Contacts of the helix formed by residues 19 - 34 (chain D) in PDB entry 1CBM
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 ASN 19 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17D LYS 3.5 4.5 + - - +
18D VAL* 1.3 72.7 - - - +
20D VAL* 1.3 58.4 + - - +
21D ASP* 3.0 13.4 + - - +
22D GLU* 2.9 49.8 + - + +
23D VAL* 3.0 31.1 + - + +
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Residues in contact with VAL 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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15D TRP* 5.5 3.1 - - + +
18D VAL* 3.4 14.1 + - + +
19D ASN* 1.3 70.0 + - - +
21D ASP* 1.3 75.4 - - - +
24D GLY* 2.8 29.6 + - - -
65D LYS* 4.2 25.2 - - + +
68D LEU* 4.3 31.5 - - + +
69D GLY* 5.7 1.1 - - - +
72D SER* 5.1 9.6 - - - +
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Residues in contact with ASP 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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19D ASN* 3.0 8.6 + - - +
20D VAL* 1.3 86.8 - - - +
22D GLU* 1.3 66.8 - - + +
25D GLY* 3.4 17.8 + - - -
61D LYS* 5.4 8.9 + - - +
65D LYS* 3.6 36.8 + - - +
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Residues in contact with GLU 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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19D ASN* 2.9 42.3 + - + +
21D ASP* 1.3 82.7 - - + +
23D VAL* 1.3 59.8 + - - +
26D GLU* 3.0 28.9 + - - +
117D HIS* 3.8 21.2 + - + -
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Residues in contact with VAL 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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18D VAL* 3.9 19.5 - - + -
19D ASN* 3.0 19.1 + - + +
22D GLU* 1.3 73.1 - - - +
24D GLY* 1.3 58.7 + - - +
26D GLU* 3.4 4.8 - - - +
27D ALA* 2.8 34.5 + - - +
68D LEU* 3.4 22.4 - - + -
110D LEU* 4.1 20.0 - - + -
113D VAL* 4.0 6.6 - - + +
114D LEU* 4.1 12.3 - - + -
117D HIS* 2.9 34.1 - - + +
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Residues in contact with GLY 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 VAL 2.8 24.0 + - - -
23D VAL* 1.3 74.6 - - - +
25D GLY* 1.3 60.4 + - - +
27D ALA* 4.1 1.3 - - - +
28D LEU* 3.1 17.2 + - - +
64D GLY* 3.3 35.8 - - - -
68D LEU* 3.7 12.9 - - - +
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Residues in contact with GLY 25 (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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21D ASP 3.4 15.9 + - - -
24D GLY* 1.3 74.2 - - - +
26D GLU* 1.3 54.2 + - - +
29D GLY* 2.7 32.8 + - - -
55D MET* 4.1 7.2 - - - +
60D VAL* 4.3 8.2 - - - +
61D LYS* 4.2 33.6 + - - -
64D GLY* 4.3 0.8 - - - -
65D LYS 4.8 0.2 - - - +
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Residues in contact with GLU 26 (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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124A PRO* 5.4 0.9 - - - +
22D GLU 3.0 22.2 + - - +
23D VAL 3.4 4.7 - - - +
25D GLY* 1.3 74.2 - - - +
27D ALA* 1.3 62.2 + - - +
30D ARG* 2.6 76.0 + - - +
55D MET* 4.1 18.5 - - - +
113D VAL* 3.8 19.5 - - + -
116D HIS* 3.7 12.4 + - + -
117D HIS* 4.0 11.9 - - + +
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Residues in contact with ALA 27 (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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23D VAL 2.8 22.1 + - - +
24D GLY* 4.1 3.8 - - - +
26D GLU* 1.3 74.5 - - - +
28D LEU* 1.4 61.6 + - - +
31D LEU* 3.0 22.5 + - - +
67D VAL* 6.5 0.7 - - + -
68D LEU* 5.0 4.7 - - + -
106D LEU* 4.1 10.1 - - + +
109D VAL* 3.4 16.8 - - + +
110D LEU* 4.0 31.6 - - + -
113D VAL* 4.1 8.5 - - + -
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Residues in contact with LEU 28 (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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24D GLY 3.1 17.2 + - - +
25D GLY 4.4 1.3 - - - +
27D ALA* 1.4 75.1 - - - +
29D GLY* 1.3 61.4 + - - +
31D LEU* 3.3 22.1 + - + +
32D LEU* 3.3 27.3 + - + +
42D PHE* 4.0 22.4 - - + -
45D PHE* 4.8 2.0 - - + -
60D VAL* 3.7 30.7 - - + +
63D HIS* 3.7 29.4 - - + -
64D GLY* 3.7 10.1 - - - +
67D VAL* 4.9 4.9 - - + -
106D LEU* 4.7 9.1 - - + +
148D CMO 3.9 15.3 - - - +
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Residues in contact with GLY 29 (chain D).
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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25D GLY 2.7 23.8 + - - -
28D LEU* 1.3 74.1 - - - +
30D ARG* 1.3 57.2 + - - +
32D LEU 3.4 1.6 + - - -
33D VAL* 3.0 33.8 + - - +
54D VAL* 3.7 14.2 - - - +
55D MET* 3.6 19.5 - - - -
60D VAL* 4.2 6.2 - - - +
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Residues in contact with ARG 30 (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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122A PHE* 2.8 32.5 + - - -
123A THR* 3.6 12.1 - - - +
124A PRO* 3.6 32.1 - - + +
127A GLN* 2.6 40.9 + - - +
26D GLU* 2.6 52.0 + - - +
29D GLY* 1.3 72.5 - - - +
31D LEU* 1.3 61.7 + - - +
33D VAL* 4.5 5.4 - - - +
34D VAL* 2.7 38.5 + - + +
109D VAL* 3.5 15.7 - - + -
112D CYS* 5.3 0.8 - - - -
113D VAL* 3.6 20.8 - - - +
116D HIS* 3.2 16.7 + - - -
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Residues in contact with LEU 31 (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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27D ALA 3.0 14.8 + - - +
28D LEU* 3.5 28.5 - - + +
29D GLY 3.3 0.2 - - - -
30D ARG* 1.3 77.0 - - - +
32D LEU* 1.3 56.1 + - + +
35D TYR* 3.0 45.6 + - + +
38D THR* 3.3 26.4 + - + +
42D PHE* 4.8 3.1 - - + -
102D ASN 4.6 2.0 - - - +
105D LEU* 4.1 7.4 - - + +
106D LEU* 3.8 44.4 - - + +
109D VAL* 4.0 8.4 - - + +
147D HEM 4.2 25.1 - - + -
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Residues in contact with LEU 32 (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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28D LEU* 3.3 22.3 + - + +
29D GLY 3.4 6.0 + - - +
31D LEU* 1.3 77.2 - - + +
33D VAL* 1.3 58.5 + - - +
36D PRO* 3.6 8.7 - - - +
38D THR* 3.4 26.2 - - - +
39D GLN* 2.8 42.3 + - + +
42D PHE* 3.5 37.9 - - + -
48D LEU* 4.1 13.5 - - + -
54D VAL* 4.1 17.0 - - + -
60D VAL* 4.1 26.7 - - + -
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Residues in contact with VAL 33 (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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124A PRO* 3.9 35.4 - - + +
125A PRO* 4.5 0.9 - - + -
128A ALA* 4.2 12.7 - - + +
29D GLY 3.0 19.5 + - - +
30D ARG 4.1 2.2 - - - +
32D LEU* 1.3 78.5 - - - +
34D VAL* 1.3 65.3 + - + +
35D TYR 3.7 0.2 + - - -
36D PRO* 4.1 9.4 - - - +
39D GLN* 4.8 2.2 - - - +
51D PRO* 3.9 44.0 - - + +
54D VAL* 4.0 17.0 - - + -
55D MET* 4.7 0.9 - - - -
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Residues in contact with VAL 34 (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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124A PRO 4.0 6.5 - - - +
127A GLN* 3.8 26.7 - - + +
128A ALA* 3.7 30.2 - - - +
131A GLN* 3.7 28.7 - - + +
30D ARG* 2.7 27.6 + - + +
33D VAL* 1.3 76.5 - - + +
35D TYR* 1.3 88.4 + - + +
36D PRO* 3.1 9.7 - - - +
37D TRP* 5.2 0.5 - - - -
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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
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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