Contacts of the helix formed by residues 52 - 65 (chain A) in PDB entry 4FAO
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 52 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A THR 4.2 1.1 - - - +
51A PRO* 1.3 76.6 - - - +
53A LYS* 1.3 65.7 - - - +
54A HIS* 3.4 6.6 + - - +
55A ALA* 2.9 26.6 + - - +
56A ILE* 3.0 21.0 + - - +
109A CYS 4.0 0.6 + - - -
110A ARG* 3.4 38.2 + - - +
79B LEU* 3.9 25.1 - - + +
101B GLY* 5.8 0.7 - - - -
73D HIS* 4.8 0.4 - - - -
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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
----------------------------------------------------------
52A THR* 1.3 71.8 - - - +
54A HIS* 1.3 65.6 + - - +
56A ILE* 2.8 20.5 + - + +
57A VAL* 2.9 17.8 + - + +
22B TRP* 6.1 2.7 - - + -
99B TYR* 3.8 14.8 - - + +
100B GLU 3.6 17.7 - - - +
101B GLY* 3.2 14.0 + - - +
102B MET* 4.0 17.7 - - - -
72D LEU 4.2 6.5 + - - -
73D HIS* 2.7 37.6 + - + +
75D GLU* 2.8 34.0 + - - +
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Residues in contact with HIS 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A THR* 3.1 6.9 + - - +
53A LYS* 1.3 75.2 - - - +
55A ALA* 1.3 66.8 + - - +
57A VAL* 3.0 8.4 + - + +
58A GLN* 2.8 58.0 + - + +
110A ARG 4.2 8.3 + - - -
13B LEU* 5.2 1.1 - - + +
32B TYR* 5.2 0.7 - - - -
34B ALA* 4.0 8.9 - - + +
35B TYR 2.9 25.0 + - - -
36B GLU* 5.2 0.4 - - - -
76B PRO* 4.4 7.0 - - + +
79B LEU* 4.2 12.8 - - + -
101B GLY 2.8 21.9 + - - +
102B MET* 3.5 27.8 - - - +
103B SER 4.2 1.6 - - - -
104B VAL* 3.4 22.2 - - + +
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Residues in contact with ALA 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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45A LEU* 4.4 10.5 - - + -
52A THR* 2.9 29.0 + - - +
54A HIS* 1.3 75.2 + - - +
56A ILE* 1.3 63.4 + - - +
58A GLN* 3.9 4.3 - - - +
59A THR* 2.9 27.8 + - - -
72A ALA* 4.3 9.6 - - + +
109A CYS 3.8 22.9 - - - +
110A ARG* 4.0 16.8 + - - +
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Residues in contact with ILE 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A PHE* 4.5 11.0 - - + -
45A LEU* 4.1 26.5 - - + +
51A PRO* 4.1 11.4 - - + -
52A THR 3.0 16.9 + - - +
53A LYS* 2.8 17.2 + - + +
55A ALA* 1.3 72.9 - - - +
57A VAL* 1.3 66.0 + - + +
59A THR* 3.1 3.4 + - - +
60A LEU* 2.9 25.2 + - + +
22B TRP* 4.9 7.0 - - + -
73D HIS* 4.1 26.2 - - + +
76D LEU* 4.1 37.2 - - + -
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Residues in contact with VAL 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LYS* 2.9 15.1 + - + +
54A HIS* 3.6 10.1 - - + +
56A ILE* 1.3 77.5 - - - +
58A GLN* 1.3 64.3 + - - +
60A LEU* 2.9 11.1 + - - +
61A VAL* 2.9 22.0 + - + +
13B LEU* 6.3 0.2 - - + -
15B VAL* 4.0 31.4 - - + -
17B PHE* 5.8 0.4 - - + -
20B ILE* 4.3 6.3 - - + -
22B TRP* 3.9 31.6 - - + -
32B TYR* 4.0 15.9 - - + +
34B ALA* 5.4 1.8 - - + -
102B MET* 4.2 20.0 - - + -
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Residues in contact with GLN 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 HIS* 2.8 48.1 + - + +
55A ALA* 3.9 4.3 - - - +
57A VAL* 1.3 75.3 - - - +
59A THR* 1.3 65.1 + - - +
61A VAL* 3.2 7.5 + - - +
62A HIS* 2.8 22.1 + - - +
69A VAL* 4.0 9.2 - - + -
70A GLY* 3.1 26.6 + - - +
71A LYS 3.7 13.2 + - - +
72A ALA* 4.8 5.2 - - + +
110A ARG* 4.9 5.6 + - - +
13B LEU* 4.8 9.6 - - + -
35B TYR 4.4 2.9 - - - +
36B GLU* 4.3 26.2 + - - +
37B CYS 5.0 4.9 + - - +
76B PRO* 5.3 1.4 - - - +
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Residues in contact with THR 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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41A CYS 4.3 10.0 + - - +
43A PHE* 3.4 44.2 - - + +
45A LEU* 4.1 12.9 - - + +
55A ALA 2.9 23.3 + - - -
56A ILE* 3.4 4.9 - - - -
58A GLN* 1.3 73.5 - - - +
60A LEU* 1.3 63.2 + - - +
62A HIS* 3.3 10.0 + - - +
63A LEU* 3.0 24.6 + - + +
71A LYS* 4.9 1.5 - - - +
72A ALA* 4.0 20.6 + - - +
58D GLU* 5.7 1.1 - - - +
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Residues in contact with LEU 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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43A PHE* 3.6 33.7 - - + -
56A ILE* 2.9 17.4 + - + +
57A VAL* 2.9 8.0 + - - +
59A THR* 1.3 71.7 - - - +
61A VAL* 1.3 66.7 + - - +
63A LEU* 2.8 36.4 + - + +
64A LYS 3.1 4.5 + - - -
20B ILE* 3.7 27.6 - - + +
22B TRP* 4.1 34.5 - - + +
76D LEU* 4.3 9.9 - - + -
84D PHE* 4.1 8.1 - - + -
85D VAL* 4.8 14.6 - - + -
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Residues in contact with VAL 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 VAL* 2.9 17.8 + - + +
58A GLN* 3.5 8.1 - - - +
60A LEU* 1.3 72.0 - - - +
62A HIS* 1.3 57.4 + - - +
64A LYS* 2.9 6.5 + - - +
65A PHE* 2.8 41.5 + - + +
69A VAL* 3.8 26.5 - - + -
13B LEU* 4.7 8.7 - - + -
14B ARG 6.2 0.4 - - - +
15B VAL* 4.0 32.5 - - + -
19B ASP* 6.3 1.3 - - + -
20B ILE* 3.7 19.9 - - + +
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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 GLN 2.8 15.9 + - - +
59A THR* 3.4 13.3 + - - +
61A VAL* 1.3 68.7 - - - +
63A LEU* 1.3 79.0 + - + +
65A PHE 3.0 0.6 + - - +
66A PRO* 2.9 49.2 + - + +
69A VAL* 2.7 40.9 - - + +
70A GLY* 3.7 7.6 - - - +
71A LYS* 3.4 54.4 + - + +
58D GLU* 5.7 0.4 + - - -
59D GLU* 4.3 6.1 - - - -
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Residues in contact with LEU 63 (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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43A PHE* 4.2 19.5 - - + -
59A THR* 3.0 20.1 + - + +
60A LEU* 2.8 35.0 + - + +
62A HIS* 1.3 81.2 + - + +
64A LYS* 1.3 57.4 + - - +
66A PRO* 3.7 10.8 - - - +
56D VAL* 4.3 11.4 - - + -
57D ARG 3.5 15.5 - - - +
58D GLU* 3.3 37.2 - - + +
84D PHE* 3.9 29.7 - - + +
85D VAL* 5.0 2.0 - - + -
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Residues in contact with LYS 64 (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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60A LEU 3.1 4.5 + - - +
61A VAL* 2.9 7.0 + - - +
63A LEU* 1.3 75.2 - - - +
65A PHE* 1.3 93.4 + - + +
66A PRO* 3.3 10.4 - - - +
18B GLU 5.0 1.0 + - - -
19B ASP* 3.4 45.2 + - + +
20B ILE* 5.8 0.4 - - + -
80D ARG* 5.9 1.4 - - - +
83D GLU* 3.6 32.7 + - + -
84D PHE* 3.2 22.9 - - + -
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Residues in contact with PHE 65 (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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61A VAL* 2.8 33.5 + - + +
62A HIS 3.0 3.6 + - - -
64A LYS* 1.3 114.4 - - + +
66A PRO* 1.3 54.5 - - - +
67A THR* 2.6 18.7 + - - -
68A LYS* 2.8 43.0 + - + -
69A VAL* 3.0 16.0 + - + +
19B ASP* 4.0 24.5 - - + -
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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