Contacts of the helix formed by residues 67 - 83 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ASN* 3.1 14.7 + - - -
66B THR* 1.3 81.2 + - - +
68B GLU* 1.3 63.7 + - - +
69B LYS* 3.4 7.3 + - - +
70B GLU* 3.1 39.1 + - - +
71B VAL* 3.2 24.1 + - - +
127B ASN* 3.7 2.7 - - - -
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Residues in contact with GLU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 4.7 12.2 + - + +
112A GLU* 5.2 7.2 - - - +
66B THR 3.8 3.4 + - - -
67B SER* 1.3 70.6 + - - +
69B LYS* 1.3 76.2 + - + +
71B VAL* 4.0 0.9 - - - +
72B GLN* 3.0 27.4 + - + +
127B ASN* 3.8 12.2 - - - +
130B ARG* 2.8 35.2 + - - +
131B LEU* 4.2 9.6 - - + +
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Residues in contact with LYS 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B SER* 3.4 6.1 + - - +
68B GLU* 1.3 89.7 + - + +
70B GLU* 1.3 60.5 + - + +
72B GLN* 3.7 5.4 - - - +
73B ALA* 3.1 27.9 + - - +
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Residues in contact with GLU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PRO* 5.7 4.0 - - - +
62B PRO 4.8 4.1 - - - +
63B ALA* 3.6 25.6 - - + +
64B ASN* 2.9 29.8 + - - +
67B SER* 3.1 25.8 + - - +
69B LYS* 1.3 75.1 - - + +
71B VAL* 1.3 66.8 + - - +
73B ALA* 3.4 6.9 + - - +
74B ALA 3.1 17.0 + - - -
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Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 4.7 12.6 - - + -
63B ALA* 4.6 3.8 - - + -
64B ASN 3.8 14.6 - - - +
65B VAL* 3.9 13.0 - - - +
67B SER 3.2 18.6 + - - +
70B GLU* 1.3 72.7 - - - +
72B GLN* 1.3 67.1 + - - +
74B ALA* 3.1 13.3 + - - +
75B LEU* 3.1 29.4 + - + +
127B ASN* 3.8 11.7 - - - +
128B VAL* 4.3 25.4 - - + -
131B LEU* 3.8 22.9 - - + -
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Residues in contact with GLN 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLU* 3.0 22.3 + - + +
69B LYS* 3.7 6.1 - - - +
71B VAL* 1.3 80.3 - - - +
73B ALA* 1.3 61.1 + - - +
75B LEU* 3.4 14.9 + - - +
76B THR* 3.0 35.6 + - - +
131B LEU* 3.8 30.6 + - + +
135B VAL* 5.3 5.5 - - - +
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Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LYS 3.1 16.9 + - - +
70B GLU* 3.8 6.7 - - - +
71B VAL 3.3 0.2 - - - -
72B GLN* 1.3 77.3 - - - +
74B ALA* 1.3 57.4 + - - +
76B THR* 3.5 6.7 + - - -
77B LEU* 3.1 26.5 + - - +
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Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B VAL* 6.2 0.9 - - + -
38B VAL* 4.9 3.0 - - + +
40B LEU* 3.7 28.0 - - + -
61B ALA* 3.8 27.9 - - + +
62B PRO 5.2 0.9 - - - +
63B ALA* 4.3 4.9 - - + -
70B GLU 3.1 12.6 + - - +
71B VAL 3.1 8.7 + - - +
73B ALA* 1.3 76.3 - - - +
75B LEU* 1.3 58.9 + - - +
77B LEU* 3.4 6.3 + - - +
78B ALA* 3.1 25.6 + - - +
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B VAL* 4.3 22.2 - - + -
40B LEU* 5.2 3.6 - - + -
71B VAL* 3.1 26.0 + - + +
72B GLN* 3.9 10.3 - - - +
74B ALA* 1.3 74.4 - - - +
76B THR* 1.3 63.6 + - - +
78B ALA* 3.4 6.0 + - - +
79B LYS* 3.2 23.6 + - - +
85B ILE* 3.9 25.1 - - + +
128B VAL* 4.9 5.2 - - + +
131B LEU* 3.8 43.1 - - + +
132B VAL* 3.8 18.2 - - + +
135B VAL* 4.7 12.6 - - + +
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Residues in contact with THR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLN* 3.0 27.7 + - - +
73B ALA* 3.8 7.4 - - - -
74B ALA 3.4 0.2 - - - -
75B LEU* 1.3 76.8 - - - +
77B LEU* 1.3 62.8 + - - +
79B LYS* 4.6 3.1 - - - -
80B GLU* 2.6 53.0 + - + +
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B VAL* 6.2 0.2 - - + -
59B ILE* 4.3 14.1 - - + -
60B PHE 4.3 10.5 - - - +
61B ALA* 4.1 24.0 - - + -
62B PRO* 5.8 1.3 - - + -
73B ALA 3.1 14.0 + - - +
74B ALA* 3.5 9.2 - - - +
75B LEU 3.3 0.2 - - - -
76B THR* 1.3 78.5 - - - +
78B ALA* 1.3 62.3 + - - +
80B GLU* 3.7 7.1 - - + +
81B LYS* 3.0 34.7 + - + +
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL* 5.5 1.8 - - + -
14B VAL* 4.2 17.7 - - + -
38B VAL* 3.6 32.1 - - + +
59B ILE* 5.0 0.9 - - - -
74B ALA 3.1 13.2 + - - +
75B LEU 3.4 8.7 + - - +
77B LEU* 1.3 75.6 - - - +
79B LYS* 1.3 56.7 + - - +
81B LYS* 4.7 2.7 - - - -
82B PHE* 2.8 35.9 + - + +
84B ARG 4.5 2.5 - - - +
85B ILE* 4.3 9.4 - - + -
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Residues in contact with LYS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU 3.2 14.5 + - - +
76B THR* 3.8 5.2 - - - +
78B ALA* 1.3 75.4 - - - +
80B GLU* 1.3 75.1 + - - +
83B GLY* 2.6 48.0 + - - +
84B ARG* 4.2 14.8 - - - +
85B ILE* 4.9 1.3 - - + +
135B VAL* 4.9 16.8 - - + -
138B GLN* 2.6 34.6 + - - +
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Residues in contact with GLU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B THR* 2.6 49.5 + - + +
77B LEU* 3.7 10.1 - - + +
78B ALA 3.3 0.2 - - - -
79B LYS* 1.3 99.3 - - - +
81B LYS* 1.3 61.4 + - - +
83B GLY 4.6 0.9 + - - -
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Residues in contact with LYS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B GLY 4.8 9.1 + - - -
59B ILE* 4.1 28.5 - - + +
77B LEU* 3.0 25.2 + - + +
78B ALA 3.8 2.5 - - - +
80B GLU* 1.3 81.3 - - - +
82B PHE* 1.3 92.3 + - + +
83B GLY 3.7 0.2 - - - -
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Residues in contact with PHE 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL* 3.8 34.0 - - + +
36B THR* 4.0 32.8 - - + -
37B ALA 4.5 3.1 - - - -
38B VAL* 3.9 26.5 - - + -
56B GLY 4.5 14.1 - - - -
57B ASN* 4.6 9.4 - - - -
59B ILE* 4.0 26.2 - - + -
78B ALA 2.8 21.0 + - - +
81B LYS* 1.3 97.8 - - + +
83B GLY* 1.3 57.2 + - - +
84B ARG* 3.4 8.6 + - - +
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Residues in contact with GLY 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LYS* 2.6 38.4 + - - +
80B GLU 4.5 0.8 + - - -
81B LYS 3.7 1.2 - - - -
82B PHE* 1.3 70.5 - - - +
84B ARG* 1.3 61.9 + - - +
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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