Contacts of the helix formed by residues 31 - 49 (chain D) in PDB entry 4H7Y
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 31 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D PRO 2.9 11.7 + - - -
30D LEU* 1.3 74.7 - - - +
32D ASP* 1.3 61.4 + - - +
33D ALA* 3.6 5.5 + - - +
34D LEU* 3.2 31.6 + - - +
35D LEU* 2.8 27.9 + - - +
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Residues in contact with ASP 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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30D LEU 5.2 0.7 - - - +
31D SER* 1.3 75.1 - - - +
33D ALA* 1.3 58.4 + - - +
35D LEU* 3.3 12.3 + - - +
36D ASN* 2.8 30.8 + - - +
74D GLN* 4.9 2.1 + - - -
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Residues in contact with ALA 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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31D SER* 3.4 5.7 + - - +
32D ASP* 1.3 78.8 - - - +
34D LEU* 1.3 59.6 + - + +
36D ASN* 3.2 6.7 + - - +
37D LYS* 2.9 49.2 + - - +
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Residues in contact with LEU 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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26D ASN 5.5 0.4 - - - +
27D SER* 3.9 34.4 + - - +
28D VAL 4.5 3.8 - - - +
29D PRO 3.7 20.2 - - - +
30D LEU* 4.1 9.7 - - + +
31D SER* 3.2 22.2 + - - +
33D ALA* 1.3 77.7 - - + +
35D LEU* 1.3 61.1 + - - +
37D LYS* 3.9 15.1 - - + +
38D LEU* 2.9 30.5 + - - +
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Residues in contact with LEU 35 (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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30D LEU* 3.7 34.2 - - + +
31D SER 2.8 19.3 + - - +
32D ASP* 3.5 11.2 - - - +
34D LEU* 1.3 75.1 - - - +
36D ASN* 1.3 58.2 + - - +
38D LEU* 3.4 2.7 + - + +
39D ILE* 3.0 49.3 + - + +
70D LEU* 4.1 21.8 - - + +
73D ILE* 4.0 17.0 - - + -
74D GLN* 3.7 36.1 - - + +
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Residues in contact with ASN 36 (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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32D ASP 2.8 17.6 + - - +
33D ALA* 3.2 8.0 + - - +
35D LEU* 1.3 78.0 - - - +
37D LYS* 1.3 58.2 + - + +
39D ILE* 3.6 5.0 + - - +
40D GLY* 3.0 23.7 + - - -
74D GLN* 2.7 30.9 + - - +
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Residues in contact with LYS 37 (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 LEU* 4.5 5.0 - - + +
33D ALA* 2.9 35.2 + - - +
34D LEU* 4.0 14.7 - - + +
35D LEU 3.3 0.2 - - - -
36D ASN* 1.3 76.3 - - + +
38D LEU* 1.3 66.4 + - - +
40D GLY* 3.2 3.1 + - - +
41D ARG* 3.0 23.0 + - - +
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Residues in contact with LEU 38 (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 LEU* 4.0 15.3 - - + +
23D LEU* 3.8 29.3 - - + +
24D GLU* 3.8 33.7 - - + +
27D SER* 5.3 2.7 - - - +
30D LEU* 4.3 14.8 - - + -
34D LEU 2.9 19.0 + - - +
35D LEU* 3.7 4.7 - - + +
37D LYS* 1.3 77.2 - - - +
39D ILE* 1.3 60.5 + - - +
41D ARG* 3.2 4.5 + - - +
42D TYR* 3.1 43.3 + - + -
70D LEU* 3.7 30.7 - - + -
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Residues in contact with ILE 39 (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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35D LEU* 3.0 28.0 + - + +
36D ASN* 3.7 5.6 - - - +
38D LEU* 1.3 76.3 - - - +
40D GLY* 1.3 56.1 + - - +
42D TYR* 3.0 10.0 + - - +
43D SER* 2.9 30.8 + - - +
67D PHE* 3.8 10.5 - - + +
70D LEU* 3.7 43.3 - - + +
71D LYS* 3.7 31.2 - - + +
74D GLN* 3.4 31.9 - - + +
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Residues in contact with GLY 40 (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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36D ASN 3.0 15.8 + - - -
37D LYS* 3.2 5.8 + - - -
39D ILE* 1.3 77.2 - - - +
41D ARG* 1.3 58.9 + - - +
43D SER* 3.4 10.3 + - - -
44D GLN* 3.2 27.3 + - - +
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Residues in contact with ARG 41 (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 TRP* 3.8 22.2 - - + -
19D LEU* 3.8 36.4 - - + +
20D LEU* 3.7 19.9 - - + +
23D LEU* 3.9 18.1 - - + +
37D LYS 3.0 11.9 + - - +
38D LEU 3.2 9.4 + - - +
40D GLY* 1.3 74.3 - - - +
42D TYR* 1.3 67.5 + - - +
44D GLN* 2.5 45.3 + - - +
45D ALA* 3.0 20.4 + - - +
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Residues in contact with TYR 42 (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 LEU* 4.8 5.5 - - + +
20D LEU* 3.7 45.5 + - + +
21D LEU* 4.7 8.7 - - - +
24D GLU* 4.3 5.7 + - - -
38D LEU* 3.1 37.7 + - + -
39D ILE* 3.0 10.0 + - - +
41D ARG* 1.3 77.1 - - - +
43D SER* 1.3 56.8 + - - +
45D ALA* 3.1 5.5 + - - +
46D ILE* 2.9 33.9 + - - +
63D ILE* 3.6 37.7 - - + -
66D ARG* 3.3 30.0 - - + +
67D PHE* 3.7 22.7 - - + -
70D LEU* 3.7 20.6 - - + -
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Residues in contact with SER 43 (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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47A GLU 5.1 1.2 + - - -
48A ALA* 6.0 2.0 - - - -
39D ILE* 2.9 13.2 + - - +
40D GLY* 3.5 12.9 - - - -
41D ARG 3.2 0.2 - - - -
42D TYR* 1.3 77.3 - - - +
44D GLN* 1.3 57.3 + - - +
46D ILE* 3.4 7.2 + - - +
47D GLU* 3.0 29.1 + - - +
67D PHE* 3.3 26.7 - - - -
71D LYS* 5.2 1.2 - - - -
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Residues in contact with GLN 44 (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 TRP* 4.1 12.9 - - + -
40D GLY 3.2 11.0 + - - +
41D ARG* 2.5 50.4 + - - +
43D SER* 1.3 75.0 - - - +
45D ALA* 1.3 64.3 + - - +
47D GLU* 3.4 5.5 + - - +
48D ALA* 3.1 25.8 + - - +
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Residues in contact with ALA 45 (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 TRP* 3.5 39.8 - - + -
20D LEU* 3.8 20.6 - - + -
41D ARG 3.0 7.1 + - - +
42D TYR 3.3 9.0 - - - +
44D GLN* 1.3 75.1 - - - +
46D ILE* 1.3 63.5 + - - +
48D ALA* 3.2 1.6 + - - -
49D LEU* 3.1 32.8 + - + +
63D ILE* 4.2 9.4 - - + -
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Residues in contact with ILE 46 (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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44A GLN* 3.0 29.1 + - + +
47A GLU* 3.8 36.6 - - + +
42D TYR 2.9 17.1 + - - +
43D SER* 3.8 5.8 - - - +
45D ALA* 1.3 78.3 - - - +
47D GLU* 1.3 59.4 + - - +
48D ALA 3.4 0.3 + - - -
49D LEU* 3.6 10.3 + - - +
51D PRO* 5.6 0.2 - - - +
60D PHE* 5.7 2.2 - - + -
63D ILE* 4.0 19.7 - - + +
64D GLN* 4.0 22.1 + - - +
67D PHE* 3.4 49.6 - - + -
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Residues in contact with GLU 47 (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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16A TRP* 3.3 19.6 - - - -
41A ARG* 2.8 42.6 + - - -
44A GLN* 3.3 18.1 + - - +
48A ALA* 5.9 0.3 - - - +
43D SER 3.0 17.6 + - - +
44D GLN* 4.0 6.7 - - - +
46D ILE* 1.3 77.8 - - - +
48D ALA* 1.3 58.1 + - - +
49D LEU 3.5 0.2 - - - -
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Residues in contact with ALA 48 (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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44A GLN* 4.7 0.2 - - - -
11D ASN* 2.8 43.9 + - - +
16D TRP* 4.0 13.7 - - + +
44D GLN 3.1 17.1 + - - +
45D ALA 3.2 4.9 + - - +
47D GLU* 1.3 79.8 - - - +
49D LEU* 1.3 58.1 + - - +
50D PRO* 3.3 8.9 - - - +
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Residues in contact with LEU 49 (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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44A GLN* 3.5 6.6 + - - -
11D ASN* 3.6 21.5 - - - +
12D ASN* 3.7 24.7 - - - -
13D PRO* 3.8 10.3 - - + -
16D TRP* 3.8 12.1 - - + -
45D ALA 3.1 20.9 + - - +
46D ILE* 3.6 4.4 + - - +
47D GLU 3.5 1.2 - - - -
48D ALA* 1.3 77.7 - - - +
50D PRO* 1.3 69.3 - - - +
51D PRO* 3.2 9.5 - - - +
54D TYR* 3.8 19.1 - - + -
60D PHE* 3.8 27.6 - - + -
63D ILE* 3.8 29.8 - - + -
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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