Contacts of the helix formed by residues 41 - 59 (chain D) in PDB entry 4KEU
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 41 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40D TYR* 1.3 77.0 - - - +
42D GLU* 1.3 62.8 + - - +
43D ASP* 3.1 14.1 + - - +
44D GLU* 3.1 40.8 + - + +
45D GLU* 3.1 28.6 + - - +
47D ARG* 5.4 2.6 - - - +
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Residues in contact with GLU 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D ARG* 3.7 25.1 + - - +
33D ARG* 3.8 12.7 + - - +
40D TYR 4.0 1.6 + - - -
41D ASN* 1.3 70.6 + - - +
43D ASP* 1.3 64.6 + - - +
45D GLU* 3.4 9.3 + - - +
46D PHE* 2.8 30.3 + - + +
75D ASP* 4.8 2.9 - - - +
78D PHE* 3.9 17.9 - - + +
81D LYS* 5.0 13.6 + - - +
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Residues in contact with ASP 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D ASN* 3.1 9.5 + - - +
42D GLU* 1.3 79.9 - - - +
44D GLU* 1.3 64.1 + - - +
46D PHE* 3.3 5.7 + - - +
47D ARG* 3.0 44.4 + - - +
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Residues in contact with GLU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D ASN* 3.1 33.9 + - + +
43D ASP* 1.3 78.4 - - - +
45D GLU* 1.3 64.4 + - + +
47D ARG* 3.2 26.6 + - - +
48D ASN* 3.0 46.9 + - - +
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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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25D LEU 4.9 0.7 - - - +
26D ARG* 2.7 47.1 + - - +
33D ARG* 2.8 31.4 + - - -
40D TYR* 3.7 13.0 - - - -
41D ASN 3.1 24.8 + - - +
42D GLU* 3.4 7.7 - - - +
44D GLU* 1.3 77.8 - - + +
46D PHE* 1.3 62.2 + - - +
48D ASN* 3.6 1.6 + - - +
49D ALA* 3.2 24.1 + - - +
78D PHE* 3.7 5.7 - - + -
260D THR* 3.5 38.7 + - + +
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Residues in contact with PHE 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 GLU* 2.8 19.2 + - + +
43D ASP* 3.6 7.0 - - - +
45D GLU* 1.3 75.9 - - - +
47D ARG* 1.3 69.1 + - + +
49D ALA* 3.4 2.1 + - - +
50D VAL* 3.0 49.9 + - + +
78D PHE* 3.7 17.6 - + + -
81D LYS* 3.6 58.8 - - + +
82D VAL* 3.8 12.6 - - + -
85D ALA* 3.8 10.3 - - + -
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Residues in contact with ARG 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D ASN* 5.4 2.6 + - - +
43D ASP* 3.0 37.1 + - - +
44D GLU* 3.6 35.1 - - - +
46D PHE* 1.3 82.0 - - + +
48D ASN* 1.3 64.9 + - - +
50D VAL* 3.4 5.5 + - - +
51D ASN* 2.9 34.9 + - - +
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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
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44D GLU* 3.0 38.1 + - - +
45D GLU 3.9 3.4 - - - +
47D ARG* 1.3 77.7 + - - +
49D ALA* 1.3 64.8 + - - +
51D ASN* 2.7 22.6 + - - +
52D GLU* 3.2 18.2 + - + +
259D CYS* 3.7 27.1 + - + +
260D THR* 3.8 8.3 + - - +
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Residues in contact with ALA 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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25D LEU* 3.8 28.5 - - + +
45D GLU 3.2 16.0 + - - +
46D PHE 3.9 2.9 - - - +
48D ASN* 1.3 78.7 - - - +
50D VAL* 1.3 63.5 + - - +
52D GLU* 3.5 1.2 + - - +
53D VAL* 3.1 30.2 + - - +
78D PHE* 4.2 5.4 - - + -
82D VAL* 4.1 19.5 - - + -
259D CYS* 3.8 12.5 - - + +
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Residues in contact with VAL 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 PHE* 3.0 55.7 + - + +
47D ARG* 3.8 6.3 - - - +
48D ASN 3.2 0.2 - - - -
49D ALA* 1.3 76.3 - - - +
51D ASN* 1.3 59.8 + - + +
53D VAL 3.4 0.9 + - - -
54D LYS* 3.2 47.6 + - + +
82D VAL* 4.5 8.1 - - + -
85D ALA* 4.1 14.1 - - + +
86D THR* 3.7 18.8 - - + +
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Residues in contact with ASN 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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47D ARG* 2.9 18.0 + - - +
48D ASN* 2.7 34.6 + - - +
50D VAL* 1.3 75.8 - - + +
52D GLU* 1.4 69.4 + - - +
54D LYS* 3.5 16.5 - - + +
55D ARG* 3.1 26.0 + - - +
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Residues in contact with GLU 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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48D ASN* 3.2 20.1 + - + +
49D ALA 3.8 3.6 - - - +
51D ASN* 1.4 85.1 + - - +
53D VAL* 1.4 63.6 - - - +
55D ARG* 2.4 48.6 + - - +
56D ALA 3.0 17.2 + - - -
257D TYR* 3.7 27.8 + - + +
259D CYS* 3.9 14.8 - - + -
279D SER* 4.0 1.8 - - - -
280D ILE* 3.1 39.6 + - + +
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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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25D LEU* 3.6 27.4 - - + -
49D ALA 3.1 21.5 + - - +
50D VAL 3.7 4.5 - - - +
52D GLU* 1.4 77.5 - - + +
54D LYS* 1.3 57.6 + - - +
56D ALA* 3.1 9.3 + - - +
57D MET* 2.8 29.7 + - + +
64D ILE* 4.3 13.0 - - + -
82D VAL* 4.2 8.3 - - + -
86D THR* 3.7 19.3 - - + +
88D ILE* 3.7 35.4 - - + -
280D ILE* 5.0 2.9 - - + -
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Residues in contact with LYS 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 VAL* 3.2 32.6 + - + +
51D ASN* 3.5 20.4 - - + +
53D VAL* 1.3 76.6 - - - +
55D ARG* 1.3 61.3 + - - +
57D MET* 3.3 15.9 + - + +
58D GLN* 2.9 40.7 + - + +
85D ALA 3.9 18.0 + - - -
86D THR* 4.4 6.1 - - + +
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Residues in contact with ARG 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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51D ASN* 3.1 19.7 + - - +
52D GLU* 2.4 51.4 + - - +
53D VAL 3.2 0.2 - - - -
54D LYS* 1.3 76.8 - - - +
56D ALA* 1.3 63.9 + - - +
58D GLN* 3.1 29.3 + - - +
59D PHE* 3.2 27.1 + - + -
279D SER* 3.2 16.7 + - - -
280D ILE* 4.0 0.4 - - - +
281D THR* 2.9 40.7 + - + +
285D GLU* 4.8 2.7 + - - -
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Residues in contact with ALA 56 (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 LEU* 4.6 2.5 - - + -
52D GLU 3.0 14.0 + - - +
53D VAL* 3.2 12.6 - - - +
55D ARG* 1.3 76.3 - - - +
57D MET* 1.3 60.6 - - + +
59D PHE* 3.1 9.4 + - - +
60D GLY 3.3 0.2 + - - -
61D VAL* 3.0 45.9 + - + +
64D ILE* 4.6 3.8 - - + -
280D ILE* 4.1 20.2 - - + +
281D THR* 3.7 12.2 - - + +
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Residues in contact with MET 57 (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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53D VAL* 2.8 25.3 + - - +
54D LYS* 3.6 14.1 - - - +
55D ARG 3.2 0.2 - - - -
56D ALA* 1.3 77.7 - - + +
58D GLN* 1.3 56.7 + - - +
60D GLY* 3.0 18.7 + - - -
61D VAL 3.5 11.8 - - - +
62D LYS* 6.4 0.2 - - - -
86D THR* 3.5 28.9 - - - +
87D GLY 4.2 4.7 - - - +
88D ILE* 3.6 45.3 - - + +
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Residues in contact with GLN 58 (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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54D LYS* 2.9 31.6 + - + +
55D ARG* 3.1 23.7 + - - +
57D MET* 1.3 76.9 - - + +
59D PHE* 1.3 63.9 + - + +
60D GLY* 3.1 1.1 + - - -
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Residues in contact with PHE 59 (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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18D PHE* 5.9 1.0 - - - -
55D ARG* 3.2 32.1 + - + -
56D ALA 3.1 9.2 + - - +
58D GLN* 1.3 78.9 - - + +
60D GLY* 1.3 59.3 + - - +
61D VAL 3.6 0.7 - - - -
281D THR* 3.7 29.2 - - + -
284D PHE* 3.4 59.2 - + + -
285D GLU* 4.5 14.1 - - + -
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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
------------------------------------------------------------
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