Contacts of the helix formed by residues 40 - 62 (chain A) in PDB entry 4FPR
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 THR 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A PRO* 1.3 77.3 - - - +
41A LYS* 1.3 64.6 + - - +
42A THR* 3.7 5.6 + - - -
43A GLU* 2.9 30.3 + - - +
44A ALA* 3.1 19.4 + - - +
69B ASP* 3.3 19.5 - - + +
144B HIS* 3.7 36.8 - - + +
146B HIS* 3.7 14.8 - - + +
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Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A PRO 4.0 1.5 + - - +
40A THR* 1.3 71.9 - - - +
42A THR* 1.3 62.2 + - - +
44A ALA* 3.4 7.0 + - - +
45A LEU* 3.0 25.5 + - - +
74A VAL* 4.7 3.4 - - + +
76A CYS* 4.0 40.2 + - + +
77A ALA 4.4 7.3 + - - -
78A PRO* 5.1 4.8 - - - +
69B ASP* 2.8 11.5 + - - +
71B THR* 4.0 5.9 - - + +
97B HIS* 3.5 52.7 - - + +
140B ARG* 5.8 4.3 - - - +
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Residues in contact with THR 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A THR* 3.0 6.7 - - - -
41A LYS* 1.3 78.7 - - - +
43A GLU* 1.3 64.4 + - - +
45A LEU* 3.4 3.4 + - - +
46A ASN* 3.0 23.4 + - + +
56B ILE* 5.8 1.8 - - + +
68B ILE 4.6 2.6 + - - -
69B ASP* 2.6 25.5 + - - -
70B MET 3.5 20.4 + - - +
71B THR* 4.2 7.8 - - - +
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Residues in contact with GLU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A TYR* 5.0 5.9 - - - -
39A PRO* 3.2 21.7 - - + +
40A THR* 2.9 39.8 + - - +
42A THR* 1.3 81.0 - - - +
44A ALA* 1.3 57.0 + - - +
46A ASN* 3.0 9.9 + - + +
47A ASP* 2.8 37.6 + - - +
146B HIS* 3.3 23.2 + - - -
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Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE* 5.4 0.9 - - - +
33A TYR* 3.5 22.3 + - + +
39A PRO* 4.6 3.8 - - + -
40A THR 3.1 12.4 + - - +
41A LYS* 3.7 8.7 - - - +
43A GLU* 1.3 78.1 - - - +
45A LEU* 1.3 57.3 + - - +
47A ASP* 3.2 3.5 + - - +
48A CYS* 2.9 28.8 + - - +
74A VAL* 4.2 8.7 - - + +
76A CYS* 3.7 30.3 - - - -
90A CYS* 4.0 3.3 - - + +
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Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LYS 3.0 17.6 + - - +
42A THR* 3.8 4.9 - - - +
44A ALA* 1.3 77.1 - - - +
46A ASN* 1.3 57.6 + - - +
48A CYS* 3.4 2.8 + - + +
49A ASN* 2.8 49.7 + - - +
72A ALA* 3.8 31.0 - - + +
73A LYS* 4.3 4.0 - - - -
74A VAL* 3.5 25.2 - - + +
49B ASN* 5.7 3.6 - - - +
71B THR* 4.1 26.5 - - + -
72B ALA 4.7 14.4 - - - +
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Residues in contact with ASN 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A THR* 3.0 16.5 + - + +
43A GLU* 3.0 13.7 + - - +
45A LEU* 1.3 75.7 - - - +
47A ASP* 1.3 64.9 + - - +
49A ASN* 3.1 10.7 + - - +
50A LYS* 3.1 46.9 + - - +
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Residues in contact with ASP 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE* 4.3 6.7 - - + -
33A TYR* 2.6 37.2 + - - +
43A GLU* 2.8 20.5 + - - +
44A ALA 3.5 7.4 - - - +
46A ASN* 1.3 73.4 + - - +
48A CYS* 1.3 59.5 + - - +
50A LYS* 2.8 53.6 + - - +
51A VAL* 3.5 7.3 + - - +
118A ILE* 3.7 18.6 - - + +
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Residues in contact with CYS 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE* 4.2 4.0 - - + +
44A ALA 2.9 16.0 + - - +
45A LEU* 3.5 10.3 - - + +
47A ASP* 1.3 77.7 - - - +
49A ASN* 1.3 56.1 + - - +
51A VAL* 3.1 23.7 + - - +
52A THR* 3.2 9.8 + - - -
72A ALA* 3.8 16.8 - - - -
73A LYS 3.8 14.1 - - - -
74A VAL* 4.4 6.5 - - + -
92A CYS* 2.0 56.6 - - + -
94A ILE* 4.0 1.6 - - - -
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Residues in contact with ASN 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU* 2.8 43.1 + - - +
46A ASN* 3.1 9.9 + - - +
48A CYS* 1.3 73.2 - - - +
50A LYS* 1.3 61.7 + - - +
51A VAL 3.3 0.2 - - - -
52A THR* 3.2 23.7 + - - +
53A LYS* 3.1 21.7 + - - +
71A THR* 5.5 0.3 - - - -
72A ALA* 3.3 14.8 + - - +
45B LEU* 5.8 5.4 - - - +
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Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ASN* 3.1 32.7 + - - +
47A ASP* 2.8 42.2 + - - +
49A ASN* 1.3 72.3 - - - +
51A VAL* 1.3 58.6 + - - +
53A LYS* 3.3 6.4 + - - +
54A GLY 2.9 22.9 + - - -
116A GLY* 3.5 22.3 - - - +
118A ILE* 4.4 11.2 - - + -
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE* 4.3 7.6 - - + -
47A ASP 3.6 10.1 - - - +
48A CYS* 3.2 15.3 - - - +
50A LYS* 1.3 71.4 - - - +
52A THR* 1.3 61.7 + - - +
54A GLY* 3.6 0.3 - - - -
55A LEU* 2.8 40.6 + - + +
92A CYS* 4.3 3.1 - - - -
94A ILE* 3.5 25.6 - - + -
116A GLY 3.1 20.0 - - - +
117A VAL* 4.3 4.0 - - - +
118A ILE* 3.7 19.1 - - + +
119A PHE* 3.9 27.4 - - + +
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Residues in contact with THR 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A CYS 3.2 8.4 + - - -
49A ASN* 3.2 31.2 + - - +
50A LYS 3.2 0.2 - - - -
51A VAL* 1.3 79.6 - - - +
53A LYS* 1.3 63.1 + - - +
55A LEU* 3.2 4.0 + - - +
56A ILE* 3.0 35.1 + - + +
70A MET* 3.9 36.7 - - + +
71A THR* 4.6 1.6 - - - +
72A ALA* 3.4 16.6 - - - +
94A ILE* 3.5 13.6 - - + +
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Residues in contact with LYS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ASN 3.1 10.1 + - - +
50A LYS* 3.7 9.2 - - - +
52A THR* 1.3 79.3 - - - +
54A GLY* 1.3 66.3 + - - +
56A ILE* 3.2 14.9 + - + +
57A ASP* 2.7 63.6 + - - +
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Residues in contact with GLY 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LYS 2.9 13.6 + - - -
51A VAL 3.3 4.0 + - - -
52A THR 3.3 0.4 - - - -
53A LYS* 1.3 79.0 - - - +
55A LEU* 1.3 58.7 + - - +
57A ASP* 3.3 7.9 + - - +
58A PHE* 3.0 27.2 + - - +
114A ALA* 5.5 1.6 - - - +
115A PRO* 3.4 25.3 - - - +
116A GLY* 4.4 1.8 - - - -
117A VAL* 4.4 5.2 - - - +
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ILE* 3.9 16.8 - - + -
51A VAL* 2.8 30.4 + - + +
52A THR 3.7 1.3 - - - +
54A GLY* 1.3 69.3 - - - +
56A ILE* 1.3 61.6 + - - +
58A PHE* 4.5 1.6 - - + -
59A SER* 2.8 32.1 + - - -
66A TRP* 3.6 23.0 - - + -
70A MET* 3.7 14.8 - - - -
94A ILE* 4.2 13.9 - - + -
111A PHE* 4.0 17.5 - - + -
117A VAL* 3.8 25.1 - - + -
119A PHE* 4.7 2.5 - - + -
131A TRP* 3.6 27.8 - - + -
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Residues in contact with ILE 56 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A THR* 3.0 33.0 + - + +
53A LYS* 3.2 14.1 + - + +
55A LEU* 1.3 75.7 - - - +
57A ASP* 1.3 63.5 + - - +
59A SER* 3.7 2.0 - - - -
60A GLN* 2.9 34.7 + - - +
67A GLY 4.9 0.2 - - - -
68A ILE* 4.0 37.4 - - + +
70A MET* 3.8 31.4 - - + +
42B THR* 5.7 2.9 - - + +
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Residues in contact with ASP 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LYS* 2.7 55.6 + - - +
54A GLY* 3.5 9.9 - - - +
56A ILE* 1.3 78.2 - - - +
58A PHE* 1.3 66.4 + - - +
60A GLN* 3.1 9.0 - - - +
61A SER* 3.0 25.3 + - - -
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Residues in contact with PHE 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLY 3.0 15.6 + - - +
55A LEU* 3.8 5.2 - - + +
57A ASP* 1.3 73.0 - - - +
59A SER* 1.3 67.3 + - - +
61A SER* 3.0 6.7 + - - -
62A HIS* 2.7 71.4 + + + -
66A TRP* 3.5 31.2 - + + -
106A ILE* 4.1 13.9 - - + -
110A SER* 3.4 34.3 - - - -
111A PHE* 3.6 18.8 - - + -
114A ALA* 4.1 16.4 - - + -
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Residues in contact with SER 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LEU 2.8 21.9 + - - -
56A ILE 3.7 2.5 - - - -
58A PHE* 1.3 73.2 - - - +
60A GLN* 1.3 54.3 + - - +
62A HIS* 2.9 17.9 + - - +
64A ARG* 2.8 33.1 + - - +
65A ALA* 4.6 1.3 - - - +
66A TRP* 3.0 39.8 + - - +
67A GLY 2.9 30.0 + - - -
70A MET* 4.0 1.1 - - - -
106A ILE* 6.4 0.2 - - - -
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Residues in contact with GLN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ILE* 2.9 24.2 + - - +
57A ASP* 3.1 10.8 - - - +
59A SER* 1.3 78.7 - - - +
61A SER* 1.3 59.1 + - - +
62A HIS 3.2 3.1 + - - -
63A GLN* 3.7 7.3 + - - -
64A ARG* 2.5 54.9 + - - +
68A ILE* 3.8 18.5 - - - +
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Residues in contact with SER 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ASP 3.0 12.7 + - - -
58A PHE* 3.1 13.2 + - - -
60A GLN* 1.3 75.2 - - - +
62A HIS* 1.3 74.5 + - - +
63A GLN* 3.7 1.6 + - - +
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Residues in contact with HIS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A PHE* 2.7 77.0 + + + +
59A SER* 2.9 6.4 + - - +
61A SER* 1.3 91.7 + - - +
63A GLN* 1.3 78.8 + - - +
64A ARG 3.4 0.7 + - - -
65A ALA* 3.4 14.2 + - - +
106A ILE* 4.5 16.0 - - + +
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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