Contacts of the helix formed by residues 45 - 64 (chain D) in PDB entry 3UF2
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 ASP 45 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D LEU* 3.6 3.9 - - + +
44D LYS* 1.3 76.1 - - - +
46D PRO* 1.3 71.4 - - - +
47D VAL* 3.8 6.0 + - - +
48D CYS* 3.0 27.7 + - + +
49D TYR* 2.9 28.6 + - - +
137D LYS* 2.6 33.0 + - - -
142D SER* 3.5 17.1 + - - +
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Residues in contact with PRO 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D LYS 3.3 9.6 - - - +
45D ASP* 1.3 93.4 - - - +
47D VAL* 1.3 65.2 + - + +
49D TYR* 3.3 9.3 + - + +
50D LEU* 3.2 28.5 + - + +
123D GLU* 6.1 1.3 - - - +
127D LEU* 5.6 3.4 - - + -
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Residues in contact with VAL 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D ASP* 3.4 10.6 + - - +
46D PRO* 1.3 79.8 - - + +
48D CYS* 1.3 59.7 + - - +
50D LEU* 3.1 7.3 + - - +
51D LYS* 3.1 28.3 + - + +
127D LEU* 4.5 9.6 - - + -
134D ILE* 3.6 42.6 - - + +
135D PHE* 3.8 23.2 - - + -
137D LYS* 4.3 21.3 - - + +
139D CYS* 4.9 0.4 - - - -
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Residues in contact with CYS 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D LEU* 3.4 13.5 - - + +
45D ASP* 3.0 29.8 + - + +
46D PRO 3.4 0.4 - - - -
47D VAL* 1.3 75.1 - - - +
49D TYR* 1.3 63.2 + - - +
50D LEU 3.3 0.2 - - - -
51D LYS* 3.6 2.8 - - - +
52D LYS 3.2 15.8 + - - -
137D LYS* 3.7 6.1 - - - -
139D CYS* 2.0 57.9 - - + -
142D SER* 3.3 23.6 - - - -
143D PHE* 3.5 10.3 - - + -
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Residues in contact with TYR 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D PHE* 3.5 23.3 - + - -
38D VAL* 3.7 33.1 + - + +
40D GLN* 3.7 42.5 + - + +
43D LEU* 3.7 26.7 - - - +
44D LYS 5.0 0.4 - - - +
45D ASP 2.9 14.9 + - - +
46D PRO* 3.3 14.1 - - + +
47D VAL 3.1 0.2 - - - -
48D CYS* 1.3 79.5 - - - +
50D LEU* 1.3 69.6 + - + +
52D LYS* 3.5 1.6 + - - +
53D ALA* 2.8 44.9 + - + +
120D VAL* 5.2 4.0 - - + -
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Residues in contact with LEU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D PRO* 3.2 14.8 + - + +
47D VAL 3.1 3.0 + - - +
49D TYR* 1.3 88.2 - - + +
51D LYS* 1.3 65.4 + - - +
53D ALA* 4.1 2.4 - - + +
54D PHE* 3.2 25.1 + - - +
91D PHE* 3.6 4.9 - - - -
120D VAL* 4.1 16.2 - - + +
123D GLU* 4.0 38.1 - - + +
124D THR* 3.7 16.6 + - - +
127D LEU* 3.5 32.3 - - + -
135D PHE* 3.6 22.9 - - + -
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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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47D VAL* 3.1 18.5 + - + +
48D CYS* 3.6 8.1 - - - +
49D TYR 3.2 0.2 - - - -
50D LEU* 1.3 80.2 - - - +
52D LYS* 1.3 62.8 + - - +
54D PHE* 3.5 3.1 + - - +
55D LEU* 3.2 26.7 + - + +
91D PHE* 3.8 20.0 - - + -
92D THR* 2.7 37.2 + - - +
94D ASP* 2.9 17.5 + - - +
135D PHE* 3.5 32.7 + - + +
137D LYS 3.2 16.4 + - - +
139D CYS* 3.2 24.9 - - - -
143D PHE* 4.4 6.5 - - + -
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Residues in contact with LYS 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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38D VAL* 3.8 20.0 - - + -
43D LEU* 4.1 8.7 - - + -
48D CYS 3.2 13.1 + - - +
49D TYR 4.0 1.3 - - - +
51D LYS* 1.3 78.7 - - - +
53D ALA* 1.3 64.0 + - - +
55D LEU* 3.0 38.0 + - + +
56D LEU* 3.2 25.9 + - + +
100D LYS* 4.2 12.9 - - - +
101D ALA* 3.3 31.2 - - - +
102D CYS* 4.9 1.6 - - + -
103D VAL* 4.1 13.4 - - + +
143D PHE* 3.7 33.5 - - + -
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Residues in contact with ALA 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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37D PHE* 4.2 6.1 - - + -
38D VAL* 3.4 18.6 - - + +
49D TYR* 2.8 41.2 + - + +
50D LEU* 4.1 4.9 - - - -
51D LYS 3.4 0.2 - - - -
52D LYS* 1.3 73.2 - - - +
54D PHE* 1.3 57.4 + - - +
56D LEU* 3.3 2.9 + - - +
57D VAL* 3.0 33.9 + - - +
120D VAL* 4.0 19.1 - - + -
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Residues in contact with PHE 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 LEU 3.2 19.8 + - - +
51D LYS 3.8 2.5 - - - +
52D LYS 3.2 1.0 - - - -
53D ALA* 1.3 74.4 - - - +
55D LEU* 1.3 74.8 + - + +
57D VAL* 3.7 6.0 + - + +
58D GLN* 3.3 45.1 + - + +
84D SER* 3.9 13.2 - - - -
87D LEU* 3.5 41.3 - - + -
88D LYS* 4.0 20.6 - - + -
91D PHE* 3.7 35.4 - + + -
120D VAL* 4.4 16.1 - - + +
121D PHE* 4.4 12.3 - + - -
124D THR* 5.2 4.5 - - + +
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Residues in contact with LEU 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 LYS* 3.2 18.2 - - + +
52D LYS* 3.0 33.3 + - + +
54D PHE* 1.3 88.4 - - + +
56D LEU* 1.3 63.7 + - + +
58D GLN* 3.5 17.3 - - - +
59D ASP* 3.4 13.6 - - - +
88D LYS* 6.4 1.1 - - + -
91D PHE* 5.7 8.1 - - + -
143D PHE* 5.9 3.4 - - + -
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Residues in contact with LEU 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D GLU* 3.9 19.6 - - + +
37D PHE* 3.6 25.1 - - + +
38D VAL* 3.4 32.5 - - + +
52D LYS* 3.2 16.2 + - + +
53D ALA 3.3 4.7 + - - +
55D LEU* 1.3 76.8 - - + +
57D VAL* 1.3 65.2 + - - +
58D GLN 3.0 2.7 - - - -
59D ASP* 3.1 24.8 + - + +
60D ILE* 3.2 15.0 + - - +
100D LYS 5.9 0.7 - - - +
103D VAL* 4.1 31.4 - - + -
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Residues in contact with VAL 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D PHE* 4.1 15.9 - - + -
53D ALA 3.0 20.8 + - - +
54D PHE* 4.0 8.1 - - + +
55D LEU 3.4 0.4 - - - -
56D LEU* 1.3 76.4 - - - +
58D GLN* 1.3 60.1 + - - +
60D ILE* 3.2 9.0 + - - +
61D MET* 2.9 36.1 + - + +
117D VAL* 3.9 20.6 - - + -
120D VAL* 4.1 24.5 - - + -
121D PHE* 3.7 33.0 - - + -
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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 PHE* 3.3 46.6 + - + +
55D LEU* 3.5 11.9 - - - +
56D LEU 3.0 0.4 - - - -
57D VAL* 1.3 80.1 - - - +
59D ASP* 1.3 63.6 + - - +
61D MET* 3.2 23.5 + - - +
62D GLU* 3.1 24.8 + - - +
81D GLN* 5.0 4.0 + - - +
84D SER* 3.2 29.8 + - - -
88D LYS* 4.3 24.0 - - - +
121D PHE* 4.9 0.2 - - - -
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Residues in contact with ASP 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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55D LEU 3.4 15.2 - - - +
56D LEU* 3.1 17.0 + - + +
58D GLN* 1.3 78.2 - - - +
60D ILE* 1.3 58.6 + - + +
62D GLU* 4.5 4.0 - - - -
63D ASP* 3.0 46.2 + - - +
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Residues in contact with ILE 60 (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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35D PHE* 4.3 13.5 - - + -
36D GLU 4.1 12.6 - - - +
37D PHE* 3.7 33.2 - - + -
56D LEU 3.2 12.9 + - - +
57D VAL* 3.4 11.9 - - - +
58D GLN 3.2 0.2 - - - -
59D ASP* 1.3 79.8 - - + +
61D MET* 1.3 58.0 + - - +
64D THR* 3.0 15.2 + - - +
65D MET* 3.0 39.6 + - + -
113D LEU* 3.7 43.1 - - + -
117D VAL* 4.1 6.7 - - + -
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Residues in contact with MET 61 (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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57D VAL* 2.9 26.2 + - + +
58D GLN* 3.2 37.4 + - - +
60D ILE* 1.3 76.0 - - - +
62D GLU* 1.3 60.9 + - - +
65D MET* 3.4 46.4 - - + +
66D ARG* 5.0 0.7 - - - +
77D ILE* 3.9 17.5 - - + +
80D LEU* 4.0 29.2 - - - +
81D GLN* 4.3 20.1 + - + +
84D SER* 3.5 15.9 - - - +
117D VAL* 5.0 0.9 - - + -
121D PHE* 4.1 14.1 - - + -
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Residues in contact with GLU 62 (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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58D GLN 3.1 16.8 + - - +
59D ASP* 4.0 6.1 - - - +
60D ILE 3.3 0.2 - - - -
61D MET* 1.3 79.7 - - - +
63D ASP* 1.3 71.6 + - - +
66D ARG* 4.0 13.8 - - - +
81D GLN* 3.0 22.9 + - - +
85I LEU* 5.8 0.5 - - - +
88I LYS* 2.6 34.0 + - - +
93I LYS* 5.2 0.9 + - - -
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Residues in contact with ASP 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D ASP* 3.0 28.9 + - - +
62D GLU* 1.3 93.5 - - - +
64D THR* 1.3 64.4 + - - +
66D ARG* 3.2 31.3 + - - +
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Residues in contact with THR 64 (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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27C MET* 4.1 1.7 - - + +
28C GLU 3.5 16.3 - - - +
29C THR* 3.8 18.1 - - + +
33D ILE* 3.9 15.9 - - + -
34D THR 4.3 13.1 + - - +
35D PHE* 4.8 4.3 - - - +
60D ILE* 3.0 15.3 + - - +
63D ASP* 1.3 82.1 - - - +
65D MET* 1.3 61.5 + - - +
66D ARG 2.8 9.8 + - - -
113D LEU* 3.6 30.8 - - + +
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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) + - + + + + + -
------------------------------------------------------------
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