Contacts of the helix formed by residues 75 - 87 (chain D) in PDB entry 3SAJ
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 THR 75 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46D ILE 2.8 29.5 + - - +
47D SER 3.6 19.7 - - - -
49D SER* 3.7 16.2 - - - +
52D MET* 3.7 16.8 - - + -
71D TYR* 3.4 4.8 - - - +
72D GLU* 3.0 20.9 + - - -
74D ARG* 1.3 79.8 - - - +
76D VAL* 1.3 64.7 + - - +
77D ASN 3.2 2.7 - - - -
78D MET* 3.2 5.0 + - + +
79D LEU* 3.2 35.0 + - - +
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Residues in contact with VAL 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D TYR* 2.8 47.8 - - + -
72D GLU 3.1 12.1 + - - +
73D ARG* 3.4 21.5 + - + +
75D THR* 1.3 77.0 - - - +
77D ASN* 1.3 72.9 + - - +
79D LEU* 3.4 3.1 + - - +
80D THR* 2.9 37.5 + - - +
97D VAL* 3.6 21.3 - - + -
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Residues in contact with ASN 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B SER* 4.0 3.4 + - - +
73B ARG* 4.1 15.6 + - - +
74B ARG* 3.2 53.5 - - + +
77B ASN* 4.8 17.3 - - + +
73D ARG 5.0 0.8 + - - -
74D ARG 5.4 0.8 - - - +
75D THR 3.2 1.0 - - - -
76D VAL* 1.3 87.5 - - - +
78D MET* 1.3 65.1 + - - +
80D THR* 4.0 6.1 - - - +
81D SER* 3.0 26.3 + - - -
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Residues in contact with MET 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B SER* 3.9 15.1 + - - +
53B THR* 5.5 1.1 - - - +
78B MET* 5.9 4.3 - - + -
12D LEU* 6.4 0.2 - - + -
49D SER* 3.8 20.8 + - - +
52D MET* 2.9 52.9 - - + +
53D THR* 3.4 21.3 - - - +
56D PHE* 5.0 5.2 - - + -
74D ARG 5.7 0.2 + - - -
75D THR* 3.2 8.8 + - - +
77D ASN* 1.3 77.4 - - - +
79D LEU* 1.3 76.0 + - + +
81D SER* 3.2 0.9 + - - -
82D PHE* 2.7 68.3 + - + -
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Residues in contact with LEU 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 5.1 0.7 - - + -
52D MET* 4.0 18.2 - - + -
56D PHE* 5.2 9.4 - - + -
71D TYR* 3.6 17.7 - - + -
75D THR* 3.2 23.6 + - - +
76D VAL* 3.8 4.3 - - - +
78D MET* 1.3 106.0 - - + +
80D THR* 1.3 57.0 + - - +
82D PHE* 4.4 2.0 - - - +
83D CYS* 2.7 43.2 + - - +
90D PHE* 3.1 53.4 - - + -
104D VAL* 5.1 2.2 - - + -
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Residues in contact with THR 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D VAL* 2.9 25.8 + - - +
77D ASN* 4.0 6.7 - - - +
79D LEU* 1.3 75.7 - - - +
81D SER* 1.3 59.6 + - - +
83D CYS* 3.8 0.2 - - - +
84D GLY* 2.9 14.4 + - - -
97D VAL* 5.1 2.1 - - - +
99D THR 4.7 4.0 + - - +
100D SER* 3.9 29.6 - - - -
101D ASN* 2.7 43.5 + - + +
104D VAL* 4.4 11.8 - - - +
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Residues in contact with SER 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ASP* 2.7 28.9 + - - +
49B SER* 3.1 14.6 + - - -
50B PHE* 3.1 17.3 + - - +
77D ASN 3.0 21.0 + - - -
78D MET 3.5 2.9 - - - -
80D THR* 1.3 78.5 - - - +
82D PHE* 1.3 60.7 + - - +
84D GLY* 3.5 0.6 + - - -
85D ALA* 3.0 30.1 + - - +
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Residues in contact with PHE 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B SER 4.3 0.4 - - - -
50B PHE* 3.5 54.7 - + + -
53B THR* 3.9 20.2 - - + -
53D THR* 3.6 21.1 - - + -
56D PHE* 3.9 33.0 - + + -
57D CYS* 3.8 23.6 - - - -
78D MET* 2.7 55.3 + - + +
79D LEU 4.1 1.6 - - - +
81D SER* 1.3 71.3 - - - +
83D CYS* 1.3 60.4 + - - +
86D LEU* 3.0 39.1 + - + +
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Residues in contact with CYS 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D PHE* 4.0 17.0 - - - -
79D LEU* 2.7 30.7 + - - +
80D THR 3.8 3.1 - - - +
82D PHE* 1.3 72.0 - - - +
84D GLY* 1.3 59.2 + - - +
87D HIS* 2.8 31.9 + - - -
88D VAL 3.5 23.5 + - - +
89D CYS 4.6 0.2 - - - -
90D PHE* 3.5 31.9 - - - -
101D ASN* 4.3 4.5 - - - +
103D PHE* 3.8 16.0 - - + -
104D VAL* 4.3 6.7 - - + -
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Residues in contact with GLY 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D THR 2.9 18.3 + - - -
81D SER* 3.9 0.9 - - - -
83D CYS* 1.3 76.2 - - - +
85D ALA* 1.3 60.6 + - - +
87D HIS* 3.2 22.5 + - - -
101D ASN* 3.6 13.0 - - - +
103D PHE* 4.2 11.1 - - - -
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Residues in contact with ALA 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ASP* 5.4 2.9 - - - +
50B PHE* 3.9 34.1 - - + -
81D SER 3.0 18.6 + - - +
82D PHE 4.2 2.2 - - - +
83D CYS 3.3 0.2 - - - -
84D GLY* 1.3 77.4 - - - +
86D LEU* 1.3 64.2 + - + +
87D HIS* 4.4 4.6 + - - -
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Residues in contact with LEU 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B PHE* 3.9 32.5 - - + -
56D PHE* 3.6 24.5 - - + -
57D CYS* 5.7 3.4 - - - -
60D PHE* 4.1 45.2 - - + -
82D PHE* 3.0 25.8 + - + +
85D ALA* 1.3 82.7 - - - +
87D HIS* 1.3 73.0 + - - +
88D VAL* 3.3 7.7 + - + +
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Residues in contact with HIS 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D CYS 2.8 10.2 + - - -
84D GLY 3.2 20.9 + - - -
85D ALA 4.4 3.6 - - - -
86D LEU* 1.3 81.3 + - - +
88D VAL* 1.3 58.7 + - - +
89D CYS* 4.2 1.6 + - - -
103D PHE* 3.2 45.8 - + + -
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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