Contacts of the helix formed by residues 74 - 88 (chain L) in PDB entry 6PST
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 GLU 74 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73L ASP* 1.3 92.7 + - + +
75L ASP* 1.3 63.9 + - - +
76L ALA 3.3 1.6 - - - -
77L ALA* 3.0 13.9 - - + +
78L GLU* 3.0 26.5 + - - +
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Residues in contact with ASP 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121J PRO* 3.0 39.9 - - - +
123J ARG* 4.4 3.3 + - - -
219J LYS* 3.5 27.8 + - - +
73L ASP 3.8 0.2 - - - -
74L GLU* 1.3 80.0 - - - +
76L ALA* 1.3 58.5 + - - +
78L GLU* 3.1 11.2 + - - +
79L ALA* 2.9 25.6 + - - +
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Residues in contact with ALA 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120J LEU* 3.5 25.1 - - + +
121J PRO* 4.7 2.7 - - + +
1330J ARG* 4.7 12.1 - - - +
50L ASP* 3.4 24.3 - - - +
51L MET 5.0 0.4 - - - -
72L ALA 4.3 13.4 + - - +
74L GLU* 3.3 1.0 - - - +
75L ASP* 1.3 77.5 - - - +
77L ALA* 1.3 61.0 + - - +
79L ALA* 4.0 1.1 - - - +
80L ALA* 2.9 33.3 + - - +
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Residues in contact with ALA 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L LYS* 4.5 13.3 + - - +
51L MET* 3.9 25.7 + - - +
72L ALA 4.9 1.0 + - - -
73L ASP* 4.8 4.0 - - + -
74L GLU* 3.0 30.7 + - + +
76L ALA* 1.3 78.8 - - - +
78L GLU* 1.3 54.1 + - - +
80L ALA* 3.8 3.1 - - - +
81L ALA* 2.9 31.3 + - - +
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Residues in contact with GLU 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216J LYS* 3.1 28.8 + - - +
74L GLU 3.0 11.5 + - - +
75L ASP* 3.1 13.4 + - - +
77L ALA* 1.3 76.3 - - - +
79L ALA* 1.3 61.5 + - + +
81L ALA* 3.3 3.9 + - - +
82L GLN* 2.9 66.9 + - - +
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Residues in contact with ALA 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120J LEU* 3.3 38.1 - - + +
121J PRO* 4.2 5.6 - - + +
75L ASP* 2.9 17.4 + - - +
76L ALA 4.0 3.1 - - - +
78L GLU* 1.3 80.1 - - + +
80L ALA* 1.3 62.9 + - - +
82L GLN* 3.3 5.4 + - - +
83L VAL* 3.0 32.4 + - + +
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Residues in contact with ALA 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120J LEU* 4.2 1.0 - - - +
47L MET* 3.4 19.2 - - + +
50L ASP* 3.0 27.8 - - - +
51L MET* 3.4 27.6 - - + -
76L ALA 2.9 13.6 + - - +
77L ALA 3.8 1.3 - - - +
79L ALA* 1.3 77.0 - - - +
81L ALA* 1.3 57.1 + - - +
83L VAL 3.2 1.2 + - - -
84L LEU* 2.9 32.4 + - - +
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Residues in contact with ALA 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10L LYS* 3.9 14.4 + - - +
13L VAL* 5.9 1.6 - - + -
17L LYS* 5.2 5.4 - - - +
51L MET* 3.1 17.3 - - + +
77L ALA 2.9 18.1 + - - +
78L GLU* 3.3 5.1 + - - +
80L ALA* 1.3 75.3 - - - +
82L GLN* 1.3 69.6 + - - +
84L LEU* 3.3 2.7 + - - +
85L SER* 2.8 35.0 + - - -
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Residues in contact with GLN 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216J LYS* 5.5 0.4 - - - +
10L LYS* 5.7 0.6 - - - +
78L GLU* 2.9 53.2 + - - +
79L ALA* 3.9 6.1 - - - +
80L ALA 3.3 0.2 - - - -
81L ALA* 1.3 87.3 + - - +
83L VAL* 1.3 62.9 + - + +
85L SER* 4.1 9.7 + - - -
86L SER* 3.7 18.0 + - - -
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Residues in contact with VAL 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120J LEU* 5.6 1.6 - - + +
132J LEU* 4.7 20.6 - - + -
133J ARG* 3.4 35.6 - - + +
47L MET* 3.4 36.3 - - + -
79L ALA* 3.0 20.4 + - + +
80L ALA 3.7 1.6 - - - +
82L GLN* 1.3 77.3 - - + +
84L LEU* 1.3 60.1 + - + +
86L SER* 3.1 5.2 + - - -
87L VAL* 2.9 36.9 + - + +
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Residues in contact with LEU 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L LEU* 4.0 23.6 - - + +
10L LYS* 5.3 3.1 - - - +
13L VAL* 3.8 15.9 - - + -
44L ILE* 3.5 43.3 - - + +
47L MET* 4.0 12.1 - - + -
48L ILE* 4.3 8.3 - - + -
51L MET* 3.3 39.7 - - + -
80L ALA 2.9 12.6 + - - +
81L ALA* 3.3 4.2 + - - +
83L VAL* 1.3 76.8 - - + +
85L SER* 1.3 59.7 + - - +
87L VAL* 3.0 28.4 + - + +
88L GLU* 3.9 8.1 + - - +
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Residues in contact with SER 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L LEU* 6.4 0.2 - - - -
10L LYS* 2.8 35.3 + - - +
81L ALA 2.8 14.6 + - - -
82L GLN* 4.5 12.5 + - - -
83L VAL 3.3 0.2 - - - -
84L LEU* 1.3 78.0 - - - +
86L SER* 1.3 57.2 + - - +
88L GLU* 3.2 28.9 - - - +
89L SER* 4.5 3.6 + - - -
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Residues in contact with SER 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133J ARG* 5.5 10.0 - - - +
137J ARG* 5.6 4.2 + - - -
82L GLN 3.7 15.4 + - - -
83L VAL* 3.1 5.8 + - - -
85L SER* 1.3 79.3 - - - +
87L VAL* 1.3 65.4 + - - +
88L GLU 3.2 2.5 - - - -
89L SER* 3.1 21.6 + - - -
90L GLU* 3.9 9.5 + - - +
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Residues in contact with VAL 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133J ARG* 4.5 15.7 - - + +
9L LEU* 4.6 3.8 - - + -
35L ILE* 5.6 2.9 - - - +
40L GLN* 4.2 17.4 + - - +
44L ILE* 4.3 23.1 - - + -
83L VAL* 2.9 39.7 + - + +
84L LEU* 3.0 39.7 - - + +
86L SER* 1.3 77.9 - - - +
88L GLU* 1.3 64.3 + - - +
90L GLU* 3.1 27.7 - - - +
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Residues in contact with GLU 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L SER 4.5 15.4 + - - -
8L GLN* 5.1 2.9 + - - +
9L LEU* 4.0 24.7 + - + +
32L PRO* 4.2 28.5 - - + +
34L ASP* 6.0 1.2 - - - +
35L ILE* 6.2 1.8 - - - -
84L LEU 4.1 5.4 - - - +
85L SER* 3.2 31.9 - - - +
87L VAL* 1.3 83.7 - - + +
89L SER* 1.3 66.8 + - - +
90L GLU 4.6 0.4 - - - -
91L ILE* 4.7 7.3 - - - +
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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