Contacts of the helix formed by residues 30 - 41 (chain D) in PDB entry 4HSZ
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 30 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D GLU* 3.0 31.8 + - - +
24D GLY* 5.6 0.6 - - - -
29D LEU* 1.3 78.8 - - - +
31D LYS* 1.3 60.3 + - - +
32D SER* 2.9 11.8 + - - -
33D GLU* 2.7 55.4 + - - +
34D LEU* 3.0 24.6 + - - +
59D MET* 4.1 2.7 - - - -
68D ASN 4.2 2.0 - - - +
69D GLU* 3.7 26.7 + - + +
101D CA 4.0 2.8 - - - -
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Residues in contact with LYS 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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30D ASN* 1.3 74.7 - - - +
32D SER* 1.3 65.9 + - - +
35D LYS* 3.1 21.0 + - - +
55D PHE* 3.2 20.8 - - + -
56D GLN* 2.7 42.0 - - + +
59D MET* 3.3 35.7 - - + -
68D ASN* 3.5 41.6 + - - +
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Residues in contact with SER 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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23D GLU* 3.9 19.9 + - - -
30D ASN* 2.9 9.9 + - - -
31D LYS* 1.3 78.2 + - - +
33D GLU* 1.3 62.5 + - - +
35D LYS* 3.2 22.0 + - - +
36D GLU* 3.3 9.0 + - - +
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Residues in contact with GLU 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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19D TYR* 3.0 30.9 - - - +
20D SER 2.8 13.1 - - - +
22D LYS* 4.3 11.4 - - + -
23D GLU* 2.7 32.6 + - - +
28D LYS 3.0 3.5 - - - +
29D LEU* 4.1 9.9 - - + -
30D ASN* 2.7 46.0 + - - +
32D SER* 1.3 73.1 - - - +
34D LEU* 1.3 63.1 + - - +
35D LYS 3.3 0.2 + - - -
36D GLU* 3.5 4.4 + - - +
37D LEU* 3.2 23.0 + - - +
101D CA 2.3 22.0 - - - -
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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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29D LEU* 4.0 28.6 - - + +
30D ASN 3.0 19.6 + - - +
33D GLU* 1.3 75.6 - - - +
35D LYS* 1.3 56.8 + - - +
37D LEU* 3.6 8.8 + - + +
38D LEU* 2.9 52.8 + - + +
55D PHE* 3.5 19.3 - - + -
58D LEU* 4.8 0.7 - - + -
59D MET* 3.2 33.9 - - + -
62D LEU* 4.0 27.1 - - + -
70D VAL* 4.6 8.1 - - + -
75D TYR* 6.0 2.2 - - + -
78D PHE* 5.4 4.0 - - + -
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Residues in contact with LYS 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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31D LYS 3.1 21.7 + - - +
32D SER* 3.2 13.2 + - - +
34D LEU* 1.3 72.3 - - - +
36D GLU* 1.3 61.8 + - - +
38D LEU* 3.1 5.4 + - - +
39D THR* 2.8 38.7 + - - +
50D THR* 3.2 28.9 + - + +
51D ASP 4.0 0.6 + - - -
52D GLU* 3.9 22.7 - - - +
55D PHE* 3.6 42.3 - - + +
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Residues in contact with GLU 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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19D TYR* 4.0 14.7 - - + -
22D LYS* 3.6 29.5 + - - +
32D SER 3.3 8.3 + - - +
33D GLU* 4.2 3.8 - - - +
35D LYS* 1.3 78.1 - - - +
37D LEU* 1.3 55.5 + - - +
39D THR* 4.3 5.6 - - - +
40D ARG* 2.6 80.8 + - + +
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Residues in contact with LEU 37 (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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5C LEU* 4.5 15.3 - - + -
15D THR* 3.6 22.4 - - + +
16D PHE* 4.3 4.5 - - - -
19D TYR* 3.6 43.3 - - + -
29D LEU* 4.2 16.2 - - + -
33D GLU 3.2 16.1 + - - +
34D LEU* 3.7 8.7 - - + +
36D GLU* 1.3 78.2 - - - +
38D LEU* 1.3 75.9 + - + +
41D GLU* 2.8 35.2 + - + +
42D LEU* 3.6 3.2 + - + -
75D TYR* 4.4 20.2 - - + -
78D PHE* 6.0 1.1 - - + -
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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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34D LEU* 2.9 37.3 + - + +
35D LYS* 3.6 3.4 - - - +
37D LEU* 1.3 92.3 - - + +
39D THR* 1.3 62.1 + - - +
42D LEU* 3.3 28.2 - - + +
46D LEU* 3.1 29.4 - - + +
55D PHE* 3.9 12.1 - - + -
58D LEU* 3.2 36.1 - - + -
78D PHE* 3.8 28.5 - - + -
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Residues in contact with THR 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 LYS* 2.8 25.8 + - - +
36D GLU* 3.8 6.7 - - - -
38D LEU* 1.3 80.3 - - - +
40D ARG* 1.3 64.3 + - + +
43D PRO* 3.6 21.7 - - - +
46D LEU* 3.7 20.0 - - + +
50D THR* 5.0 13.5 - - + +
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Residues in contact with ARG 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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3C CYS* 4.1 10.4 - - - +
19D TYR* 3.4 19.5 - - - +
36D GLU* 2.6 59.0 + - + +
39D THR* 1.3 79.0 - - + +
41D GLU* 1.3 64.3 + - - +
43D PRO* 3.9 7.5 - - - +
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Residues in contact with GLU 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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3C CYS* 3.6 8.3 - - - +
4C PRO* 4.3 21.0 - - - +
5C LEU* 3.9 19.3 + - + +
6C GLU* 3.3 18.9 - - - +
15D THR* 3.7 21.7 + - + +
18D LYS* 3.2 20.2 + - - -
19D TYR* 2.6 42.6 + - + +
37D LEU* 2.8 24.0 + - + +
40D ARG* 1.3 79.7 - - - +
42D LEU* 1.3 59.7 + - + +
43D PRO* 3.3 7.0 - - - +
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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