Contacts of the helix formed by residues 75 - 90 (chain K) in PDB entry 3SDI
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 75 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C LEU 4.7 3.8 + - - -
41K LEU* 5.8 0.9 - - - -
66K HIS* 5.1 1.4 + - - -
73K ARG 3.6 2.4 + - - -
74K ILE* 1.3 79.0 - - - +
76K VAL* 1.3 61.4 + - - +
77K ALA* 3.8 4.9 + - - +
78K ALA* 3.2 24.5 + - - +
79K ALA* 2.9 27.3 + - - +
105K THR* 4.2 15.5 - - - -
106K GLU* 3.4 23.1 + - - -
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Residues in contact with VAL 76 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41K LEU* 4.2 9.2 - - + -
74K ILE 3.9 0.6 + - - -
75K SER* 1.3 68.1 - - - +
77K ALA* 1.3 68.0 + - - +
79K ALA* 3.2 5.3 + - - +
80K SER* 2.9 23.6 + - - -
101K ILE* 3.6 34.8 - - + +
103K GLY* 3.7 36.3 - - - +
104K TYR 4.3 5.6 - - - +
105K THR* 4.8 1.5 - - + +
106K GLU* 2.8 21.9 + - - +
107K GLY 5.4 0.2 - - - +
109K THR* 3.8 15.9 - - - +
111K TYR* 3.7 16.2 - - + -
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Residues in contact with ALA 77 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LEU 5.0 2.9 - - - +
104C GLU* 4.2 14.4 - - + +
75K SER* 3.2 4.9 - - - +
76K VAL* 1.3 76.5 - - - +
78K ALA* 1.3 56.2 + - - +
80K SER* 2.9 16.6 + - - -
81K LYS* 3.2 11.1 + - - +
106K GLU* 2.8 18.9 + - + +
111K TYR* 3.5 29.8 - - + +
119K ARG* 3.2 15.2 + - - +
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Residues in contact with ALA 78 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C THR 4.6 4.6 - - - +
103C LEU* 3.8 37.9 + - + +
74K ILE* 3.7 18.4 - - + -
75K SER* 3.2 17.5 + - - +
76K VAL 3.1 0.2 - - - -
77K ALA* 1.3 76.6 - - - +
79K ALA* 1.3 66.1 + - - +
80K SER 3.2 1.3 - - - -
81K LYS* 3.3 6.5 + - - +
82K ILE* 3.1 27.4 + - + +
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Residues in contact with ALA 79 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41K LEU* 3.8 19.1 - - + -
59K LEU* 3.1 29.7 - - + +
63K CYS* 3.7 26.2 - - - -
74K ILE* 3.8 9.8 - - + +
75K SER 2.9 17.1 + - - +
76K VAL 3.8 3.6 - - - +
78K ALA* 1.3 75.8 - - - +
80K SER* 1.3 63.5 + - - +
82K ILE* 3.3 6.4 + - - -
83K LEU 3.4 1.0 + - - -
101K ILE* 4.4 7.4 - - + -
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Residues in contact with SER 80 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76K VAL 2.9 14.1 + - - -
77K ALA 2.9 11.6 + - - -
79K ALA* 1.3 77.3 - - - +
81K LYS* 1.3 57.4 + - - +
83K LEU* 3.2 4.2 + - - +
84K SER* 2.8 29.5 + - - -
101K ILE* 4.1 17.4 - - - +
111K TYR* 3.5 29.5 - - - -
113K VAL* 3.9 11.3 - - - +
119K ARG* 2.8 28.7 + - - -
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Residues in contact with LYS 81 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C ARG 5.0 0.2 + - - -
101C LEU* 2.9 25.0 + - - +
102C THR 3.8 17.7 - - - +
104C GLU* 2.9 35.5 + - + +
53J VAL* 6.1 1.1 - - - -
54J GLN* 5.8 0.9 - - - -
57J GLU* 2.8 31.0 + - - -
77K ALA 3.2 12.6 + - - +
78K ALA* 3.3 2.2 + - - +
79K ALA 3.2 0.2 - - - -
80K SER* 1.3 79.3 + - - +
82K ILE* 1.3 66.5 + - - +
84K SER* 3.4 5.3 - - - -
85K ASN* 2.8 50.2 + - - +
119K ARG* 3.6 27.1 - - - +
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Residues in contact with ILE 82 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C THR 5.2 3.8 + - - +
103C LEU* 6.1 2.0 - - + -
58K TRP* 3.6 29.5 - - + -
59K LEU* 3.7 9.6 - - + -
62K GLN* 4.1 28.0 - - + +
63K CYS* 5.2 0.4 - - - -
66K HIS* 5.8 0.7 - - + -
74K ILE* 3.6 31.2 - - + -
78K ALA* 3.1 13.0 + - + +
79K ALA* 3.7 8.7 - - - +
81K LYS* 1.3 80.5 - - - +
83K LEU* 1.3 61.2 + - - +
85K ASN* 3.9 3.9 - - - +
86K LEU* 3.1 20.6 + - - +
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Residues in contact with LEU 83 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55K TRP* 4.1 25.8 - - + +
56K GLU* 4.3 11.2 - - + -
58K TRP* 4.7 4.5 - - + -
59K LEU* 4.1 18.2 - - + -
79K ALA 3.4 3.4 + - - +
80K SER* 3.2 8.1 + - - +
81K LYS 3.2 0.2 - - - -
82K ILE* 1.3 75.6 - - - +
84K SER* 1.3 67.5 + - - +
86K LEU* 3.2 7.0 + - + +
87K VAL* 3.0 29.9 + - + +
97K MET* 3.9 23.6 - - + -
99K THR* 3.5 34.1 - - + +
101K ILE* 4.0 16.2 - - + -
113K VAL* 4.2 9.0 - - + -
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Residues in contact with SER 84 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54J GLN* 4.8 2.4 + - - +
80K SER 2.8 20.8 + - - -
81K LYS* 3.4 7.1 - - - +
83K LEU* 1.3 74.7 - - - +
85K ASN* 1.3 63.2 + - - +
87K VAL* 3.7 5.8 + - - +
88K TYR* 3.0 26.0 + - - +
113K VAL* 3.7 16.8 - - - +
117K GLY* 3.8 13.8 + - - -
119K ARG* 3.7 33.1 - - - +
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Residues in contact with ASN 85 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C LEU 5.1 0.7 - - - +
102C THR* 4.2 19.2 - - - +
54J GLN* 2.8 30.2 + - - +
81K LYS* 2.8 46.7 + - - +
82K ILE* 3.9 4.7 - - - +
84K SER* 1.3 75.5 + - - +
86K LEU* 1.3 64.7 + - - +
88K TYR* 3.4 5.4 + - - +
89K GLN* 3.2 27.9 + - - +
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Residues in contact with LEU 86 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55K TRP* 3.5 50.9 - - + +
58K TRP* 3.8 32.1 - - + -
82K ILE 3.1 16.6 + - - +
83K LEU* 3.6 4.9 - - + +
85K ASN* 1.3 74.1 - - - +
87K VAL* 1.3 74.1 + - + +
89K GLN* 2.9 28.0 + - + +
90K TYR* 3.4 30.3 - - + -
95K LEU* 4.9 0.7 - - + -
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Residues in contact with VAL 87 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83K LEU* 3.0 20.1 + - + +
84K SER* 3.8 7.4 - - - +
86K LEU* 1.3 85.9 - - + +
88K TYR* 1.3 63.6 + - - +
90K TYR* 3.0 13.9 + - - +
91K LYS* 3.4 9.4 + - - -
95K LEU* 4.3 14.1 - - + +
97K MET* 3.8 40.4 - - + -
113K VAL* 5.2 2.5 - - + -
114K ASP 3.4 12.3 - - - +
115K SER* 3.4 33.9 - - - +
117K GLY* 4.1 5.2 - - - +
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Residues in contact with TYR 88 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50J GLY 3.9 0.2 - - - -
51J ASP* 3.0 39.0 + - - -
54J GLN* 3.6 49.6 - - + +
93J ARG* 3.2 22.9 + - - -
95J TYR* 3.5 27.4 - + - -
84K SER 3.0 18.6 + - - +
85K ASN* 3.6 6.3 - - - +
86K LEU 3.1 0.4 - - - -
87K VAL* 1.3 78.5 - - - +
89K GLN* 1.3 73.5 + - - +
90K TYR 3.2 0.3 + - - -
91K LYS* 3.3 28.9 + - + +
117K GLY* 4.5 15.3 - - - -
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Residues in contact with GLN 89 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92J ARG* 5.6 3.8 + - - -
85K ASN* 3.2 17.9 + - - +
86K LEU* 2.9 17.2 + - + +
88K TYR* 1.3 88.6 - - - +
90K TYR* 1.3 68.1 + - + +
91K LYS 3.3 1.4 + - - +
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Residues in contact with TYR 90 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55K TRP* 3.8 31.8 - + - -
86K LEU* 3.4 39.0 + - + -
87K VAL 3.0 4.9 + - - +
89K GLN* 1.3 84.9 - - + +
91K LYS* 1.3 65.4 + - - +
92K GLY 3.2 0.5 + - - -
93K ALA* 2.9 27.7 + - + +
94K GLY 4.5 1.2 + - - -
95K LEU* 3.5 30.4 + - + +
88L TYR* 6.5 0.2 - + - -
92L PHE* 3.8 35.9 - + - -
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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
------------------------------------------------------------
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