Residues in contact with LEU 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D GLN* 2.9 28.0 + - + +
18D SER* 3.2 15.0 + - - +
20D ALA* 1.3 75.8 - - - +
22D MET* 1.3 63.5 + - + +
24D GLU* 3.1 24.0 + - - +
25D SER* 3.0 21.5 + - - -
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Residues in contact with MET 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D SER 2.8 14.3 + - - +
19D LEU 3.4 6.3 - - - +
21D LEU* 1.3 75.6 - - + +
23D LEU* 1.3 65.5 + - - +
25D SER* 3.1 25.8 + - - +
27D ASP* 4.0 7.6 - - + -
28D GLY* 3.3 11.5 + - - -
32D ILE* 3.7 31.9 - - + -
36D LYS* 3.7 37.2 - - + +
37D LEU* 3.6 34.1 - - - -
40D SER* 3.6 23.6 - - - +
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Residues in contact with LEU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 2.7 38.4 + - + +
20D ALA* 3.2 9.6 + - - +
22D MET* 1.3 73.9 - - - +
24D GLU* 1.3 51.9 + - - +
28D GLY* 3.5 7.8 - - - +
32D ILE* 3.7 26.5 - - + -
59D PHE* 3.9 22.0 - - + -
62D LEU* 4.0 4.5 - - + -
104D GLY* 3.5 24.7 - - - +
105D LEU* 5.5 0.2 - - + -
107D ARG* 2.6 40.3 + - + -
108D ILE* 3.9 15.9 - - + -
113D ALA* 3.8 24.0 - - + -
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Residues in contact with GLU 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D ALA 2.8 12.9 + - - +
21D LEU* 3.3 26.3 - - - +
22D MET 3.0 0.2 - - - -
23D LEU* 1.3 75.8 - - - +
25D SER* 1.3 65.8 + - - +
101D ARG 5.5 0.5 - - - +
102D ASN* 5.6 0.2 - - - -
103D PRO* 3.7 36.5 - - + +
104D GLY* 3.4 11.6 - - - +
107D ARG* 4.2 0.4 - - - +
178D PHE* 3.4 19.3 - - + -
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Residues in contact with SER 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LEU 3.0 12.6 + - - -
22D MET* 3.1 17.1 + - - -
24D GLU* 1.3 75.3 - - - +
26D SER* 1.3 60.6 + - - +
27D ASP* 2.9 24.2 + - - +
28D GLY 2.8 17.5 + - - -
107D ARG* 2.9 15.0 + - - -
178D PHE* 5.5 0.2 - - - -
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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