Contacts of the helix formed by residues 45 - 58 (chain A) in PDB entry 1FS6
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 PRO 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A PRO* 3.8 27.6 - - + +
41A THR* 3.5 23.8 - - - +
42A GLY 3.2 19.1 - - - +
44A THR* 1.4 95.2 - - + +
46A MET* 1.3 62.3 + - - -
47A THR 3.5 0.7 - - - -
48A THR* 3.0 5.5 + - - -
49A TYR* 3.0 45.2 + - + -
88A PHE* 4.4 0.2 - - + -
135A MET* 4.3 2.7 - - + -
202A LEU* 3.8 15.0 - - + -
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Residues in contact with MET 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 GLY 3.6 11.9 + - - +
43A GLY* 2.9 33.9 - - - +
44A THR 3.1 1.4 - - - -
45A PRO* 1.3 78.4 - - - +
47A THR* 1.3 67.3 + - + +
49A TYR* 3.4 3.8 + - + +
50A LYS* 3.1 23.6 + - + +
88A PHE* 3.6 19.5 - - + -
92A ASN* 3.0 34.3 - - + +
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Residues in contact with THR 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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9A ALA* 2.7 46.1 + - + +
10A GLU* 3.9 21.4 - - + +
12A VAL* 5.1 0.9 - - - +
13A GLY* 3.4 10.1 + - - -
44A THR 4.2 8.2 + - - -
46A MET* 1.3 81.4 - - + +
48A THR* 1.3 59.6 + - - +
50A LYS* 3.6 15.3 - - + +
51A ALA* 3.0 28.2 + - - +
204A LEU* 5.0 2.3 - - - +
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Residues in contact with THR 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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12A VAL* 5.2 0.3 - - - +
13A GLY* 3.4 19.1 - - - -
16A ALA* 3.6 15.7 - - + +
17A ALA* 3.6 26.6 - - - +
20A ILE* 4.3 5.6 - - + -
44A THR 4.8 0.3 + - - -
45A PRO 3.0 10.6 + - - -
47A THR* 1.3 78.8 + - - +
49A TYR* 1.3 60.9 + - - +
51A ALA* 3.1 2.4 + - - +
52A LEU* 2.8 31.6 + - + +
135A MET* 3.9 24.9 - - + -
202A LEU* 3.7 15.9 - - - +
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Residues in contact with TYR 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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39A LEU* 3.3 26.5 - - + +
40A PRO* 2.6 43.7 + - + +
45A PRO* 3.0 37.1 + - + +
46A MET* 3.8 5.8 - - + +
48A THR* 1.3 76.2 - - - +
50A LYS* 1.3 57.4 + - - +
52A LEU* 3.6 12.0 - - + +
53A VAL* 3.0 36.8 + - - +
88A PHE* 3.8 24.7 - + - -
89A MET* 3.5 17.7 - - + +
92A ASN* 3.6 23.1 - - + +
93A PHE* 3.8 26.4 - + + -
135A MET* 4.2 6.3 - - + -
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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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10A GLU* 3.2 37.6 + - - +
46A MET* 3.1 19.4 + - + +
47A THR* 3.6 13.1 - - + +
49A TYR* 1.3 79.8 - - - +
51A ALA* 1.3 60.2 + - - +
53A VAL* 3.5 6.5 + - - +
54A GLU* 3.2 41.4 + - + +
92A ASN 5.5 0.4 - - - -
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Residues in contact with ALA 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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10A GLU* 6.0 0.7 - - - +
13A GLY 3.6 6.7 - - - +
14A LYS* 3.9 17.9 - - + +
17A ALA* 3.4 22.7 - - + -
47A THR 3.0 18.4 + - - +
48A THR 3.1 0.4 + - - +
50A LYS* 1.3 76.9 - - - +
52A LEU* 1.3 64.3 + - - +
54A GLU* 3.2 17.1 + - - +
55A MET* 3.0 31.1 + - + +
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Residues in contact with LEU 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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17A ALA* 3.6 29.1 - - + +
20A ILE* 4.0 29.4 - - + -
21A VAL* 4.0 11.0 - - + -
37A LEU* 5.3 3.4 - - + -
39A LEU* 5.5 0.4 - - + -
48A THR* 2.8 24.2 + - + +
49A TYR* 3.6 22.0 - - + +
50A LYS 3.4 0.2 - - - -
51A ALA* 1.3 73.6 - - - +
53A VAL* 1.3 61.4 + - - +
55A MET* 3.5 4.5 + - - +
56A HIS* 3.0 23.4 + - - +
61A VAL* 4.4 2.1 - - - +
63A PHE* 3.8 21.8 - - + -
93A PHE* 3.9 29.6 - - + -
135A MET* 5.4 0.4 - - + -
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Residues in contact with VAL 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 TYR 3.0 25.3 + - - +
50A LYS* 3.7 7.2 - - - +
52A LEU* 1.3 73.3 - - - +
54A GLU* 1.3 60.5 + - + +
56A HIS* 3.2 6.9 + - - +
57A LYS* 2.9 48.4 + - + +
92A ASN 4.1 15.5 - - - +
93A PHE* 4.1 13.7 - - + -
96A HIS* 3.7 37.9 - - + +
97A VAL* 4.4 4.7 - - + -
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Residues in contact with GLU 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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10A GLU* 5.6 0.2 - - - +
14A LYS* 4.4 16.5 + - - +
50A LYS* 3.2 32.8 + - + +
51A ALA* 3.2 20.5 + - - +
53A VAL* 1.3 79.6 - - + +
55A MET* 1.3 53.2 + - + +
57A LYS* 3.1 9.1 + - - +
58A ALA* 2.8 35.9 + - - +
60A GLN* 5.1 0.2 - - - -
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Residues in contact with MET 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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14A LYS 5.1 1.3 - - - +
17A ALA* 4.0 7.2 - - - -
18A ARG* 3.9 35.0 - - + -
21A VAL* 3.6 36.8 - - + -
22A ASN* 5.5 0.7 - - - +
51A ALA* 3.0 18.7 + - + +
52A LEU* 3.8 4.9 - - - +
54A GLU* 1.3 76.3 - - + +
56A HIS* 1.3 53.6 + - - +
58A ALA 3.3 0.3 + - - -
59A GLY 3.2 4.2 + - - -
60A GLN* 2.7 70.0 + - - +
61A VAL* 4.0 10.3 - - + -
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Residues in contact with HIS 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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52A LEU 3.0 14.7 + - - +
53A VAL 3.4 7.6 - - - +
54A GLU 3.1 0.2 - - - -
55A MET* 1.3 74.7 - - - +
57A LYS* 1.3 64.9 + - + +
59A GLY* 2.8 24.9 + - - -
61A VAL* 2.7 35.1 - - - +
62A SER* 4.2 1.1 - - - -
63A PHE* 4.0 12.1 - + + -
96A HIS 3.2 19.2 + - - -
97A VAL* 3.4 29.7 - - + -
98A ASP* 3.4 30.8 + - + +
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Residues in contact with LYS 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 VAL* 2.9 35.6 + - + +
54A GLU* 3.6 6.3 - - - +
56A HIS* 1.3 79.1 + - + +
58A ALA* 1.3 57.3 + - - +
59A GLY* 2.9 9.2 + - - -
96A HIS* 2.9 40.0 + - - +
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Residues in contact with ALA 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 GLU 2.8 14.1 + - - +
55A MET 3.5 1.1 - - - +
56A HIS 3.1 0.2 - - - -
57A LYS* 1.3 76.1 - - - +
59A GLY* 1.3 61.0 + - - +
60A GLN* 3.3 33.5 + - + +
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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