Contacts of the helix formed by residues 75 - 85 (chain B) in PDB entry 3SF8
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 GLY 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLY 3.7 6.3 - - - -
15B GLU* 3.7 22.5 - - - +
18B GLU* 3.5 6.5 + - - -
47B SER* 5.0 2.9 - - - -
48B ARG* 5.9 1.1 - - - -
74B GLY* 1.3 72.4 - - - -
76B ASN* 1.3 66.9 + - - +
77B LEU 3.3 2.9 - - - -
78B GLY 3.8 1.1 - - - -
79B ALA* 2.8 25.5 + - - +
106B CYS* 5.1 1.4 - - - +
107B ALA* 4.5 8.3 - - - +
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Residues in contact with ASN 76 (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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13B GLY 4.5 0.6 + - - -
47B SER* 5.7 1.4 - - - -
75B GLY* 1.3 72.5 - - - +
77B LEU* 1.3 65.1 + - - +
79B ALA* 4.0 2.3 - - - +
80B GLN* 3.2 22.9 + - - +
107B ALA* 4.8 10.4 - - - +
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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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12B LYS* 3.7 27.1 - - + +
13B GLY* 3.9 20.5 + - - +
75B GLY 3.3 0.2 - - - -
76B ASN* 1.3 80.8 - - + +
78B GLY* 1.3 66.8 + - - +
80B GLN* 3.2 28.5 + - - +
81B ASN* 2.9 39.7 + - - +
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Residues in contact with GLY 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA* 3.8 6.2 - - - +
12B LYS 3.4 14.1 - - - -
13B GLY 3.1 23.1 + - - -
14B ALA* 3.6 9.0 - - - -
74B GLY 4.3 2.7 - - - -
75B GLY 3.3 2.4 + - - -
77B LEU* 1.3 76.9 - - - +
79B ALA* 1.3 56.6 + - - +
81B ASN* 3.2 3.8 + - - +
82B LEU* 2.9 36.4 + - - +
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Residues in contact with ALA 79 (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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73B PRO 5.1 0.7 - - - -
74B GLY* 4.5 2.3 + - - -
75B GLY 2.8 20.9 + - - +
76B ASN 4.0 2.7 - - - +
78B GLY* 1.3 69.5 - - - -
80B GLN* 1.3 67.2 + - - +
82B LEU* 3.3 12.8 + - - +
83B SER* 2.9 28.7 + - - -
107B ALA* 3.5 35.4 - - + +
108B GLY* 4.3 6.5 - - - +
110B THR* 4.0 7.6 - - - +
111B ALA* 4.4 1.4 - - - +
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Residues in contact with GLN 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 ASN* 3.2 15.2 + - - +
77B LEU* 3.2 29.4 + - - +
79B ALA* 1.3 79.8 - - - +
81B ASN* 1.3 68.4 + - - +
83B SER* 3.1 9.9 + - - -
84B GLU* 3.0 50.3 + - + +
132B LYS* 6.0 4.7 - - - +
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Residues in contact with ASN 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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11B ALA* 4.0 12.6 - - + -
12B LYS* 2.9 37.2 + - - +
38B LEU* 3.7 11.9 - - + +
77B LEU* 2.9 29.0 + - - +
78B GLY 3.2 4.5 + - - +
80B GLN* 1.3 89.6 + - - +
82B LEU* 1.3 60.7 + - - +
84B GLU* 3.3 19.0 + - - +
85B SER* 3.4 14.9 + - - -
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Residues in contact with LEU 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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9B ILE* 3.6 37.0 - - + +
11B ALA* 4.2 15.7 - - + +
38B LEU* 4.5 2.2 - - + -
72B LEU* 4.0 24.7 - - + -
73B PRO* 3.6 28.5 - - + +
78B GLY 2.9 20.4 + - - +
79B ALA* 3.3 10.1 + - - +
81B ASN* 1.3 75.4 - - - +
83B SER* 1.3 54.2 + - - +
85B SER 3.3 7.4 + - - -
88B VAL* 3.6 23.7 - - + +
108B GLY* 5.4 0.7 - - - -
111B ALA* 4.0 13.0 - - + -
115B HIS* 2.8 25.7 + - - -
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Residues in contact with SER 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 ALA 2.9 22.9 + - - -
80B GLN* 3.3 9.3 - - - -
82B LEU* 1.3 78.1 - - - +
84B GLU* 1.3 61.0 + - - +
89B LYS* 5.0 1.0 + - - -
110B THR* 3.9 5.2 + - - -
111B ALA* 3.3 22.2 + - - -
114B ALA* 3.6 23.6 - - - +
115B HIS* 3.0 24.2 - - - -
132B LYS* 5.8 2.9 + - - -
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Residues in contact with GLU 84 (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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80B GLN* 3.0 47.0 + - + +
81B ASN* 3.3 11.6 + - - +
82B LEU 3.2 0.4 - - - -
83B SER* 1.3 79.6 - - - +
85B SER* 1.3 61.6 + - - +
86B ALA 3.6 2.6 + - - -
115B HIS* 4.7 0.2 - - - -
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Residues in contact with SER 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 3.6 18.1 - - - +
81B ASN 3.4 13.7 + - - -
82B LEU 3.3 2.4 + - - -
83B SER 3.4 0.2 - - - -
84B GLU* 1.3 76.3 - - - +
86B ALA* 1.3 60.8 + - - +
87B ALA* 3.2 8.8 + - - +
88B VAL* 3.1 35.1 + - - +
89B LYS* 3.1 16.3 + - - -
115B HIS* 3.2 12.3 + - - -
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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