Contacts of the strand formed by residues 9 - 14 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A PHE* 5.6 1.4 - - - -
8J ASP* 3.4 32.5 - - + -
9J PHE 5.7 2.0 - - - -
10J VAL* 5.9 0.9 - - + -
48J PHE* 4.0 17.0 - + + -
65J THR* 3.8 24.2 - - - -
66J ARG* 4.1 11.4 - - + -
67J HIS* 3.1 59.7 + + - -
7K SER 4.5 5.4 - - - -
8K ASP* 1.3 82.0 + - - +
10K VAL* 1.3 71.8 + - - +
11K VAL* 3.9 6.3 - - + -
45K ILE* 3.5 22.0 - - + -
46K ALA 3.2 20.9 - - - +
47K GLN* 3.9 9.9 - - + -
48K PHE* 4.7 0.7 - - - +
65K THR* 4.5 4.0 - - - -
66K ARG 4.9 0.5 + - - -
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Residues in contact with VAL 10 (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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9A PHE* 5.5 1.3 - - + -
45A ILE* 4.3 23.3 - - + -
9K PHE* 1.3 81.2 - - - +
11K VAL* 1.3 62.1 + - - +
12K ILE* 3.3 26.9 - - + -
44K LEU 3.7 0.9 - - - +
45K ILE* 3.4 4.3 - - - +
46K ALA* 2.9 38.1 + - + +
48K PHE* 4.3 13.0 - - + -
55K ILE* 4.1 20.2 - - + -
63K ILE* 4.9 3.1 - - + -
64K GLN 3.5 7.9 - - - +
65K THR* 4.0 19.7 - - + -
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Residues in contact with VAL 11 (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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65J THR* 3.9 17.7 - - + +
67J HIS* 4.2 3.1 - - + -
70J ILE* 4.0 19.5 - - + -
9K PHE* 3.9 22.7 - - + -
10K VAL* 1.3 77.3 - - - +
12K ILE* 1.3 63.1 + - - +
43K VAL* 3.9 23.6 - - + -
44K LEU 3.6 2.9 - - - +
45K ILE* 4.2 10.5 - - + +
62K TYR 3.8 0.2 - - - +
63K ILE* 3.1 10.4 - - - +
64K GLN* 2.9 60.2 + - + +
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Residues in contact with ILE 12 (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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10K VAL* 3.3 33.0 - - + +
11K VAL* 1.3 80.1 - - - +
13K LYS* 1.3 62.5 + - - +
19K VAL* 4.7 1.1 - - + -
21K VAL* 3.9 35.4 - - + -
38K LEU* 3.8 18.8 - - + +
43K VAL* 3.4 3.4 - - - -
44K LEU* 2.8 46.1 + - + +
46K ALA* 4.7 2.7 - - + -
57K VAL* 4.2 16.4 - - + -
61K ALA* 3.8 23.6 - - + -
62K TYR 3.7 2.0 - - - -
63K ILE* 4.2 14.6 - - + -
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Residues in contact with LYS 13 (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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70J ILE* 3.9 24.7 - - + +
71J GLU* 2.9 31.7 + - - +
73J GLU* 3.0 30.6 + - - -
11K VAL* 5.0 0.2 - - - +
12K ILE* 1.3 73.4 - - - +
14K ALA* 1.3 67.6 + - - +
15K LEU* 3.6 20.0 + - + +
41K GLY* 4.4 10.1 - - - +
42K GLU 3.6 4.7 - - - +
43K VAL* 3.9 14.4 - - + -
61K ALA* 3.1 5.5 - - - -
62K TYR* 2.7 49.1 + - + +
28L ALA* 3.8 19.4 - - - +
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Residues in contact with ALA 14 (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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12K ILE 4.0 1.6 + - - -
13K LYS* 1.3 72.8 - - - +
15K LEU* 1.3 60.6 + - - +
16K GLU 3.4 5.4 - - - +
19K VAL* 3.7 19.3 - - + -
38K LEU* 3.6 25.4 - - + +
39K ASP 3.5 21.5 - - - +
40K LYS* 4.2 0.2 - - - +
41K GLY* 2.6 31.9 + - - -
42K GLU 3.1 8.6 + - - +
60K LYS 3.8 5.4 - - - -
61K ALA* 4.2 2.0 - - - -
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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