Contacts of the helix formed by residues 38 - 55 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ASP 3.9 21.1 - - - +
20B GLY* 4.8 1.3 - - - -
36B ALA* 3.7 12.3 + - + +
37B ASP* 1.3 77.7 + - - +
39B LYS* 1.3 60.8 + - + +
41B THR* 3.8 12.6 - - + -
42B GLN* 3.0 32.3 + - + +
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Residues in contact with LYS 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ASP* 3.4 12.4 + - - +
38B LEU* 1.3 79.0 - - + +
40B SER* 1.3 62.2 + - - +
42B GLN* 3.4 3.9 + - - +
43B ALA* 3.1 21.3 + - - +
121B LYS* 4.9 18.3 - - - +
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Residues in contact with SER 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR* 3.2 38.4 - - - +
37B ASP* 2.8 24.9 + - - -
39B LYS* 1.3 73.5 - - - +
41B THR* 1.3 68.4 + - - +
43B ALA* 3.2 8.5 + - - +
44B ALA 2.9 20.8 + - - -
114B GLU* 4.6 15.9 - - - +
118B LEU* 3.8 13.3 - - - +
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Residues in contact with THR 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLY* 3.8 9.7 - - - -
21B TRP* 2.9 46.8 + - + +
22B TYR* 3.3 14.5 + - - -
37B ASP 2.8 22.3 + - - -
38B LEU* 3.8 11.9 - - + -
39B LYS 3.3 0.6 - - - -
40B SER* 1.3 78.2 + - - +
42B GLN* 1.3 62.9 + - - +
44B ALA* 3.5 2.4 + - - +
45B ILE* 3.0 33.7 + - + +
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Residues in contact with GLN 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 3.0 20.1 + - + +
39B LYS* 3.8 4.7 - - - +
41B THR* 1.3 72.4 - - - +
43B ALA* 1.3 68.6 + - - +
45B ILE* 2.8 23.9 + - - +
46B ASP* 2.8 65.1 + - - +
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Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LYS 3.1 12.8 + - - +
40B SER* 3.2 9.6 + - - +
42B GLN* 1.3 77.4 - - - +
44B ALA* 1.3 63.0 + - - +
46B ASP* 4.2 5.3 + - - +
47B GLN* 2.9 31.0 + - - +
114B GLU* 3.6 24.5 - - - +
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Residues in contact with ALA 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B TRP* 3.4 32.1 - - + -
22B TYR* 3.5 28.0 - - + +
40B SER 2.9 8.1 + - - +
41B THR 3.7 1.3 - - - +
43B ALA* 1.3 76.2 - - - +
45B ILE* 1.3 62.5 + - - +
47B GLN* 3.6 9.7 + - - +
48B ILE* 3.1 27.2 + - - +
110B LEU* 4.0 3.0 - - - +
111B THR* 4.6 4.0 - - + -
114B GLU* 4.2 6.6 - - + +
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Residues in contact with ILE 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B TRP* 3.5 35.4 - - + +
41B THR* 3.0 35.8 + - + +
42B GLN* 2.8 33.5 + - - +
44B ALA* 1.3 72.2 - - - +
46B ASP* 1.3 60.8 - - - +
48B ILE* 3.2 5.3 + - - +
49B ASN* 2.8 44.3 + - - +
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Residues in contact with ASP 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLN* 2.8 52.5 + - - +
43B ALA* 4.2 5.2 + - - +
45B ILE* 1.3 73.3 - - - +
47B GLN* 1.3 57.6 + - + +
49B ASN* 3.1 9.9 + - - +
50B GLY* 2.8 27.0 + - - -
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Residues in contact with GLN 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ALA* 2.9 26.2 + - - +
44B ALA 3.8 2.9 - - - +
46B ASP* 1.3 75.7 - - + +
48B ILE* 1.3 63.6 + - - +
50B GLY* 3.0 9.8 + - - +
51B LYS* 3.1 11.6 + - - +
110B LEU* 3.7 36.6 - - + +
114B GLU* 3.3 26.2 + - - +
30E THR* 3.5 29.9 + - + +
31E ASP* 6.0 2.7 - - - +
1F GLY 5.3 6.6 + - - -
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Residues in contact with ILE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ALA 4.7 2.2 - - - +
318A THR* 3.6 47.3 - - + +
319A GLY 4.0 0.2 - - - +
330A NAG 5.1 3.1 - - - +
21B TRP* 3.6 36.1 - - + -
44B ALA 3.1 10.6 + - - +
45B ILE* 3.2 7.8 + - - +
47B GLN* 1.3 76.0 - - - +
49B ASN* 1.3 63.6 + - - +
51B LYS* 3.2 11.9 - - + +
52B LEU* 3.0 24.6 + - - +
107B THR* 4.0 16.6 - - + +
110B LEU* 4.3 9.9 - - + -
111B THR* 3.9 15.5 - - + -
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Residues in contact with ASN 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A NAG 4.2 17.0 + - - -
45B ILE* 2.8 33.7 + - - +
46B ASP* 3.1 11.4 + - - +
48B ILE* 1.3 78.8 - - - +
50B GLY* 1.3 52.8 + - - +
52B LEU* 3.1 10.6 + - - +
53B ASN* 2.7 48.1 + - - +
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Residues in contact with GLY 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ASP 2.8 13.5 + - - -
47B GLN 3.0 1.5 + - - -
49B ASN* 1.3 75.4 - - - +
51B LYS* 1.3 61.9 + - - +
53B ASN* 3.1 9.4 + - - +
54B ARG* 3.1 22.2 + - - +
30E THR 3.1 25.3 - - - -
31E ASP* 5.3 0.4 - - - -
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Residues in contact with LYS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A LEU* 5.7 7.0 - - + -
317A ALA 5.5 2.7 - - - +
47B GLN 3.1 8.5 + - - +
48B ILE* 3.2 18.8 - - + +
50B GLY* 1.3 73.9 - - - +
52B LEU* 1.3 68.2 + - - +
54B ARG* 3.1 3.3 + - - +
55B VAL* 3.0 25.1 + - - +
103B GLU* 2.8 41.0 + - + +
106B HIS* 2.7 34.5 + - - -
107B THR* 2.9 28.4 + - - +
110B LEU* 4.1 7.9 - - - -
29E ILE* 3.4 21.3 - - - +
30E THR* 3.6 16.5 + - + -
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A THR* 3.7 15.7 - - + -
316A LEU* 3.7 25.6 - - + -
318A THR* 3.7 10.1 - - + -
330A NAG 3.3 37.2 - - - +
48B ILE 3.0 18.0 + - - +
49B ASN* 3.1 16.1 + - - +
51B LYS* 1.3 78.8 - - + +
53B ASN* 1.3 64.8 + - - +
55B VAL* 3.1 8.8 - - - +
56B ILE* 3.0 41.9 + - + +
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Residues in contact with ASN 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ASN* 2.7 32.6 + - - +
50B GLY* 3.1 7.5 + - - +
52B LEU* 1.3 77.6 - - - +
54B ARG* 1.3 62.6 + - - +
56B ILE* 3.3 15.8 + - + +
57B GLU* 3.2 25.8 + - - +
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Residues in contact with ARG 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B GLY 3.1 11.0 + - - +
51B LYS 3.1 9.9 + - - +
53B ASN* 1.3 77.3 - - - +
55B VAL* 1.3 61.5 + - - +
57B GLU* 3.3 48.3 + - - +
58B LYS* 4.1 3.2 - - - +
27E LYS* 3.2 37.4 - - - +
28E THR 3.0 20.4 + - - -
29E ILE* 4.2 10.3 - - - +
31E ASP 4.1 7.2 + - - -
32E ASP* 4.0 19.4 - - - +
97F GLU* 2.8 34.9 + - - +
101F ALA* 3.7 20.9 - - - +
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Residues in contact with VAL 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 4.3 15.9 - - + -
293A PRO* 3.5 23.8 - - + +
316A LEU* 3.7 28.3 - - + -
51B LYS 3.0 12.0 + - - +
52B LEU* 3.1 15.0 - - - +
54B ARG* 1.3 78.8 - - - +
56B ILE* 1.3 65.1 + - + +
57B GLU 3.3 4.6 + - - +
99B LEU* 3.7 32.8 - - + -
103B GLU* 5.0 9.2 - - - +
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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