Contacts of the strand formed by residues 9 - 14 (chain O) in PDB entry 5EF3
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 PHE 9 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9N PHE* 5.5 1.6 - - - -
7O SER 4.7 4.5 - - - -
8O ASP* 1.3 83.5 + - - +
10O VAL* 1.3 68.1 + - - +
11O VAL* 3.7 17.7 - - + -
45O ILE* 3.5 19.5 - - + -
46O ALA 3.2 20.2 - - - +
47O GLN* 3.8 11.0 - - + -
48O PHE* 4.7 1.1 - - - +
65O THR* 4.6 3.3 - - - -
8P ASP* 3.7 29.4 - - + -
9P PHE 5.6 0.7 - - - -
10P VAL* 5.2 1.6 - - + -
48P PHE* 4.0 21.1 - + + -
65P THR* 3.8 21.3 - - + -
66P ARG* 4.2 8.7 - - + -
67P HIS* 3.3 53.4 + + - -
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Residues in contact with VAL 10 (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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9N PHE* 5.3 1.6 - - + -
45N ILE* 3.9 27.1 - - + -
9O PHE* 1.3 78.2 - - - +
11O VAL* 1.3 61.7 + - - +
12O ILE* 3.6 24.5 - - + -
44O LEU 3.6 1.2 - - - +
45O ILE* 3.4 4.3 - - - +
46O ALA* 2.8 40.8 + - + +
48O PHE* 4.5 12.3 - - + -
55O ILE* 3.9 15.7 - - + -
63O ILE* 4.8 2.0 - - + -
64O GLN 3.5 8.7 - - - +
65O THR* 3.6 24.2 - - + -
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Residues in contact with VAL 11 (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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9O PHE* 3.7 24.9 - - + -
10O VAL* 1.3 76.0 - - - +
12O ILE* 1.3 63.8 + - - +
43O VAL* 4.0 23.3 - - + -
44O LEU 3.6 2.7 - - - +
45O ILE* 4.3 9.9 - - + +
62O TYR 3.7 0.7 - - - +
63O ILE* 3.2 6.4 - - - +
64O GLN* 2.8 66.9 + - + +
65P THR* 4.0 15.0 - - + +
67P HIS* 4.7 1.6 - - + -
70P ILE* 4.2 18.2 - - + -
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Residues in contact with ILE 12 (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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45N ILE* 5.6 0.2 - - + -
10O VAL* 3.6 25.8 - - + -
11O VAL* 1.3 77.0 - - - +
13O LYS* 1.4 61.7 + - - +
14O ALA 4.8 0.2 - - - +
19O VAL* 4.8 1.1 - - + -
21O VAL* 3.7 46.7 - - + -
38O LEU* 4.1 9.8 - - + +
42O GLU 3.8 1.0 - - - +
43O VAL* 3.3 5.7 - - - -
44O LEU* 2.8 49.6 + - + +
46O ALA* 5.2 2.0 - - + -
55O ILE* 4.7 1.8 - - + -
57O VAL* 4.2 16.4 - - + -
61O ALA* 3.8 25.1 - - + -
62O TYR 3.4 2.9 - - - +
63O ILE* 4.2 13.2 - - + -
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Residues in contact with LYS 13 (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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11O VAL 4.3 0.4 - - - -
12O ILE* 1.4 73.5 - - - +
14O ALA* 1.3 69.0 + - - +
15O LEU* 3.9 16.9 - - + +
41O GLY* 4.2 16.2 - - - +
42O GLU 3.4 6.3 - - - +
43O VAL* 3.8 12.6 - - + -
61O ALA* 3.3 4.3 - - - -
62O TYR* 2.7 45.1 + - + +
70P ILE* 3.5 30.4 - - + +
71P GLU* 2.8 33.8 + - - +
73P GLU* 2.9 28.0 + - - -
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Residues in contact with ALA 14 (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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12O ILE 4.1 1.0 + - - -
13O LYS* 1.3 73.0 - - - +
15O LEU* 1.3 63.3 + - - +
16O GLU 3.3 14.6 - - - +
19O VAL* 3.7 14.6 - - + -
38O LEU* 3.8 20.7 - - + +
39O ASP 3.5 21.8 - - - +
41O GLY* 2.8 26.0 + - - -
42O GLU 3.1 9.2 + - - +
60O LYS 3.9 5.2 - - - -
61O ALA* 4.3 2.7 - - - -
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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