Contacts of the helix formed by residues 21 - 33 (chain D) in PDB entry 4CQM
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 SER 21 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D GLY 3.5 7.4 + - - +
19D ALA 3.3 1.0 - - - -
20D GLY* 1.3 80.2 - - - +
22D GLY* 1.3 68.6 + - - +
23D ILE 3.4 0.3 + - - -
24D GLY 3.4 5.4 + - - -
25D ARG* 3.4 24.1 + - - +
42D ASP* 4.4 0.8 + - - -
47D ALA* 5.8 0.2 - - - -
205D PRO* 4.0 22.7 - - - +
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Residues in contact with GLY 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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21D SER* 1.3 75.8 - - - +
23D ILE* 1.3 63.3 + - - -
25D ARG* 3.9 3.4 - - - +
26D ALA* 3.1 23.4 + - - +
204D THR* 3.9 14.4 - - - -
205D PRO* 3.8 23.7 - - - +
230D PRO* 4.1 6.8 - - - +
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Residues in contact with ILE 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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21D SER 3.4 0.8 + - - -
22D GLY* 1.3 71.2 - - - -
24D GLY* 1.3 53.8 + - - +
26D ALA* 3.1 6.3 + - - +
27D VAL* 2.7 46.6 + - + +
103D CYS* 4.1 13.5 - - + -
154D ILE* 4.7 10.8 - - + -
199D PRO* 4.4 12.8 - - + -
202D ILE* 4.4 13.2 - - + -
204D THR* 3.9 17.2 - - + +
230D PRO* 4.5 4.5 - - + +
233D VAL* 3.7 46.9 - - + -
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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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16D VAL* 3.4 7.5 - - - +
18D GLY 3.2 18.9 + - - -
19D ALA* 3.5 9.0 - - - -
21D SER 3.4 3.2 + - - -
22D GLY 3.3 0.6 - - - -
23D ILE* 1.3 79.5 - - - +
25D ARG* 1.3 58.6 + - - +
27D VAL* 3.6 0.6 + - - +
28D SER* 2.9 27.0 + - - -
103D CYS* 3.6 24.2 - - - +
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Residues in contact with ARG 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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19D ALA 3.5 14.6 + - - +
20D GLY 2.7 21.9 + - - -
21D SER* 3.4 27.2 + - - +
22D GLY 3.9 2.0 - - - +
23D ILE 3.3 0.4 - - - -
24D GLY* 1.3 73.4 - - - +
26D ALA* 1.3 61.8 + - - +
28D SER* 3.2 4.0 + - - -
29D VAL* 3.0 36.8 + - + +
47D ALA* 3.3 18.4 + - - +
50D GLU* 2.6 39.8 + - - +
51D THR* 3.0 24.2 + - + +
54D LEU* 4.1 18.1 - - + +
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Residues in contact with ALA 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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22D GLY 3.1 18.0 + - - +
23D ILE 3.1 3.6 + - - +
25D ARG* 1.3 77.7 - - - +
27D VAL* 1.3 57.9 + - - +
29D VAL* 3.5 8.3 + - - +
30D ARG* 3.0 28.2 + - - +
230D PRO* 3.6 36.8 - - + +
231D GLU* 4.3 8.7 - - + +
234D ALA* 3.5 4.9 - - + +
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Residues in contact with VAL 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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16D VAL* 3.9 13.7 - - + -
23D ILE* 2.7 37.6 + - + +
24D GLY* 3.7 6.1 - - - +
26D ALA* 1.3 70.9 - - - +
28D SER* 1.3 60.5 + - - +
30D ARG* 3.1 2.5 + - - +
31D LEU* 2.8 57.0 + - + +
101D VAL* 4.1 6.3 - - + -
103D CYS* 4.2 6.5 - - - -
234D ALA* 4.0 13.5 - - - -
237D VAL* 3.7 39.5 - - + -
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Residues in contact with SER 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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16D VAL* 3.7 6.4 - - - +
19D ALA* 3.4 17.0 - - - +
24D GLY 2.9 13.1 + - - -
25D ARG 3.2 9.1 + - - -
27D VAL* 1.3 79.6 - - - +
29D VAL* 1.3 55.8 + - - +
31D LEU* 4.7 0.2 - - - -
32D ALA* 3.0 31.7 + - - +
38D VAL* 3.4 32.3 - - - +
40D ALA* 4.6 0.2 - - - +
51D THR* 3.8 17.7 - - - -
55D LEU* 3.5 5.1 - - - +
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Residues in contact with VAL 29 (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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25D ARG* 3.0 28.1 + - + +
26D ALA* 3.7 7.2 - - - +
28D SER* 1.3 76.0 - - - +
30D ARG* 1.3 59.6 + - - +
32D ALA* 3.4 1.6 + - - +
33D GLY* 2.9 27.0 + - - -
51D THR* 5.4 0.7 - - + -
54D LEU* 4.5 17.7 - - + +
55D LEU* 3.7 17.7 - - + -
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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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5D LEU* 4.4 18.2 - - - +
8D ARG* 4.5 1.6 - - - +
26D ALA 3.0 18.2 + - - +
27D VAL* 3.5 4.5 - - - +
29D VAL* 1.3 78.8 - - - +
31D LEU* 1.3 61.5 + - + +
33D GLY* 3.3 3.6 + - - -
34D GLU* 2.3 66.4 + - - +
231D GLU* 4.9 3.2 + - - -
234D ALA* 3.5 29.6 - - + +
235D ASP* 2.5 41.8 + - - +
238D ALA* 3.8 11.4 - - + +
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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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9D LEU* 3.7 22.4 - - + -
14D ALA* 3.6 24.7 - - + -
16D VAL* 4.1 9.9 - - + -
27D VAL* 2.8 41.7 + - + +
30D ARG* 1.3 70.9 - - + +
32D ALA* 1.3 65.2 + - - +
34D GLU* 3.1 13.7 + - - +
35D GLY 3.6 0.2 + - - -
36D ALA* 3.2 28.9 + - + +
38D VAL* 4.0 11.2 - - + -
99D VAL* 4.2 4.0 - - + -
101D VAL* 4.2 10.3 - - + -
234D ALA 5.4 0.2 - - - +
237D VAL* 4.5 2.9 - - + -
238D ALA* 3.9 28.3 - - + +
241D ALA* 4.4 4.9 - - + -
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Residues in contact with ALA 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 SER 3.0 19.4 + - - +
29D VAL 3.8 3.8 - - - +
31D LEU* 1.3 76.7 - - - +
33D GLY* 1.3 60.8 + - - +
34D GLU 3.1 0.4 - - - -
35D GLY* 3.1 14.2 + - - -
36D ALA 3.3 12.0 + - - +
38D VAL* 3.8 2.6 - - + +
55D LEU* 3.9 20.9 - - + +
69D HIS* 3.6 29.6 + - + +
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Residues in contact with GLY 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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6D GLN* 3.7 17.5 - - - +
29D VAL 2.9 16.2 + - - -
30D ARG* 3.7 4.3 - - - -
31D LEU 3.2 0.4 - - - -
32D ALA* 1.3 76.4 - - - +
34D GLU* 1.3 58.8 + - - +
35D GLY 3.3 2.8 + - - -
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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