Contacts of the helix formed by residues 81 - 93 (chain O) in PDB entry 5X22
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 PRO 81 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1499N ARG* 3.4 17.5 - - - +
80O VAL* 1.3 92.9 - - + +
82O GLU* 1.3 63.8 + - - +
83O ASP* 3.4 16.8 - - - +
84O ARG* 3.2 13.3 + - + -
85O LEU* 3.0 19.9 + - - +
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Residues in contact with GLU 82 (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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1485N GLN* 2.7 34.0 + - - +
25O LYS* 5.4 4.7 + - - -
80O VAL 3.5 2.9 + - - -
81O PRO* 1.3 70.5 - - - +
83O ASP* 1.3 58.9 + - - +
85O LEU* 3.3 18.7 + - - +
86O GLN* 2.9 57.2 + - - +
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Residues in contact with ASP 83 (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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81O PRO* 3.4 19.0 - - - +
82O GLU* 1.3 76.0 + - - +
84O ARG* 1.3 61.7 + - - -
86O GLN* 3.8 12.1 - - - +
87O LYS* 2.9 42.3 + - + +
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Residues in contact with ARG 84 (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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1495N ILE* 4.0 20.8 - - + +
1498N ALA* 4.0 27.6 + - - +
1499N ARG* 5.3 3.7 - - + +
80O VAL* 4.1 4.5 - - + -
81O PRO* 3.2 24.6 + - + +
83O ASP* 1.3 81.2 + - - +
85O LEU* 1.3 58.5 + - - +
87O LYS* 3.5 6.2 + - - -
88O GLU* 2.9 54.3 + - - +
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Residues in contact with LEU 85 (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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1485N GLN* 4.7 10.5 - - + +
1486N VAL 4.5 13.2 - - - +
1487N VAL* 3.7 31.6 - - + -
1495N ILE* 3.9 19.1 - - + -
29O GLN* 4.5 9.2 - - - +
80O VAL* 3.9 21.0 - - + +
81O PRO 3.0 13.6 + - - +
82O GLU* 3.6 24.9 - - - +
84O ARG* 1.3 77.0 - - - +
86O GLN* 1.3 65.1 + - + +
88O GLU* 3.8 0.9 - - - +
89O MET* 2.9 43.5 + - + +
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Residues in contact with GLN 86 (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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32O ARG* 6.0 6.3 - - - +
33O HIS* 5.3 0.7 - - - -
82O GLU* 2.9 44.4 + - + +
83O ASP* 3.8 11.1 - - - +
85O LEU* 1.3 80.7 - - + +
87O LYS* 1.3 70.9 + - - +
89O MET* 3.4 4.8 + - - +
90O GLU* 2.9 42.2 + - - +
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Residues in contact with LYS 87 (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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83O ASP* 2.9 26.6 + - + +
84O ARG* 4.0 8.5 - - - +
86O GLN* 1.3 89.5 + - - +
88O GLU* 1.3 58.8 + - + +
90O GLU* 3.3 31.9 + - + +
91O ARG* 2.9 32.8 + - - +
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Residues in contact with GLU 88 (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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1491N THR* 4.6 4.7 - - + -
1494N ALA* 4.3 19.8 - - - +
1495N ILE* 3.6 31.0 - - + -
1498N ALA* 3.9 19.4 - - - +
84O ARG* 2.9 36.9 + - + +
85O LEU 3.8 2.9 - - - +
87O LYS* 1.3 74.6 - - + +
89O MET* 1.3 58.7 + - - +
91O ARG* 3.1 40.9 + - - +
92O LEU* 2.9 34.5 + - - +
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Residues in contact with MET 89 (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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1487N VAL* 5.3 1.1 - - - -
1488N ASP* 3.9 16.8 - - - +
1491N THR* 3.7 28.0 - - + +
26O ARG* 4.6 0.7 - - - +
29O GLN* 4.3 20.6 - - - +
33O HIS* 3.3 26.7 - - + +
37O ASN* 3.4 39.3 - - + +
85O LEU* 2.9 33.1 + - + +
86O GLN* 3.9 4.7 - - - +
88O GLU* 1.3 76.6 - - - +
90O GLU* 1.3 57.1 + - - +
92O LEU* 4.5 1.3 - - - +
93O TYR* 2.9 41.4 + - + +
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Residues in contact with GLU 90 (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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32O ARG* 5.8 4.7 - - - -
33O HIS* 4.7 10.5 - - + -
86O GLN* 2.9 33.3 + - - +
87O LYS* 3.6 34.8 + - + +
88O GLU 3.2 0.2 - - - -
89O MET* 1.3 75.6 - - - +
91O ARG* 1.3 62.2 + - - +
93O TYR 4.2 5.4 - - - +
94O PRO* 3.3 28.6 - - + +
95O VAL 5.9 2.5 - - - +
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Residues in contact with ARG 91 (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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87O LYS* 2.9 12.4 + - - +
88O GLU* 3.1 52.7 + - - +
90O GLU* 1.3 80.6 - - - +
92O LEU* 1.3 76.6 + - + +
93O TYR 3.5 0.2 + - - -
94O PRO* 3.7 10.4 - - - +
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Residues in contact with LEU 92 (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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1490N LYS* 5.0 6.7 - - + +
1491N THR* 3.8 27.4 - - + +
1494N ALA* 3.9 27.4 - - + -
88O GLU* 2.9 20.5 + - - +
89O MET* 4.7 0.2 - - - -
91O ARG* 1.3 95.8 - - + +
93O TYR* 1.3 93.3 + - + +
94O PRO* 3.7 3.9 - - - +
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Residues in contact with TYR 93 (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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1488N ASP* 3.9 9.4 + - - -
1490N LYS* 3.5 34.3 - - - +
1491N THR* 4.0 15.6 + - - -
33O HIS* 3.4 26.1 + + + +
36O LYS* 3.4 48.7 - - + -
37O ASN* 3.6 26.8 + - + -
89O MET* 2.9 30.6 + - + +
90O GLU* 3.8 1.1 - - - -
92O LEU* 1.3 107.6 - - + +
94O PRO* 1.3 67.5 - - - +
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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