Contacts of the helix formed by residues 37 - 55 (chain D) in PDB entry 3HUU
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 37 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D GLU* 4.3 2.1 + - - +
34D ILE* 3.2 18.2 + - - +
35D ARG 3.1 1.5 - - - +
36D GLN* 1.3 76.8 - - - +
38D PRO* 1.3 68.6 - - - +
39D PHE* 2.9 33.1 + - - +
40D ASN* 2.8 33.7 + - - +
41D SER* 3.8 1.7 + - - -
208D ASP* 2.6 33.1 + - - -
209D VAL* 3.8 2.1 - - - +
210D MET* 3.7 21.9 - - + +
236D ASN* 3.7 6.6 + - - -
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Residues in contact with PRO 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C GLN* 3.7 35.7 - - + +
36D GLN 3.2 8.5 - - - +
37D ASN* 1.3 88.3 - - - +
39D PHE* 1.3 63.7 + - - +
40D ASN 3.0 0.2 - - - -
41D SER* 2.9 22.3 + - - +
42D ASP* 2.9 18.5 + - - +
209D VAL* 4.1 7.2 - - + -
236D ASN* 3.9 5.8 - - - +
238D SER* 3.5 25.4 - - - +
240D LEU* 3.8 25.6 - - + -
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Residues in contact with PHE 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ASN* 2.9 20.2 + - - +
38D PRO* 1.3 77.4 - - - +
40D ASN* 1.3 72.3 + - - +
42D ASP* 3.8 5.6 - - - +
43D VAL* 3.0 42.1 + - + +
88D LEU* 4.3 19.3 - - + -
110D VAL* 4.4 22.4 - - + -
124D ASN* 5.7 0.2 - - - -
208D ASP* 5.6 1.8 - - - +
236D ASN* 3.5 15.6 - - + +
253D ILE* 3.9 22.7 - - + -
255D PRO* 4.0 11.0 - - + -
258D LEU* 4.1 22.2 - - + -
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Residues in contact with ASN 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D GLN* 4.6 13.1 - - - +
34D ILE* 2.7 36.7 + - - +
35D ARG* 3.8 16.4 - - - +
37D ASN* 2.8 22.2 + - - +
39D PHE* 1.3 86.3 - - - +
41D SER* 1.3 65.0 + - - +
43D VAL* 3.2 8.5 - - - +
44D LEU* 3.1 26.6 + - - +
60D MET* 5.7 2.5 - - + +
88D LEU* 4.9 14.7 - - - +
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Residues in contact with SER 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ARG* 3.7 32.0 - - - -
36C GLN* 3.5 21.2 - - - +
41C SER* 6.2 4.3 - - - -
35D ARG 5.2 1.7 + - - -
37D ASN 3.8 2.0 + - - -
38D PRO* 2.9 19.4 + - - +
40D ASN* 1.3 78.1 - - - +
42D ASP* 1.3 56.7 + - - +
44D LEU* 3.5 8.7 + - - +
45D ASN* 3.0 29.8 + - - +
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Residues in contact with ASP 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ARG* 2.6 41.0 + - - +
36C GLN* 3.0 16.2 + - - -
38D PRO* 2.9 28.7 + - - +
39D PHE* 3.8 1.7 - - - +
40D ASN 3.2 0.2 - - - -
41D SER* 1.3 75.2 + - - +
43D VAL* 1.3 66.8 + - - +
45D ASN* 3.2 4.2 + - - +
46D GLY 3.1 16.1 + - - -
236D ASN* 4.4 5.0 + - - +
237D THR 4.7 4.2 - - - +
255D PRO* 3.3 36.0 - - + +
256D ASP* 3.8 12.5 - - + +
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Residues in contact with VAL 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D PHE* 3.0 31.7 + - + +
40D ASN* 3.2 18.2 - - - +
42D ASP* 1.3 76.6 - - - +
44D LEU* 1.3 70.7 + - + +
46D GLY 3.0 2.3 + - - -
47D ILE* 2.9 41.9 + - + +
88D LEU* 4.2 28.5 - - + -
110D VAL* 4.7 15.9 - - + -
255D PRO* 3.6 12.9 + - - +
258D LEU* 4.6 3.6 - - + -
259D GLY* 3.4 20.8 - - - +
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Residues in contact with LEU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU* 3.7 29.8 - - + -
60C MET* 3.7 14.1 - - + -
25D LEU* 3.7 28.7 - - + -
40D ASN 3.1 16.5 + - - +
41D SER* 3.7 8.5 - - - +
43D VAL* 1.3 83.9 - - + +
45D ASN* 1.3 58.1 + - - +
47D ILE* 3.3 8.0 + - + +
48D ASN* 2.9 56.9 + - - +
58D THR* 5.1 4.5 - - + -
60D MET* 4.0 18.6 - - + -
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Residues in contact with ASN 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C GLN* 5.3 2.8 + - - -
30C SER* 3.6 25.0 + - - -
35C ARG* 3.5 35.0 - - - +
61C THR 4.9 1.0 - - - +
62C VAL* 3.9 13.0 - - - +
41D SER 3.0 19.0 + - - +
42D ASP 3.2 4.9 + - - +
44D LEU* 1.3 77.5 - - - +
46D GLY* 1.3 61.3 + - - +
48D ASN* 3.5 6.2 + - - +
49D GLN* 3.0 48.0 + - - +
256D ASP* 5.0 6.1 - - - +
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Residues in contact with GLY 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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42D ASP 3.1 7.9 + - - -
43D VAL 3.0 7.8 + - - -
45D ASN* 1.3 76.6 - - - +
47D ILE* 1.3 64.4 + - - +
49D GLN* 3.2 21.1 + - - +
50D ALA 3.3 8.7 + - - -
256D ASP* 3.6 14.1 - - - -
260D PHE* 3.3 29.5 - - - -
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Residues in contact with ILE 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ILE* 5.7 0.4 - - + -
25D LEU* 3.9 42.2 - - + -
43D VAL* 2.9 26.0 + - + +
44D LEU* 3.7 9.4 - - + +
46D GLY* 1.3 74.8 - - - +
48D ASN* 1.3 61.0 + - - +
50D ALA* 3.2 2.8 + - - +
51D CYS* 2.8 45.7 + - - -
58D THR* 5.3 3.4 - - - +
86D ILE* 4.0 20.6 - - + -
88D LEU* 4.1 21.8 - - + -
259D GLY* 3.4 21.0 + - - +
262D ALA* 4.9 0.9 - - + -
263D GLY* 4.5 4.0 - - - -
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Residues in contact with ASN 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ARG* 4.1 3.2 - - - +
60C MET* 3.0 49.6 + - + +
62C VAL* 3.8 17.5 - - + -
44D LEU* 2.9 42.4 + - - +
45D ASN* 3.8 3.4 - - - +
47D ILE* 1.3 77.0 - - - +
49D GLN* 1.3 64.8 + - - +
51D CYS* 4.5 5.8 - - - +
52D ASN* 3.0 37.7 + - - +
58D THR* 4.5 13.1 - - - +
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Residues in contact with GLN 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C SER* 5.6 0.2 + - - -
62C VAL* 3.7 36.2 + - + +
64C GLU* 5.5 4.2 + - - -
45D ASN* 3.0 38.9 + - - +
46D GLY* 3.2 14.0 + - - +
48D ASN* 1.3 76.1 - - - +
50D ALA* 1.3 60.1 + - - +
52D ASN* 4.7 0.8 - - - +
53D VAL* 3.4 27.2 + - - +
256D ASP* 5.1 5.4 - - - +
260D PHE* 3.8 22.3 - - + +
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Residues in contact with ALA 50 (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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46D GLY 3.3 4.4 + - - +
47D ILE 3.2 6.8 + - - +
48D ASN 3.2 0.4 - - - -
49D GLN* 1.3 79.1 - - - +
51D CYS* 1.3 64.7 + - - +
53D VAL* 3.1 20.0 - - - +
54D ARG* 3.3 12.5 + - - +
260D PHE* 3.7 17.2 - - + +
263D GLY* 3.9 4.5 - - - -
264D ASN* 3.6 45.3 - - - +
267D ILE* 4.5 2.5 - - - -
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Residues in contact with CYS 51 (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 ILE* 4.1 26.7 - - - -
47D ILE* 2.8 39.7 + - - +
48D ASN* 4.3 4.3 - - - +
50D ALA* 1.3 74.5 - - - +
52D ASN* 1.3 63.9 + - - +
54D ARG 3.2 1.0 + - - -
55D GLY 2.9 5.7 + - - -
56D TYR* 2.8 45.1 + - + +
57D SER 4.7 5.6 - - - +
58D THR* 5.5 3.8 - - - -
263D GLY* 4.8 6.7 - - - -
267D ILE* 4.1 15.0 - - - -
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Residues in contact with ASN 52 (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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59C ARG* 2.9 43.4 + - - +
60C MET 2.9 27.7 + - - -
62C VAL* 4.4 5.6 - - + +
72C GLU* 4.3 7.8 + - - +
76C MET* 3.9 11.1 - - + +
48D ASN* 3.0 27.6 + - - +
49D GLN* 4.7 2.0 - - - +
51D CYS* 1.3 77.1 - - - +
53D VAL* 1.3 66.8 + - + +
55D GLY* 3.3 11.8 + - - -
56D TYR 4.1 1.0 - - - +
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Residues in contact with VAL 53 (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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49D GLN 3.4 17.2 + - - +
50D ALA* 3.1 20.9 - - - +
52D ASN* 1.3 79.2 - - + +
54D ARG* 1.3 67.0 + - + +
55D GLY 3.4 0.2 - - - -
260D PHE* 5.4 4.7 - - + -
264D ASN* 5.3 2.0 - - - +
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Residues in contact with ARG 54 (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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50D ALA 3.3 15.0 + - - +
51D CYS 3.2 2.5 + - - +
52D ASN 3.2 0.8 - - - -
53D VAL* 1.3 84.8 - - + +
55D GLY* 1.3 62.4 + - - +
56D TYR* 3.6 9.3 - - + -
264D ASN* 3.0 43.3 + - - +
267D ILE* 3.3 39.9 - - + +
268D ASP* 2.6 32.3 + - - -
271D ARG* 3.7 32.3 + - - +
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Residues in contact with GLY 55 (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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59C ARG* 4.7 9.5 + - - -
81C SER* 6.4 1.1 - - - -
21D LEU* 4.0 23.2 - - - +
51D CYS 2.9 3.5 + - - -
52D ASN 3.3 10.6 + - - -
53D VAL 3.4 1.2 - - - -
54D ARG* 1.3 79.8 - - - +
56D TYR* 1.3 62.7 + - - +
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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
------------------------------------------------------------
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