Contacts of the helix formed by residues 67 - 83 (chain A) in PDB entry 1E3S
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 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ASN* 3.1 16.3 + - - -
65A VAL 3.2 0.2 - - - -
66A THR* 1.3 79.9 + - - +
68A GLU* 1.3 63.3 + - - +
69A LYS* 3.5 6.6 + - - +
70A GLU* 3.1 39.5 + - - +
71A VAL* 3.2 23.7 + - - +
127A ASN* 3.7 2.7 - - - -
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Residues in contact with GLU 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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66A THR 3.8 3.8 + - - -
67A SER* 1.3 71.9 + - - +
69A LYS* 1.3 71.9 + - + +
72A GLN* 3.0 33.1 + - + +
127A ASN* 3.8 12.6 - - - +
130A ARG* 3.0 34.4 + - - +
131A LEU* 4.1 10.4 - - + +
111B LEU* 4.8 13.1 + - + +
112B GLU* 5.2 7.7 - - - +
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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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67A SER* 3.4 6.1 + - - +
68A GLU* 1.3 90.9 + - + +
70A GLU* 1.3 60.1 + - + +
72A GLN* 3.6 5.4 + - - +
73A ALA* 3.1 27.0 + - - +
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Residues in contact with GLU 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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43A PRO* 5.8 3.3 - - - +
62A PRO 4.8 5.0 - - - +
63A ALA* 3.5 25.2 - - + +
64A ASN* 2.9 36.1 + - - +
67A SER* 3.1 25.5 + - - +
69A LYS* 1.3 74.0 - - + +
71A VAL* 1.3 65.7 + - - +
73A ALA* 3.5 6.2 + - - +
74A ALA 3.1 18.0 + - - -
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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
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40A LEU* 4.9 10.5 - - + -
63A ALA* 4.6 4.7 - - + -
64A ASN 3.9 3.4 - - - +
65A VAL* 3.9 25.1 - - + +
67A SER 3.2 18.8 + - - +
70A GLU* 1.3 73.9 - - - +
72A GLN* 1.3 67.0 + - - +
74A ALA* 3.3 4.8 + - - +
75A LEU* 3.1 37.5 + - + +
127A ASN* 3.9 10.8 - - - +
128A VAL* 4.4 26.5 - - + -
131A LEU* 3.7 22.9 - - + -
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Residues in contact with GLN 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 GLU* 3.0 23.7 + - + +
69A LYS* 3.7 7.2 - - - +
71A VAL* 1.3 79.7 - - - +
73A ALA* 1.3 56.5 + - - +
75A LEU* 3.4 9.7 + - - +
76A THR* 3.0 39.4 + - - +
131A LEU* 3.8 33.6 - - + +
135A VAL* 5.3 5.0 - - - +
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Residues in contact with ALA 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 3.1 15.0 + - - +
70A GLU* 3.8 7.0 - - - +
71A VAL 3.3 0.2 - - - -
72A GLN* 1.3 74.9 - - - +
74A ALA* 1.3 61.4 + - - +
76A THR* 3.5 7.1 + - - -
77A LEU* 3.0 27.9 + - - +
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Residues in contact with ALA 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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14A VAL* 6.2 0.7 - - - -
38A VAL* 4.9 3.4 - - + +
40A LEU* 3.7 31.2 - - + -
61A ALA* 3.8 27.6 - - + +
62A PRO 5.2 1.1 - - - +
63A ALA* 4.3 4.7 - - + -
70A GLU 3.1 16.2 + - - +
71A VAL 3.3 1.8 + - - +
73A ALA* 1.3 76.8 - - - +
75A LEU* 1.3 61.5 + - - +
77A LEU* 3.4 5.8 + - - +
78A ALA* 3.2 22.9 + - - +
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Residues in contact with LEU 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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14A VAL* 4.3 23.3 - - + -
40A LEU* 5.2 3.6 - - + -
71A VAL* 3.1 25.6 + - + +
72A GLN* 3.9 10.8 - - - +
74A ALA* 1.3 73.1 - - - +
76A THR* 1.3 65.3 + - - +
78A ALA* 3.5 3.0 + - - +
79A LYS* 3.1 24.1 + - - +
85A ILE* 3.9 25.5 - - + +
128A VAL* 4.9 5.6 - - + +
131A LEU* 3.8 32.5 - - + +
132A VAL* 3.8 28.5 - - + +
135A VAL* 4.7 11.2 - - + +
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Residues in contact with THR 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 GLN* 3.0 26.7 + - - +
73A ALA* 3.8 7.8 - - - -
75A LEU* 1.3 76.2 - - - +
77A LEU* 1.3 58.1 + - - +
79A LYS* 3.4 4.2 + - - -
80A GLU* 3.0 54.9 + - + +
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Residues in contact with LEU 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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38A VAL* 6.1 0.4 - - + -
59A ILE* 4.3 17.3 - - + -
60A PHE 4.5 7.4 - - - +
61A ALA* 4.0 24.5 - - + -
62A PRO* 5.9 1.1 - - + -
73A ALA 3.0 16.6 + - - +
74A ALA* 3.6 5.4 - - - +
75A LEU 3.3 0.2 - - - -
76A THR* 1.3 76.3 - - - +
78A ALA* 1.3 57.0 + - - +
80A GLU* 3.4 9.0 + - + +
81A LYS* 2.9 45.4 + - + +
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Residues in contact with ALA 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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12A VAL* 5.1 1.5 - - + +
14A VAL* 4.1 17.7 - - + -
38A VAL* 3.7 30.1 - - + -
59A ILE* 5.1 1.6 - - - -
74A ALA 3.2 14.2 + - - +
75A LEU 3.7 5.8 - - - +
76A THR 3.3 0.2 - - - -
77A LEU* 1.3 78.1 - - - +
79A LYS* 1.3 57.4 + - - +
81A LYS* 4.7 0.7 - - - -
82A PHE* 2.9 38.1 + - + +
84A ARG 4.3 3.7 - - - +
85A ILE* 4.3 8.3 - - + -
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Residues in contact with LYS 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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75A LEU 3.1 17.5 + - - +
76A THR* 3.9 4.3 - - - +
78A ALA* 1.3 72.8 - - - +
80A GLU* 1.3 85.2 + - - +
83A GLY* 2.8 41.1 + - - +
84A ARG* 4.2 14.6 - - - +
85A ILE* 4.7 1.5 - - + +
135A VAL* 4.8 15.5 - - + -
138A GLN* 4.3 19.0 + - - +
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Residues in contact with GLU 80 (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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76A THR* 3.0 44.2 + - + +
77A LEU* 3.5 11.7 - - + +
79A LYS* 1.3 102.0 + - - +
81A LYS* 1.3 61.3 + - - +
83A GLY* 4.3 1.6 + - - -
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Residues in contact with LYS 81 (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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56A GLY 4.9 8.3 + - - -
59A ILE* 4.2 29.4 - - + +
77A LEU* 2.9 29.1 + - + +
80A GLU* 1.3 75.7 - - - +
82A PHE* 1.3 92.8 + - + +
83A GLY 3.7 0.2 - - - -
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Residues in contact with PHE 82 (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* 3.9 32.8 - - + +
36A THR* 4.1 32.1 - - + -
37A ALA 4.7 2.5 - - - -
38A VAL* 3.9 19.1 - - + -
56A GLY 4.7 11.4 - - - -
57A ASN* 4.7 9.9 - - - -
59A ILE* 3.8 35.7 - - + -
78A ALA 2.9 19.9 + - - +
81A LYS* 1.3 97.2 - - + +
83A GLY* 1.3 56.6 + - - +
84A ARG* 3.4 8.6 + - - +
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Residues in contact with GLY 83 (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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79A LYS* 2.8 30.2 + - - +
80A GLU 4.3 1.7 + - - -
81A LYS 3.7 1.4 - - - -
82A PHE* 1.3 76.3 - - - +
84A ARG* 1.3 62.3 + - - +
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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