Contacts of the helix formed by residues 31 - 47 (chain C) in PDB entry 2HR3
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 ASP 31 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLN 4.2 0.6 - - - -
30C ALA* 1.3 75.4 - - - +
32C PRO* 1.4 75.6 - - + +
33C VAL* 3.0 11.2 + - - +
34C GLN* 3.1 42.7 + - - +
35C PHE* 3.4 6.2 + - - +
60D GLU 4.8 2.7 - - - -
61D ARG 3.9 15.1 + - - +
62D MSE 3.9 32.4 - - + +
63D ARG* 4.0 11.9 + - - +
66D ASN* 4.4 5.5 - - - +
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Residues in contact with PRO 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ARG* 5.9 4.3 - - - +
30C ALA 4.0 1.3 - - - +
31C ASP* 1.4 87.7 - - + +
33C VAL* 1.3 62.9 + - + +
34C GLN 3.6 0.2 - - - -
35C PHE* 3.3 32.4 - - + -
36C SER* 3.7 2.4 + - - -
36D SER* 3.7 22.3 - - - +
39D VAL* 3.3 36.3 - - + -
40D VAL* 5.1 1.3 - - + -
60D GLU* 4.6 9.9 - - - +
62D MSE 3.7 30.1 - - + -
70D LEU* 5.0 3.6 - - + -
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Residues in contact with VAL 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ASP* 3.0 11.2 + - - +
32C PRO* 1.3 77.2 - - - +
34C GLN* 1.3 62.6 + - - +
35C PHE 3.6 0.2 + - - -
36C SER* 3.8 9.9 + - - -
37C GLN* 3.4 16.8 + - - +
70C LEU* 4.9 2.6 - - + +
73C GLU* 4.7 13.0 - - - +
36D SER* 4.9 4.3 - - - +
62D MSE 4.5 2.0 - - + -
66D ASN* 4.1 22.9 - - + -
70D LEU* 3.9 32.1 - - + -
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Residues in contact with GLN 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C GLN 4.2 9.0 + - - +
30C ALA* 4.0 12.4 - - + +
31C ASP* 3.1 39.0 + - - +
33C VAL* 1.3 73.9 - - + +
35C PHE* 1.3 61.6 + - - +
37C GLN* 2.9 33.3 + - - +
38C LEU* 2.9 12.3 + - - +
63D ARG* 5.6 6.1 + - - -
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Residues in contact with PHE 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ARG* 3.9 33.2 - - - +
30C ALA* 4.7 10.5 - - + +
31C ASP 3.4 9.3 + - - +
32C PRO* 3.3 24.9 - - + +
33C VAL 3.3 0.2 - - - -
34C GLN* 1.3 78.1 - - - +
36C SER* 1.3 77.8 + - - +
38C LEU* 2.9 16.7 + - + +
39C VAL* 2.8 47.6 + - + +
111C ARG* 5.8 1.3 - - - +
25D ARG* 4.6 10.1 - - - -
32D PRO* 4.4 7.4 - - + -
35D PHE* 3.2 50.9 - + + -
36D SER* 4.6 2.5 - - - -
39D VAL* 5.8 0.2 - - + -
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Residues in contact with SER 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C PRO 3.7 6.1 + - - -
33C VAL* 3.9 10.8 - - - -
34C GLN 3.3 0.6 - - - -
35C PHE* 1.3 87.6 - - - +
37C GLN* 1.3 61.0 + - - +
39C VAL* 3.2 11.4 + - - +
40C VAL* 3.2 23.9 + - - +
70C LEU* 3.2 29.5 - - - +
32D PRO* 4.1 25.9 - - - +
33D VAL* 4.6 3.0 + - - +
36D SER* 5.6 3.4 - - - -
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Residues in contact with GLN 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C VAL* 3.4 19.3 + - - +
34C GLN* 2.9 22.9 + - - +
36C SER* 1.3 73.2 - - - +
38C LEU* 1.3 55.9 + - - +
40C VAL* 3.2 8.7 + - - +
41C LEU* 2.9 32.6 + - + +
70C LEU* 3.8 19.5 - - + +
73C GLU* 2.5 46.5 + - - +
74C LEU* 3.8 29.4 + - + +
79C LEU* 5.0 4.9 - - + +
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Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ALA* 5.3 2.5 - - + -
34C GLN 2.9 10.0 + - - +
35C PHE* 2.9 18.1 + - + +
37C GLN* 1.3 75.7 - - - +
39C VAL* 1.3 58.7 + - + +
41C LEU* 3.6 18.2 - - + +
42C GLY* 2.9 25.6 + - - -
103C ASN* 4.4 5.6 - - + +
104C LEU* 4.0 26.1 - - + +
107C ASN* 3.3 51.4 - - + +
111C ARG* 3.7 15.0 - - - +
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Residues in contact with VAL 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C PHE* 2.8 47.5 + - + +
36C SER* 3.2 11.4 + - - +
38C LEU* 1.3 76.6 - - + +
40C VAL* 1.3 57.2 + - + +
42C GLY* 3.5 2.5 + - - -
43C ALA* 3.0 25.6 + - - +
60C GLU* 3.1 32.1 - - + +
22D ARG* 4.3 9.1 + - - +
25D ARG* 5.1 4.7 - - - +
32D PRO* 4.0 15.9 - - + -
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Residues in contact with VAL 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C SER* 3.2 14.2 + - - +
37C GLN* 3.2 8.5 + - - +
39C VAL* 1.3 78.8 - - + +
41C LEU* 1.3 64.6 + - - +
43C ALA* 3.2 6.3 + - - +
44C ILE* 3.1 31.3 + - + +
56C LEU* 4.3 6.3 - - + -
60C GLU* 5.4 3.1 - - + -
62C MSE 4.5 10.5 - - - -
67C LEU* 4.2 20.4 - - + -
70C LEU* 4.3 16.8 - - + -
71C LEU* 4.0 19.7 - - + -
74C LEU* 3.8 21.3 - - + -
32D PRO* 5.8 0.2 - - + -
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Residues in contact with LEU 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C GLN* 2.9 18.0 + - + +
38C LEU* 3.4 28.9 + - + +
40C VAL* 1.3 76.5 - - - +
42C GLY* 1.3 62.5 + - - +
44C ILE* 3.3 5.2 + - - +
45C ASP* 3.2 22.7 + - - +
74C LEU* 3.8 25.6 - - + -
79C LEU* 4.1 14.8 - - + +
80C ILE* 4.1 11.7 - - + -
96C LEU* 3.5 28.4 - - + +
100C GLY* 4.2 18.2 - - - +
103C ASN* 4.4 12.6 - - + -
104C LEU* 3.8 13.7 - - + +
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Residues in contact with GLY 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LEU 2.9 19.3 + - - -
39C VAL* 3.7 3.1 - - - -
41C LEU* 1.3 71.6 - - - +
43C ALA* 1.3 52.8 + - - +
45C ASP* 3.3 4.7 + - - +
46C ARG* 2.8 36.1 + - - +
104C LEU* 4.0 5.0 - - - +
108C ARG* 4.0 22.8 + - - -
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Residues in contact with ALA 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C VAL 3.0 16.4 + - - +
40C VAL 3.2 2.8 + - - +
42C GLY* 1.3 73.6 - - - +
44C ILE* 1.3 57.8 + - - +
46C ARG* 2.9 20.3 + - - +
47C LEU* 2.8 37.3 + - + +
56C LEU* 3.4 26.7 - - + -
59C ALA* 5.5 0.4 - - + -
60C GLU* 3.7 23.1 - - + +
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Residues in contact with ILE 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C VAL* 3.1 28.1 + - + +
41C LEU 3.5 6.1 - - - +
42C GLY 3.2 0.2 - - - -
43C ALA* 1.3 77.6 - - - +
45C ASP* 1.3 54.5 + - - +
47C LEU* 3.6 2.1 + - - +
48C GLY 3.4 3.5 + - - -
49C GLY* 2.5 53.8 + - - -
50C ASP 4.2 1.2 + - - +
51C VAL* 4.4 12.0 - - + +
56C LEU* 4.2 17.7 - - + -
80C ILE* 3.6 21.3 - - + -
94C VAL* 3.6 28.0 - - + +
95C SER* 4.2 4.0 - - - -
96C LEU* 3.8 26.5 - - + +
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Residues in contact with ASP 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LEU 3.2 13.6 + - - +
42C GLY 3.7 3.0 - - - +
43C ALA 3.2 0.2 - - - -
44C ILE* 1.3 79.3 - - - +
46C ARG* 1.3 64.4 + - - +
48C GLY* 3.5 10.4 + - - -
49C GLY* 4.2 6.2 + - - +
96C LEU* 4.0 11.0 - - + -
104C LEU* 3.7 12.2 - - + +
105C TYR* 2.7 28.1 + - - -
108C ARG* 3.6 21.0 + - - -
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Residues in contact with ARG 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C GLY 2.8 17.1 + - - +
43C ALA* 2.9 18.7 + - - +
45C ASP* 1.3 81.3 - - - +
47C LEU* 1.3 77.4 + - - +
48C GLY* 3.2 3.6 + - - -
59C ALA* 3.9 17.0 + - - +
60C GLU* 3.1 13.1 + - - -
22D ARG* 2.9 39.1 - - - +
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Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ALA* 2.8 22.3 + - - +
44C ILE 3.6 0.2 + - - -
46C ARG* 1.3 101.0 - - - +
48C GLY* 1.3 59.0 + - - +
49C GLY 3.6 2.0 + - - -
50C ASP 5.0 1.4 + - - +
51C VAL* 3.6 32.7 - - + +
55C GLU* 4.0 35.7 - - + +
56C LEU* 4.4 6.7 - - + +
59C ALA* 4.3 14.4 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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