Contacts of the helix formed by residues 84 - 97 (chain K) in PDB entry 5O6I
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 84 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36K TYR 2.8 12.4 + - - +
38K VAL* 4.8 1.2 - - - +
65K VAL* 3.5 13.7 - - - +
67K SER* 3.2 20.2 - - - -
82K VAL* 3.3 8.7 + - - -
83K SER* 1.3 74.9 - - - +
85K LYS* 1.3 57.9 + - - +
86K LYS* 3.3 6.8 + - - +
87K LEU* 2.9 30.6 + - - +
88K TYR* 2.9 30.5 + - - +
5N C 3.7 6.1 + - - -
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Residues in contact with LYS 85 (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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36K TYR* 3.5 34.5 + - + +
84K SER* 1.3 71.3 - - - +
86K LYS* 1.3 62.9 + - - +
88K TYR* 3.6 0.5 - - - +
89K TYR* 3.2 51.1 + - + -
4N G 2.7 38.3 + - - +
5N C 2.8 27.0 + - - +
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Residues in contact with LYS 86 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63K LEU* 2.7 33.8 + - + -
64K ASN* 4.1 12.7 + - - +
65K VAL* 4.1 18.6 - - + -
84K SER* 3.2 7.5 + - - +
85K LYS* 1.3 80.4 - - - +
87K LEU* 1.3 62.4 + - - +
89K TYR* 3.5 3.1 + - - +
90K TYR* 3.1 22.4 + - + +
5N C 4.9 2.1 + - - +
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Residues in contact with LEU 87 (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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38K VAL* 3.8 12.6 - - + -
56K MET* 3.9 19.5 - - - -
59K LEU* 4.2 9.2 - - + -
60K ILE* 3.6 28.5 - - + -
63K LEU* 3.8 26.5 - - + -
65K VAL* 4.5 7.2 - - + +
82K VAL* 3.7 19.5 - - + -
84K SER* 2.9 22.4 + - - +
86K LYS* 1.3 73.4 - - - +
88K TYR* 1.3 66.2 + - - +
90K TYR* 3.3 4.7 + - + +
91K PHE* 3.2 42.6 + - + -
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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
----------------------------------------------------------
24K LEU* 3.7 14.7 + - + +
25K TYR 3.6 35.4 - - - -
26K LYS* 3.6 24.4 + - + +
36K TYR* 3.6 25.8 - + + -
37K ARG 3.9 10.8 - - - -
38K VAL* 3.8 11.4 - - + +
84K SER 2.9 19.0 + - - +
85K LYS 3.6 3.4 - - - +
86K LYS 3.2 0.2 - - - -
87K LEU* 1.3 79.9 - - - +
89K TYR* 1.3 89.7 + + - +
91K PHE* 3.3 2.3 + - - +
92K THR* 2.8 53.3 + - + +
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Residues in contact with TYR 89 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26K LYS* 4.2 19.8 + - - +
36K TYR* 4.0 6.1 + + - -
85K LYS* 3.2 54.0 + - + +
86K LYS* 4.2 3.1 - - - +
88K TYR* 1.3 101.5 - + - +
90K TYR* 1.3 60.0 + - - +
92K THR* 4.0 11.7 - - + -
93K ASN* 2.8 53.9 + - - +
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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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7K VAL* 4.4 8.0 - - - +
8K SER* 4.9 2.9 - - - -
11K SER* 2.6 37.2 + - - -
59K LEU* 4.0 13.0 - - + +
63K LEU* 3.8 41.1 - - + -
86K LYS* 3.1 15.9 + - + +
87K LEU* 3.5 18.4 - - + +
88K TYR 3.2 0.2 - - - -
89K TYR* 1.3 77.6 - - - +
91K PHE* 1.3 75.0 + + - +
93K ASN* 4.3 2.7 - - - +
94K MET* 3.2 29.3 + - + +
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Residues in contact with PHE 91 (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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11K SER 3.7 21.5 - - - -
14K LEU* 4.1 9.2 - - + -
15K LEU* 4.0 22.9 - - + +
18K ILE* 3.7 15.9 - - + -
24K LEU* 3.9 21.5 - - + -
38K VAL* 3.7 25.6 - - + -
56K MET* 4.4 2.2 - - - -
59K LEU* 3.4 26.5 - - + -
87K LEU* 3.2 46.5 + - + +
90K TYR* 1.3 89.0 - + - +
92K THR* 1.3 62.6 + - - +
94K MET* 3.2 7.8 + - - +
95K LEU* 2.8 29.8 + - - +
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Residues in contact with THR 92 (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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24K LEU* 3.8 15.1 - - - +
88K TYR* 2.8 47.0 + - + +
89K TYR* 4.0 17.5 - - + -
91K PHE* 1.3 76.1 - - - +
93K ASN* 1.3 66.8 + - - +
95K LEU* 3.1 14.6 + - + +
96K GLU* 3.1 32.2 + - + +
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Residues in contact with ASN 93 (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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89K TYR* 2.8 44.4 + - - +
90K TYR* 4.3 2.8 - - - +
92K THR* 1.3 75.5 - - - +
94K MET* 1.3 60.4 + - - +
96K GLU* 3.4 17.4 + - - +
97K ARG* 3.3 34.8 + - - +
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Residues in contact with MET 94 (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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8K SER* 4.0 5.8 - - - +
11K SER* 3.8 26.7 - - - +
12K ALA* 3.5 37.9 - - + +
15K LEU* 4.0 17.0 - - + +
90K TYR* 3.2 26.5 + - + +
91K PHE* 3.2 14.7 + - - +
93K ASN* 1.3 77.9 - - - +
95K LEU* 1.3 60.2 - - - +
97K ARG* 3.4 6.3 + - - +
98K ILE* 3.3 20.6 + - - +
101K CYS* 5.4 9.8 - - - -
105K GLU* 4.5 11.9 - - - +
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Residues in contact with LEU 95 (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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15K LEU* 4.2 11.0 - - + +
19K ILE* 3.7 35.2 - - + -
24K LEU* 4.7 9.2 - - + -
91K PHE 2.8 13.1 + - - +
92K THR* 3.1 11.6 + - + +
94K MET* 1.3 75.7 - - - +
96K GLU* 1.3 67.0 + - + +
98K ILE* 3.2 45.4 + - + +
134K LEU* 5.6 5.6 - - + -
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Residues in contact with GLU 96 (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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92K THR* 3.1 31.8 + - + +
93K ASN* 3.9 17.4 - - - +
94K MET 3.4 0.2 - - - -
95K LEU* 1.3 78.2 - - + +
97K ARG* 1.3 62.5 + - + +
98K ILE* 3.3 2.9 + - - +
99K ARG* 5.0 11.4 + - - +
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Residues in contact with ARG 97 (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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93K ASN* 3.3 23.1 + - - +
94K MET* 3.5 7.4 - - - +
95K LEU 3.2 0.6 - - - -
96K GLU* 1.3 79.7 - - + +
98K ILE* 1.3 63.2 + - - +
99K ARG* 3.2 3.4 - - - -
100K LEU* 3.2 53.9 + - + +
101K CYS* 4.1 4.0 + - - -
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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