Contacts of the helix formed by residues 65 - 79 (chain A) in PDB entry 1SFE
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 LEU 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ALA* 2.7 17.4 + - - +
64A ASP* 1.3 71.0 + - - +
66A MET* 1.3 58.1 + - + +
68A GLN* 3.5 5.7 + - - +
69A GLN* 3.2 30.9 + - - +
72A ARG* 4.7 1.6 + - - -
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Residues in contact with MET 66 (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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15A ARG* 6.1 1.8 - - - +
30A GLU* 5.7 2.0 - - - +
64A ASP* 3.2 7.1 + - - +
65A LEU* 1.3 75.8 - - + +
67A PHE* 1.3 64.2 + - - +
69A GLN* 3.5 8.6 + - - +
70A HIS* 3.3 49.1 + - + +
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Residues in contact with PHE 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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15A ARG* 3.8 16.6 - - + +
16A TYR* 3.5 46.0 - - - -
17A ALA* 3.6 12.6 - - + -
28A VAL* 3.9 6.5 - - + -
30A GLU* 3.6 47.1 - - + +
35A ILE* 5.6 0.2 - - + -
61A ALA* 3.8 13.7 - - + -
64A ASP* 2.6 31.0 + - + +
66A MET* 1.3 70.7 - - - +
68A GLN* 1.3 87.2 + - - +
70A HIS* 3.1 4.4 + - + +
71A VAL* 3.0 43.0 + - + +
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Residues in contact with GLN 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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17A ALA* 4.2 15.4 - - - +
61A ALA 2.7 30.3 + - - +
62A PRO* 3.4 21.7 - - - +
64A ASP 3.0 18.1 + - - +
65A LEU* 4.0 5.6 - - - +
66A MET 3.4 0.2 - - - -
67A PHE* 1.3 93.5 - - - +
69A GLN* 1.3 58.8 + - - +
71A VAL* 3.7 9.8 + - - +
72A ARG* 3.3 33.3 + - - +
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Residues in contact with GLN 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 LEU 3.2 15.0 + - - +
66A MET* 3.6 12.1 - - - +
67A PHE 3.2 0.4 - - - -
68A GLN* 1.3 72.3 - - - +
70A HIS* 1.3 69.8 + - + +
72A ARG* 2.9 60.5 + - - +
73A GLU* 2.9 19.5 + - + +
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Residues in contact with HIS 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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30A GLU* 2.5 33.4 + - - +
35A ILE* 4.8 4.8 - - + +
66A MET* 3.3 39.8 + - + +
67A PHE* 3.1 9.1 + - + +
69A GLN* 1.3 80.5 - - + +
71A VAL* 1.3 51.4 + - - +
73A GLU* 3.1 9.0 + - - +
74A VAL* 2.8 39.7 + - - +
87A LEU* 3.4 37.3 - - + +
88A PRO* 5.9 3.6 - - + -
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA* 4.0 17.5 - - + +
19A ALA* 4.8 11.2 - - + -
28A VAL* 3.7 20.9 - - + -
67A PHE* 3.0 52.2 + - + +
68A GLN* 3.8 14.8 - - - +
69A GLN 3.2 0.2 - - - -
70A HIS* 1.3 75.0 - - - +
72A ARG* 1.3 60.9 + - + +
74A VAL* 3.4 7.0 + - - +
75A ILE* 2.8 38.3 + - + +
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Residues in contact with ARG 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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65A LEU 4.7 1.8 + - - -
68A GLN* 3.3 14.5 + - - +
69A GLN* 2.9 72.9 + - - +
71A VAL* 1.3 78.6 - - + +
73A GLU* 1.3 64.6 + - - +
75A ILE* 3.5 5.9 + - - +
76A ALA* 3.1 22.7 + - - +
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Residues in contact with GLU 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 GLN* 2.9 18.2 + - + +
70A HIS* 3.2 12.8 - - - +
72A ARG* 1.3 73.0 - - - +
74A VAL* 1.3 67.7 + - - +
76A ALA* 3.2 16.6 + - - +
77A SER* 3.3 11.6 + - - -
85A LEU* 4.4 7.9 - - + +
86A THR* 5.0 13.4 - - - +
87A LEU* 3.3 35.8 - - + +
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Residues in contact with VAL 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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28A VAL* 3.6 29.2 - - + -
35A ILE* 3.8 25.1 - - + -
38A ILE* 3.8 24.5 - - + -
70A HIS 2.8 25.0 + - - +
71A VAL 3.7 4.5 - - - +
73A GLU* 1.3 73.9 - - - +
75A ILE* 1.3 63.9 + - - +
77A SER* 3.1 4.9 + - - -
78A LEU* 3.1 25.2 + - + +
85A LEU* 3.9 16.1 - - + +
87A LEU* 3.7 16.4 - - + -
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Residues in contact with ILE 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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19A ALA* 3.8 16.6 - - + -
20A ASP 3.6 20.9 - - - +
21A CYS* 4.0 5.6 - - + -
26A CYS* 3.2 34.3 - - - -
28A VAL* 5.1 3.1 - - + -
71A VAL* 2.8 29.5 + - + +
72A ARG* 3.9 7.2 - - - +
73A GLU 3.3 0.2 - - - -
74A VAL* 1.3 72.3 - - - +
76A ALA* 1.3 63.7 + - - +
78A LEU* 3.1 10.4 + - + +
79A ASN* 2.9 43.0 + - - +
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Residues in contact with ALA 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 ARG 3.1 14.7 + - - +
73A GLU* 3.3 12.1 - - - +
75A ILE* 1.3 76.2 - - - +
77A SER* 1.3 63.8 + - - +
79A ASN* 3.3 5.8 + - - +
80A GLN* 3.2 37.0 + - - +
83A THR* 6.0 1.3 - - + -
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Residues in contact with SER 77 (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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73A GLU 3.3 4.7 + - - -
74A VAL 3.1 11.1 + - - -
76A ALA* 1.3 75.6 - - - +
78A LEU* 1.3 68.2 + - - +
80A GLN* 2.9 24.6 + - - +
83A THR* 2.9 35.1 + - - +
84A PRO 3.2 3.3 + - - -
85A LEU* 3.2 36.6 + - - +
142A ILE* 5.2 4.3 - - - +
143A VAL* 5.2 2.9 - - - -
172A ARG* 4.4 1.2 + - - -
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Residues in contact with LEU 78 (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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21A CYS* 4.7 12.8 - - + -
23A LEU* 3.9 8.4 - - - +
26A CYS* 4.0 26.5 - - + -
38A ILE* 3.9 33.7 - - + -
40A LEU* 5.0 1.8 - - + -
74A VAL* 3.1 26.6 + - + +
75A ILE* 3.1 15.7 + - + +
77A SER* 1.3 81.6 - - - +
79A ASN* 1.3 57.5 + - - +
141A ALA 4.3 2.5 - - - +
142A ILE* 4.0 35.1 - - + +
143A VAL* 4.6 7.0 - - + -
172A ARG* 2.9 26.8 + - - +
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Residues in contact with ASN 79 (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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20A ASP 4.9 0.4 + - - -
21A CYS* 3.1 13.0 - - - +
22A GLU* 2.4 71.5 + - - +
75A ILE* 2.9 42.0 + - - +
76A ALA* 3.3 5.5 + - - +
77A SER 3.3 0.2 - - - -
78A LEU* 1.3 74.5 - - - +
80A GLN* 1.3 62.4 + - + +
81A ARG 4.1 0.9 + - - -
172A ARG* 3.8 3.9 + - - -
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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