Contacts of the helix formed by residues 52 - 76 (chain A) in PDB entry 3F4M
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 SER 52 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LYS* 3.5 6.2 + - - -
50A THR* 3.1 12.2 + - - -
51A HIS* 1.3 80.5 - - - +
53A ARG* 1.3 62.1 + - - +
54A PRO* 3.4 10.9 - - - +
55A GLN* 3.0 49.5 + - - +
56A ALA* 3.1 20.4 + - - +
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Residues in contact with ARG 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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43A TYR* 3.4 25.7 + - - +
47A LYS* 4.2 26.9 - - + +
51A HIS 4.2 1.2 + - - -
52A SER* 1.3 72.3 - - - +
54A PRO* 1.3 72.4 - - + +
56A ALA* 3.3 2.4 + - - +
57A GLN* 2.9 56.2 + - - +
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Residues in contact with PRO 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A SER* 3.4 10.8 - - - +
53A ARG* 1.3 96.4 - - + +
55A GLN* 1.3 57.2 + - + +
57A GLN* 3.7 12.7 - - - +
58A ARG* 3.0 47.6 + - - +
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Residues in contact with GLN 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A SER* 4.7 0.7 - - - -
50A THR* 3.6 29.7 - - + +
52A SER* 3.0 35.7 + - - +
54A PRO* 1.3 76.3 - - + +
56A ALA* 1.3 63.5 + - - +
58A ARG* 3.3 13.0 + - - +
59A VAL* 3.1 31.8 + - + +
145A HIS* 5.0 0.2 - - - -
149A HIS* 5.1 4.7 - - + -
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TYR* 3.5 25.4 - - + +
46A SER* 3.5 23.5 + - - +
47A LYS* 3.6 22.9 - - + +
52A SER 3.1 14.1 + - - +
53A ARG 3.8 0.9 - - - +
55A GLN* 1.3 73.9 - - - +
57A GLN* 1.3 66.0 + - - +
59A VAL* 3.4 2.0 + - - +
60A ILE* 3.1 29.6 + - - +
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Residues in contact with GLN 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TYR* 3.7 20.0 + - + +
53A ARG* 2.9 61.5 + - - +
54A PRO* 3.7 10.6 - - - +
56A ALA* 1.3 75.3 - - - +
58A ARG* 1.3 57.4 + - - +
60A ILE* 3.8 2.7 - - - +
61A LYS* 2.9 30.7 + - - +
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Residues in contact with ARG 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A PRO* 3.0 36.0 + - - +
55A GLN* 3.5 13.2 - - - +
56A ALA 3.2 0.2 - - - -
57A GLN* 1.3 74.8 - - - +
59A VAL* 1.3 66.7 + - - +
61A LYS* 3.3 24.6 + - - +
62A ASP* 3.0 27.0 + - - +
145A HIS* 4.0 17.5 - - + +
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A SER* 4.6 1.6 - - - +
55A GLN* 3.1 17.8 + - + +
56A ALA* 4.0 4.3 - - - +
58A ARG* 1.3 76.3 - - - +
60A ILE* 1.3 58.4 + - + +
62A ASP 3.4 0.7 + - - -
63A LEU* 2.9 26.3 + - - +
145A HIS* 3.3 28.3 - - + +
146A VAL* 3.6 24.4 - - + +
149A HIS* 3.8 33.0 - - + +
150A PHE* 3.7 29.8 - - + -
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Residues in contact with ILE 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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39A LEU* 4.0 32.3 - - + +
42A LEU* 4.3 9.0 - - + -
43A TYR* 3.8 42.8 - - + +
46A SER* 5.8 0.9 - - - -
56A ALA* 3.1 17.2 + - - +
57A GLN* 4.0 3.4 - - - +
59A VAL* 1.3 74.1 - - + +
61A LYS* 1.3 66.1 + - - +
63A LEU* 3.6 6.3 - - + +
64A ILE* 3.0 40.0 + - + +
150A PHE* 4.3 16.2 - - + -
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Residues in contact with LYS 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 GLN 2.9 19.5 + - - +
58A ARG* 3.6 25.2 - - - +
60A ILE* 1.3 79.1 - - - +
62A ASP* 1.3 75.1 + - - +
64A ILE* 3.4 8.6 + - - +
65A LYS* 2.9 48.0 + - + +
142A ARG* 4.0 11.4 - - - +
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Residues in contact with ASP 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 ARG* 3.0 20.2 + - - +
59A VAL 3.7 1.1 - - - +
61A LYS* 1.3 80.4 + - - +
63A LEU* 1.3 66.8 + - - +
65A LYS* 3.4 4.6 + - - +
66A VAL* 2.9 30.0 + - - +
142A ARG* 2.7 52.9 + - + +
145A HIS* 2.8 26.8 + - - +
146A VAL* 3.7 17.9 - - + -
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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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39A LEU* 3.9 29.4 - - + -
42A LEU* 4.5 16.6 - - + -
59A VAL 2.9 17.1 + - - +
60A ILE* 3.6 15.3 - - + +
61A LYS 3.3 0.2 - - - -
62A ASP* 1.3 77.2 - - - +
64A ILE* 1.3 61.5 + - + +
66A VAL* 3.4 4.4 + - - +
67A ALA* 3.0 33.2 + - + +
146A VAL* 3.4 28.9 - - + +
150A PHE* 4.7 5.6 - - + -
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Residues in contact with ILE 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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31A ILE* 5.5 13.9 - - + -
39A LEU* 3.8 30.3 - - + -
60A ILE* 3.0 29.8 + - + +
61A LYS* 3.7 6.3 - - - +
63A LEU* 1.3 78.6 - - + +
65A LYS* 1.3 68.6 + - + +
67A ALA* 3.3 4.5 + - - +
68A ILE* 3.1 34.2 + - + +
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Residues in contact with LYS 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 LYS* 2.9 41.6 + - + +
62A ASP 3.4 4.2 + - - +
64A ILE* 1.3 81.3 - - + +
66A VAL* 1.3 62.8 + - - +
68A ILE* 3.3 4.2 + - - +
69A LYS* 2.9 49.3 + - - +
142A ARG* 3.7 41.8 - - - +
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Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASP 2.9 21.5 + - - +
63A LEU* 3.7 5.8 - - - +
65A LYS* 1.3 74.7 - - - +
67A ALA* 1.3 65.7 + - - +
69A LYS* 3.3 8.1 + - + +
70A VAL* 3.0 30.9 + - + +
127A LEU* 4.1 16.8 - - + -
135A LEU* 5.8 3.1 - - + -
139A SER* 4.3 5.4 - - - +
142A ARG* 3.7 28.7 - - + +
143A ILE* 3.7 34.3 - - + +
146A VAL* 5.2 1.3 - - + -
147A PHE* 6.0 1.3 - - + -
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Residues in contact with ALA 67 (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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63A LEU* 3.0 25.7 + - + +
64A ILE* 3.8 6.5 - - - +
66A VAL* 1.3 78.9 - - - +
68A ILE* 1.3 61.5 + - + +
70A VAL* 3.5 5.9 + - - +
71A ALA* 2.9 26.9 + - - +
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Residues in contact with ILE 68 (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* 6.5 0.9 - - + -
64A ILE* 3.1 30.2 + - + +
65A LYS* 3.9 4.7 - - - +
67A ALA* 1.3 78.5 - - + +
69A LYS* 1.3 62.4 + - + +
71A ALA* 3.1 10.9 + - + +
72A VAL* 2.9 39.5 + - + +
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Residues in contact with LYS 69 (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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65A LYS* 2.9 47.6 + - - +
66A VAL* 3.7 7.9 - - + +
68A ILE* 1.3 79.5 - - + +
70A VAL* 1.3 61.0 + - - +
72A VAL* 3.4 8.2 + - - +
73A LEU* 3.2 26.9 + - - +
135A LEU* 4.1 20.8 - - + +
139A SER* 3.5 29.5 + - - +
142A ARG* 4.8 10.5 - - - +
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Residues in contact with VAL 70 (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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66A VAL* 3.0 29.9 + - + +
67A ALA* 3.8 5.8 - - - +
69A LYS* 1.3 72.7 - - - +
71A ALA* 1.3 65.6 + - - +
73A LEU* 3.2 9.4 + - - +
74A HIS* 3.1 41.7 + - + +
79A PHE* 4.5 3.4 - - + -
127A LEU* 4.2 15.5 - - + -
130A LEU* 4.5 15.0 - - + -
131A VAL* 4.0 23.3 - - + -
135A LEU* 4.5 4.3 - - + -
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Residues in contact with ALA 71 (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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67A ALA 2.9 15.6 + - - +
68A ILE* 3.1 20.8 + - + +
70A VAL* 1.3 77.4 - - - +
72A VAL* 1.3 57.0 + - + +
74A HIS* 3.2 10.8 + - - +
75A ARG* 3.0 37.5 + - + +
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Residues in contact with VAL 72 (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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68A ILE* 2.9 33.1 + - + +
69A LYS* 3.7 8.3 - - - +
71A ALA* 1.3 75.2 - - + +
73A LEU* 1.3 61.4 + - + +
75A ARG* 3.2 11.0 + - + +
76A ASN* 2.9 47.9 + - - +
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Residues in contact with LEU 73 (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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69A LYS 3.2 15.3 + - - +
70A VAL* 3.2 10.4 + - - +
72A VAL* 1.3 77.0 - - + +
74A HIS* 1.3 61.6 + - - +
76A ASN* 3.5 0.4 + - - -
77A GLY* 3.3 2.8 + - - -
78A SER* 3.1 49.1 + - - +
79A PHE* 3.5 32.4 - - + -
131A VAL* 4.2 8.1 - - + -
134A HIS* 3.6 36.3 - - + +
135A LEU* 4.0 22.7 - - + -
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Residues in contact with HIS 74 (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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70A VAL* 3.1 36.9 + - + +
71A ALA* 3.2 10.7 + - - +
73A LEU* 1.3 77.5 - - - +
75A ARG* 1.3 62.2 + - + +
76A ASN 3.5 0.2 + - - -
77A GLY* 3.5 10.2 + - - -
79A PHE* 3.5 29.1 - + - -
84A LEU* 4.4 13.1 - - + +
87A ALA* 3.7 27.2 - - + +
130A LEU* 4.8 1.2 - - - +
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Residues in contact with ARG 75 (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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71A ALA* 3.0 26.2 + - + +
72A VAL* 3.2 11.6 + - - +
74A HIS* 1.3 76.8 - - + +
76A ASN* 1.3 69.3 + - - +
77A GLY 3.5 0.5 + - - -
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Residues in contact with ASN 76 (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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72A VAL* 2.9 37.0 + - - +
73A LEU 3.5 0.2 + - - -
74A HIS 3.3 0.2 - - - -
75A ARG* 1.3 85.4 + - - +
77A GLY* 1.3 63.2 + - - +
78A SER* 3.7 15.0 + - - +
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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
------------------------------------------------------------
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