Contacts of the helix formed by residues 72 - 81 (chain O) in PDB entry 5KZ5
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 ARG 72 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E LEU* 5.6 0.4 - - - +
77F ASN* 3.5 22.8 + - - +
81F SER 3.0 39.0 + - - +
82F GLY* 3.7 11.2 - - - -
83F THR* 3.5 22.5 - - - +
86F HIS* 6.1 1.2 + - - -
70O ASP* 3.3 14.7 - - - +
71O PRO* 1.4 80.9 - - - +
73O VAL* 1.4 55.8 + - - +
75O ASP* 3.2 11.8 + - - +
76O ALA 3.1 18.7 + - - -
155e LEU* 3.4 25.0 - - - +
160e LYS* 4.2 11.1 - - - +
163e GLU* 4.8 2.0 + - - -
82f LYS* 4.1 10.5 - - - +
83f GLY 4.6 1.8 + - - -
84f LYS* 3.6 30.5 - - - +
111f GLY 5.9 0.7 - - - -
113f THR* 3.3 35.3 - - - +
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Residues in contact with VAL 73 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E ASP* 3.5 32.3 - - + +
47E ASP* 5.1 2.0 - - + +
48E ALA* 3.9 14.8 - - + +
49E THR 3.3 22.3 - - - +
79F ARG* 3.8 9.9 - - + -
80F LYS 3.4 19.3 - - - +
81F SER 4.7 0.4 - - - +
208F LYS* 3.6 29.6 - - + +
70O ASP* 3.3 24.3 + - - +
71O PRO 3.3 0.6 + - - -
72O ARG* 1.4 72.1 - - - +
74O LEU* 1.4 61.5 + - - +
76O ALA* 3.1 11.1 + - - +
77O MET* 3.3 2.9 + - - +
412O ARG* 5.1 3.6 - - - +
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Residues in contact with LEU 74 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205F TYR* 4.6 3.4 - - - -
206F SER* 3.4 44.6 - - - +
208F LYS* 3.8 24.7 - - - +
209F ASP 3.7 19.7 - - - +
71O PRO 2.9 13.5 + - - +
73O VAL* 1.4 76.4 - - - +
75O ASP* 1.4 55.5 + - - +
77O MET* 3.2 33.3 + - - +
78O LEU* 3.0 33.7 + - + +
81O LEU* 3.9 18.4 - - + -
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Residues in contact with ASP 75 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F SER 4.1 1.6 - - - +
83F THR* 3.5 26.3 - - - +
84F LEU 2.9 22.9 - - - +
85F GLY* 3.1 16.6 + - - +
86F HIS* 3.0 32.5 + - - -
71O PRO* 2.9 33.0 + - - +
72O ARG* 3.2 18.5 + - - +
74O LEU* 1.4 76.9 - - - +
76O ALA* 1.4 58.7 + - - +
78O LEU* 3.4 18.1 + - - +
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Residues in contact with ALA 76 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E THR* 3.8 5.8 - - - +
50E CYS* 3.6 35.6 - - - -
51E THR* 5.4 0.9 + - - -
54E ARG* 3.7 28.6 + - + -
81F SER* 4.0 11.9 - - - +
83F THR 4.1 3.3 + - - -
72O ARG 3.1 11.1 + - - +
73O VAL* 3.1 10.5 + - - +
75O ASP* 1.4 76.2 - - - +
77O MET* 1.4 60.9 + - - +
78O LEU 3.5 0.2 + - - -
79O PRO* 3.6 8.3 - - - +
80O TYR* 5.2 2.1 - - - -
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Residues in contact with MET 77 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E ALA* 4.5 0.4 - - + -
49E THR* 3.7 45.2 + - + +
208F LYS* 3.3 27.8 - - - +
209F ASP 4.7 2.2 - - - +
210F ALA* 3.8 10.8 - - - +
73O VAL 3.3 6.3 + - - +
74O LEU* 3.2 25.5 + - + +
76O ALA* 1.4 76.6 - - - +
78O LEU* 1.4 62.7 + - - +
79O PRO 3.5 0.4 - - - -
80O TYR* 3.3 23.5 + - + +
81O LEU* 3.5 26.4 + - + +
301O VAL* 3.7 32.3 - - + +
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Residues in contact with LEU 78 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F GLY* 3.8 8.3 - - - +
86F HIS* 5.7 0.2 - - - +
87F PRO* 3.6 34.8 - - + +
89F SER* 3.5 30.3 - - - +
204F ALA 5.4 0.9 - - - +
205F TYR* 3.8 18.6 - - + -
74O LEU* 3.0 21.3 + - + +
75O ASP* 3.4 30.1 - - - +
76O ALA 3.3 0.2 - - - -
77O MET* 1.4 74.2 - - - +
79O PRO* 1.3 63.3 - - + +
81O LEU* 3.2 10.2 + - + -
82O ILE* 3.2 34.5 + - + +
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Residues in contact with PRO 79 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E ARG* 3.4 33.7 - - + +
84F LEU* 3.3 28.0 - - + +
89F SER* 3.8 13.2 - - - +
75O ASP 3.6 1.8 - - - +
76O ALA 3.6 3.8 - - - +
77O MET 3.6 3.8 - - - -
78O LEU* 1.3 90.7 - - + +
80O TYR* 1.4 61.1 + - + +
82O ILE* 3.2 23.2 - - + +
83O ASN* 3.9 2.1 - - - +
453S LYS* 3.4 24.5 + - - -
66e ALA* 3.9 16.8 - - + +
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Residues in contact with TYR 80 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E THR* 5.2 11.0 - - + -
51E THR* 4.3 9.3 + - - +
54E ARG* 3.3 41.7 + - - -
76O ALA 5.3 1.3 - - - -
77O MET* 3.3 20.3 + - + +
79O PRO* 1.4 74.1 - - - +
81O LEU* 1.4 58.3 + - - +
83O ASN 3.0 25.6 - - - +
84O TYR* 3.2 32.1 - + + +
300O LEU 5.0 4.5 - - - +
301O VAL* 6.0 2.7 - - - +
449S LEU 5.0 1.9 + - - -
451S SER* 3.2 30.3 + - - -
452S ILE* 3.7 30.2 + - - -
453S LYS* 4.4 9.6 - - + +
454S TRP* 5.0 7.0 - + - -
67e PRO* 5.1 4.6 - - + +
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Residues in contact with LEU 81 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109F PHE* 5.5 5.8 - - + -
204F ALA* 3.3 29.8 - - - +
205F TYR* 5.2 0.2 - - - -
206F SER* 5.4 2.9 - - - +
209F ASP 5.9 0.2 - - - +
74O LEU* 3.9 24.5 - - + -
77O MET* 3.5 33.1 + - + +
78O LEU* 3.2 13.9 + - + +
80O TYR* 1.4 76.9 - - - +
82O ILE* 1.3 63.4 + - - +
83O ASN 3.6 0.2 + - - -
84O TYR* 4.6 5.1 + - - +
85O TYR* 3.4 49.0 - - + +
300O LEU* 5.1 1.6 - - + -
301O VAL* 3.8 21.8 - - + +
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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