Contacts of the helix formed by residues 38 - 55 (chain D) in PDB entry 5HMG
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 LEU 38 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ASP 3.9 21.3 - - - +
20D GLY* 4.8 1.1 - - - -
36D ALA* 3.7 12.3 + - + +
37D ASP* 1.3 77.7 + - - +
39D LYS* 1.3 61.5 + - + +
41D THR* 3.8 13.3 - - + -
42D GLN* 3.0 32.7 + - + +
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Residues in contact with LYS 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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37D ASP* 3.4 12.8 + - - +
38D LEU* 1.3 75.3 - - + +
40D SER* 1.3 66.1 + - - +
42D GLN* 3.4 4.4 + - - +
43D ALA* 3.1 21.3 + - - +
121D LYS* 4.9 18.7 - - - +
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Residues in contact with SER 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D TYR* 3.1 39.3 - - - +
37D ASP* 2.8 25.1 + - - -
39D LYS* 1.3 73.3 - - - +
41D THR* 1.3 67.7 + - - +
43D ALA* 3.3 8.5 + - - +
44D ALA 3.0 20.3 + - - -
114D GLU* 4.6 15.5 - - - +
118D LEU* 3.8 13.3 - - - +
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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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20D GLY* 3.8 9.3 - - - -
21D TRP* 2.9 40.0 + - + +
22D TYR* 3.3 14.7 + - - -
37D ASP 2.7 22.5 + - - -
38D LEU* 3.8 11.9 - - + -
39D LYS 3.3 0.8 - - - -
40D SER* 1.3 78.8 + - - +
42D GLN* 1.3 61.3 + - + +
44D ALA* 3.6 2.3 + - - +
45D ILE* 3.1 40.5 + - + +
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Residues in contact with GLN 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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38D LEU* 3.0 20.1 + - + +
39D LYS* 3.9 4.5 - - - +
41D THR* 1.3 76.1 - - - +
43D ALA* 1.3 56.0 + - - +
45D ILE* 2.8 23.9 + - - +
46D ASP* 2.8 74.3 + - - +
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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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39D LYS 3.1 11.8 + - - +
40D SER* 3.5 9.2 - - - +
42D GLN* 1.3 77.5 - - - +
44D ALA* 1.3 63.9 + - - +
46D ASP* 4.2 5.4 + - - +
47D GLN* 2.9 32.4 + - - +
114D GLU* 3.6 24.0 - - - +
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Residues in contact with ALA 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D TRP* 3.4 31.0 - - + -
22D TYR* 3.5 28.5 - - + +
40D SER 3.0 8.3 + - - +
41D THR 3.8 1.3 - - - +
43D ALA* 1.3 75.5 - - - +
45D ILE* 1.3 62.7 + - - +
47D GLN* 3.6 9.7 + - - +
48D ILE* 3.2 26.9 + - - +
110D LEU* 4.1 3.2 - - - +
111D THR* 4.5 4.9 - - + -
114D GLU* 4.2 5.8 - - + +
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Residues in contact with ILE 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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21D TRP* 3.5 35.7 - - + +
41D THR* 3.1 35.9 + - + +
42D GLN* 2.8 33.7 + - - +
44D ALA* 1.3 72.3 - - - +
46D ASP* 1.3 61.3 + - - +
48D ILE* 3.1 5.5 + - - +
49D ASN* 2.8 44.7 + - - +
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Residues in contact with ASP 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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30A THR 4.9 0.2 - - - +
42D GLN* 2.8 52.9 + - - +
43D ALA* 4.2 4.6 + - - +
45D ILE* 1.3 73.0 - - - +
47D GLN* 1.3 58.9 + - + +
49D ASN* 3.1 9.9 + - - +
50D GLY* 2.8 27.2 + - - -
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Residues in contact with GLN 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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30A THR* 3.4 30.3 + - + +
31A ASP* 6.1 1.1 - - - +
1B GLY 5.4 5.5 + - - -
43D ALA* 2.9 27.4 + - - +
44D ALA 3.8 3.1 - - - +
46D ASP* 1.3 74.9 - - + +
48D ILE* 1.3 65.3 + - - +
50D GLY* 3.1 1.8 + - - +
51D LYS* 3.1 20.5 + - - +
110D LEU* 3.7 37.3 - - + +
114D GLU* 3.3 26.4 + - - +
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Residues in contact with ILE 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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317C ALA 4.7 2.2 - - - +
318C THR* 3.7 48.9 - - + +
319C GLY 4.1 0.4 - - - +
330C NAG 5.1 1.3 - - - +
21D TRP* 3.6 35.4 - - + -
44D ALA 3.2 7.6 + - - +
45D ILE* 3.1 9.9 + - - +
47D GLN* 1.3 76.0 - - - +
49D ASN* 1.3 62.3 + - - +
51D LYS* 3.2 11.1 - - + +
52D LEU* 2.9 29.2 + - + +
107D THR* 4.0 15.5 - - + +
110D LEU* 4.3 9.4 - - + -
111D THR* 3.9 16.2 - - + -
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Residues in contact with ASN 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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330C NAG 4.2 16.6 + - - -
45D ILE* 2.8 38.0 + - - +
46D ASP* 3.1 11.7 + - - +
48D ILE* 1.3 75.5 - - - +
50D GLY* 1.3 52.4 + - - +
52D LEU* 3.1 9.4 + - - +
53D ASN* 2.7 48.8 + - - +
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Residues in contact with GLY 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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30A THR 3.2 24.2 - - - -
46D ASP 2.8 13.7 + - - -
47D GLN 3.1 1.9 + - - -
49D ASN* 1.3 77.1 - - - +
51D LYS* 1.3 62.5 + - - +
53D ASN* 3.1 9.0 + - - +
54D ARG* 3.1 23.4 + - - +
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Residues in contact with LYS 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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29A ILE* 3.5 22.4 - - + +
30A THR* 3.8 15.6 + - + +
316C LEU* 5.6 7.2 - - + -
317C ALA 5.5 2.9 - - - +
47D GLN 3.1 9.4 + - - +
48D ILE* 3.2 18.2 - - + +
50D GLY* 1.3 73.2 - - - +
52D LEU* 1.3 67.4 + - + +
54D ARG* 3.1 3.9 + - - +
55D VAL* 3.1 25.4 + - - +
103D GLU* 2.8 40.7 + - + +
106D HIS* 2.7 35.1 + - - -
107D THR* 2.9 28.7 + - + +
110D LEU* 4.1 7.9 - - - -
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Residues in contact with LEU 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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40C THR* 3.7 16.8 - - + +
316C LEU* 3.7 24.7 - - + -
318C THR* 3.7 9.0 - - + -
330C NAG 3.3 35.9 - - - +
48D ILE 2.9 18.4 + - - +
49D ASN* 3.1 16.4 + - - +
51D LYS* 1.3 78.9 - - + +
53D ASN* 1.3 65.5 + - - +
55D VAL* 3.1 8.7 - - - +
56D ILE* 3.0 43.1 + - + +
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Residues in contact with ASN 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 ASN* 2.7 33.4 + - - +
50D GLY* 3.1 6.5 + - - +
52D LEU* 1.3 77.1 - - - +
54D ARG* 1.3 62.3 + - - +
56D ILE* 3.3 15.8 + - + +
57D GLU* 3.2 25.1 + - - +
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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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27A LYS* 3.3 35.8 - - - +
28A THR 3.0 21.2 + - - -
29A ILE 4.1 11.7 - - - +
31A ASP 4.2 7.2 + - - +
32A ASP* 4.2 17.7 - - - +
97B GLU* 2.8 35.5 + - - +
101B ALA* 3.6 20.9 - - - +
50D GLY 3.1 11.0 + - - +
51D LYS 3.1 7.4 + - - +
53D ASN* 1.3 76.7 - - - +
55D VAL* 1.3 63.9 + - - +
57D GLU* 3.3 48.1 + - - +
58D LYS* 4.0 2.8 - - - +
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Residues in contact with VAL 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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42C LEU* 4.3 16.2 - - + -
293C PRO* 3.5 23.7 - - + +
316C LEU* 3.7 28.5 - - + -
51D LYS 3.1 12.6 + - - +
52D LEU 3.1 15.3 - - - +
54D ARG* 1.3 77.2 - - - +
56D ILE* 1.3 67.3 + - + +
57D GLU 3.5 4.1 + - - +
99D LEU* 3.8 32.3 - - + -
103D GLU* 4.9 8.7 - - - +
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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