Contacts of the helix formed by residues 36 - 46 (chain D) in PDB entry 2HVY
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 GLY 36 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D LYS* 1.3 73.0 - - - +
37D THR* 1.3 58.0 + - - -
39D GLU 3.4 0.7 + - - -
40D THR* 2.8 32.6 + - - -
97D ALA* 4.6 1.6 - - - +
99D SER 2.9 17.8 + - - -
31E A 3.6 18.3 + - - -
32E U 3.6 9.2 - - - -
33E G 3.2 12.1 - - - -
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Residues in contact with THR 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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36D GLY* 1.3 71.0 - - - -
38D ASN* 1.3 56.4 + - - +
40D THR* 3.9 0.3 - - - -
41D THR* 2.6 38.6 + - - +
63D ILE* 3.3 33.3 - - + +
64D VAL* 3.5 8.1 - - + +
66D HIS* 3.7 16.4 - - + -
67D LEU* 4.5 2.2 - - + -
98D ALA* 3.4 14.2 - - - +
99D SER* 3.3 17.9 + - - +
31E A 4.1 0.2 + - - -
32E U 2.7 31.0 + - - -
33E G 3.5 1.8 + - - -
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Residues in contact with ASN 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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41C TYR* 5.3 3.8 + - - -
37D THR* 1.3 77.4 - - - +
39D GLU* 1.3 57.6 + - - +
41D THR* 3.4 3.9 + - - -
42D LYS* 3.0 62.7 + - - +
21E G 4.4 13.5 + - - -
22E G 4.9 3.0 + - - -
23E U 4.7 3.8 + - - -
24E G 2.6 25.5 + - - +
33E G 3.2 22.8 + - + +
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Residues in contact with GLU 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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33D ILE 5.0 0.5 - - - +
34D ARG* 3.4 39.1 + - + +
35D LYS* 3.2 32.6 + - - +
38D ASN* 1.3 72.3 - - - +
40D THR* 1.3 65.7 + - - +
42D LYS* 3.5 7.0 + - - +
43D ALA* 3.1 23.7 + - - +
24E G 2.7 56.8 + - + +
31E A 4.1 0.5 - - - -
33E G 2.7 30.5 + - - +
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Residues in contact with THR 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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34D ARG* 3.5 2.7 + - - +
36D GLY 2.8 22.3 + - - -
37D THR 3.9 1.1 - - - -
39D GLU* 1.3 75.4 - - - +
41D THR* 1.3 62.9 + - - +
43D ALA* 3.3 4.3 + - - +
44D VAL* 3.1 27.0 + - - +
52D VAL* 3.8 22.4 - - + -
67D LEU* 4.4 6.7 - - + -
99D SER* 3.0 32.3 + - - +
100D VAL* 3.4 18.4 - - - +
101D ALA* 3.4 25.2 + - + -
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Residues in contact with THR 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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41C TYR* 3.4 40.8 - - + +
37D THR* 2.6 24.4 + - - +
38D ASN* 3.8 5.6 - - - -
40D THR* 1.3 73.8 - - - +
42D LYS* 1.3 59.7 + - - +
44D VAL* 3.3 4.8 + - - +
45D GLU* 2.9 26.5 + - - +
66D HIS* 2.9 31.2 + - - +
67D LEU* 3.7 12.2 - - - +
70D LEU* 3.7 10.9 - - + +
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Residues in contact with LYS 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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41C TYR* 3.0 21.9 + - - -
38D ASN* 3.0 50.8 + - - +
39D GLU* 3.8 7.0 - - - +
41D THR* 1.3 75.4 - - - +
43D ALA* 1.3 53.5 + - - +
45D GLU* 3.2 14.9 + - - +
46D ARG* 2.8 66.0 + - - +
21E G 2.6 31.5 + - - -
22E G 3.3 33.4 + - - +
23E U 5.0 2.9 - - - +
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Residues in contact with ALA 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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34D ARG* 4.3 4.7 - - + -
39D GLU 3.1 15.4 + - - +
40D THR 3.4 9.4 - - - +
42D LYS* 1.3 76.6 - - - +
44D VAL* 1.3 56.2 + - - +
46D ARG 3.6 0.3 + - - -
47D GLY 3.1 5.2 + - - -
48D GLN* 2.8 42.8 + - - +
49D ALA* 3.3 10.5 + - + -
101D ALA* 4.0 6.3 - - + -
103D ILE* 3.6 29.8 - - + -
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Residues in contact with VAL 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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40D THR 3.1 17.5 + - - +
41D THR 3.6 6.5 - - - +
43D ALA* 1.3 75.2 - - - +
45D GLU* 1.3 63.7 + - - +
47D GLY* 3.2 12.6 + - - -
49D ALA* 4.2 5.4 - - + -
52D VAL* 3.6 30.3 - - + -
67D LEU* 4.4 6.1 - - + -
70D LEU* 3.9 33.0 - - + +
71D CYS* 4.3 13.7 - - - +
74D LYS* 3.8 19.7 - - + +
76D ILE* 3.8 21.9 - - + +
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Residues in contact with GLU 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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40C PRO* 5.6 0.3 - - - +
41C TYR* 2.9 42.9 + - - -
44C TYR* 6.1 0.2 - - - -
41D THR 2.9 14.4 + - - +
42D LYS* 3.4 22.2 + - - +
44D VAL* 1.3 76.9 - - - +
46D ARG* 1.3 62.0 + - + +
70D LEU* 5.2 7.0 - - + -
74D LYS* 3.7 28.0 + - - +
22E G 5.3 0.7 + - - -
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Residues in contact with ARG 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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34D ARG* 5.5 7.9 - - - +
42D LYS* 2.8 36.5 + - - +
43D ALA 4.2 0.7 - - - +
45D GLU* 1.3 79.4 - - + +
47D GLY* 1.3 62.8 + - - +
48D GLN* 3.4 39.2 + - - +
22E G 2.8 34.8 + - - -
23E U 2.8 42.7 + - - -
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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