Contacts of the strand formed by residues 34 - 42 (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 34 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27K LEU 3.3 14.8 - - - -
28K LYS* 3.8 15.3 - - - -
29K TYR* 4.4 5.1 - - - +
32K ASN 4.7 1.6 - - - -
33K ARG* 1.3 79.1 - - - +
35K GLU* 1.3 65.9 + - - +
36K TYR* 3.9 3.9 - - - -
3N C 3.5 3.0 - - - +
4N G 2.6 60.9 + - - -
5N C 3.3 13.2 + - - -
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Residues in contact with GLU 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25K TYR 3.7 0.3 - - - +
26K LYS* 3.6 2.9 - - - +
27K LEU* 2.7 38.1 + - + +
29K TYR* 2.8 35.1 + - + +
34K SER* 1.3 76.8 - - - +
36K TYR* 1.3 68.1 + - - +
37K ARG* 2.9 30.6 + - + +
70K GLN* 5.0 0.3 + - - -
81K ARG* 4.5 2.4 + - - -
83K SER* 3.0 35.8 + - - +
4N G 5.1 0.9 - - - -
5N C 3.8 12.8 - - + -
6N C 2.8 30.8 + - - -
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Residues in contact with TYR 36 (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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25K TYR 3.4 4.5 - - - -
26K LYS* 3.6 34.2 + - + -
28K LYS* 3.8 12.5 + - - -
34K SER* 3.9 6.7 - - - -
35K GLU* 1.3 79.5 - - - +
37K ARG* 1.3 59.3 + - - +
83K SER* 3.2 5.1 + - - -
84K SER 2.8 32.2 + - - +
85K LYS* 3.5 45.4 + - + +
88K TYR* 3.6 29.6 - + + -
89K TYR* 4.0 14.4 + + - -
4N G 2.9 46.1 + - - -
5N C 3.8 7.9 + - - -
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Residues in contact with ARG 37 (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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23K GLY 3.9 0.5 - - - +
24K LEU* 3.5 6.1 - - - -
25K TYR* 2.9 41.4 + - + +
27K LEU* 4.0 11.7 - - + -
29K TYR* 3.5 5.2 + - - -
35K GLU* 2.9 38.1 + - - +
36K TYR* 1.3 77.2 - - - +
38K VAL* 1.3 64.2 + - - +
39K VAL* 4.0 16.8 - - + -
79K GLU* 4.5 0.6 + - - -
81K ARG* 3.4 42.2 - - + +
82K VAL 3.5 2.2 - - - +
83K SER* 4.7 1.6 - - - -
88K TYR* 3.9 3.8 - - - -
17L T 3.5 23.7 + - - -
18L C 3.5 9.1 - - - +
7N G 2.8 29.1 + - - -
8N G 2.9 22.0 + - - -
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Residues in contact with VAL 38 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18K ILE* 3.6 31.2 - - + -
23K GLY 3.9 2.5 - - - -
24K LEU* 3.9 9.6 - - + -
37K ARG* 1.3 76.3 - - - +
39K VAL* 1.3 62.2 + - - +
56K MET* 4.3 10.1 - - + -
80K LEU* 3.6 3.0 - - - +
81K ARG* 3.4 4.3 - - - -
82K VAL* 2.9 37.6 + - + +
84K SER 4.8 0.9 - - - +
87K LEU* 3.8 23.1 - - + +
88K TYR* 3.8 32.3 - - + +
91K PHE* 3.7 13.2 - - + -
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Residues in contact with VAL 39 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18K ILE* 3.7 6.6 - - - +
22K GLY* 3.2 7.9 - - - -
23K GLY 3.0 32.3 + - - +
25K TYR* 3.8 29.8 - - + -
37K ARG* 4.0 14.6 - - + -
38K VAL* 1.3 79.1 - - - +
40K ILE* 1.3 72.8 + - - +
41K THR* 3.7 26.5 - - + -
79K GLU* 3.7 28.0 - - + +
80K LEU* 3.2 2.9 - - - +
81K ARG* 4.4 4.9 - - + -
16L T 4.5 5.6 - - + -
17L T 5.7 0.7 - - + -
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Residues in contact with ILE 40 (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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14K LEU* 4.4 7.4 - - + -
17K LEU* 3.8 39.0 - - + +
18K ILE* 3.6 22.9 - - + -
21K ASP* 4.0 7.6 - - + -
22K GLY* 4.1 0.2 - - - -
39K VAL* 1.3 80.6 - - - +
41K THR* 1.3 67.7 + - - +
48K ILE* 3.8 3.4 - - + +
52K PHE* 3.9 35.2 - - + -
56K MET* 4.2 19.7 - - + -
80K LEU* 2.7 50.7 + - + +
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Residues in contact with THR 41 (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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21K ASP* 2.6 35.0 + - - +
22K GLY* 5.0 0.9 - - - -
39K VAL* 3.7 20.6 - - + -
40K ILE* 1.3 78.4 - - - +
42K GLN* 1.3 77.7 + - - +
77K ARG* 3.7 18.6 - - - +
78K TYR 3.2 8.5 - - - -
79K GLU* 4.1 15.5 - - + -
14L A 3.3 24.1 - - - +
15L G 3.8 16.6 - - + -
16L T 4.6 0.7 - - + -
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Residues in contact with GLN 42 (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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21K ASP* 2.6 31.9 + - - +
41K THR* 1.3 80.9 + - - +
43K LYS* 1.3 62.0 + - - +
44K SER* 4.0 11.2 - - - +
47K LEU* 3.7 27.3 - - + +
48K ILE* 3.6 22.0 - - + +
52K PHE* 4.1 20.8 - - + -
77K ARG* 3.9 4.0 - - - +
78K TYR* 2.8 38.4 + - - +
115K VAL* 4.6 9.0 - - - +
120K LYS* 5.9 1.7 - - - -
14L A 3.6 20.7 + - - +
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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