Contacts of the strand formed by residues 61 - 66 (chain T) in PDB entry 4C4K
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 LEU 61 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12O PHE* 4.5 13.0 - - + +
13O LEU 5.0 2.9 - - - +
14O THR* 4.5 6.7 - - - -
15O ARG* 3.8 37.0 - - + +
16O PRO* 4.8 2.0 - - + -
25T ALA* 4.1 11.4 - - + -
26T CYS 3.5 32.8 - - - +
27T ALA 3.8 3.4 - - - +
28T PHE* 3.5 5.4 - - - -
56T GLU 3.9 0.9 - - - +
57T ASN* 3.5 1.7 - - - -
58T THR* 2.8 46.6 + - + +
60T ASP* 1.3 83.9 - - - +
62T THR* 1.3 63.8 + - - +
63T THR* 4.2 14.1 - - - +
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Residues in contact with THR 62 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24T VAL 3.9 0.9 - - - +
25T ALA* 3.4 0.9 - - - +
26T CYS* 2.9 43.3 + - + +
28T PHE* 3.7 13.4 - - + -
36T VAL* 3.6 6.9 - - + +
38T TRP* 2.9 26.3 + - + +
55T ILE* 4.1 0.7 - - - +
56T GLU 3.4 3.8 + - - -
57T ASN* 2.5 23.6 + - - -
61T LEU* 1.3 73.8 - - - +
63T THR* 1.3 65.9 + - - +
79T LEU* 3.8 35.2 - - + -
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Residues in contact with THR 63 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11O ARG* 5.3 7.6 + - + +
12O PHE 5.5 1.4 + - - -
23T THR* 4.2 11.7 - - - -
24T VAL 3.4 12.8 - - - +
25T ALA* 3.8 14.0 - - + +
38T TRP* 4.5 1.3 - - - -
54T HIS 3.7 0.7 - - - +
55T ILE* 3.3 8.1 - - - +
56T GLU* 2.8 51.5 + - + +
61T LEU* 4.2 12.0 - - - +
62T THR* 1.3 81.4 + - - +
64T LEU* 1.3 63.5 + - - +
65T ILE* 3.9 23.4 + - + +
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Residues in contact with LEU 64 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22T LEU* 3.8 1.4 - - + +
23T THR* 3.3 5.0 - - - -
24T VAL* 2.9 41.0 + - + +
38T TRP* 4.0 42.6 - - + -
45T ILE* 5.0 6.1 - - + -
53T PHE* 4.6 15.3 - - + -
54T HIS 3.7 2.9 - - - +
55T ILE* 3.9 25.4 - - + -
63T THR* 1.3 70.5 - - - +
65T ILE* 1.3 66.7 + - - +
66T ILE* 4.2 10.8 - - + -
77T TYR* 3.9 28.5 - - + -
92T VAL* 5.6 0.2 - - + -
94T ILE* 4.3 14.1 - - + -
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Residues in contact with ILE 65 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11O ARG* 4.8 7.0 - - - +
21T VAL* 4.3 4.0 - - + -
22T LEU 3.4 3.1 - - - +
23T THR* 3.6 27.1 - - + -
53T PHE* 3.3 5.2 - - - +
54T HIS* 2.7 60.5 + - + +
56T GLU* 3.5 28.9 - - + +
63T THR* 3.9 15.3 - - + +
64T LEU* 1.3 75.5 - - - +
66T ILE* 1.3 67.4 + - - +
67T MET* 3.8 26.2 - - + -
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Residues in contact with ILE 66 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21T VAL* 3.5 0.9 - - - -
22T LEU* 2.8 59.6 + - + +
52T ARG* 3.6 15.7 - - - +
53T PHE* 3.6 36.1 - - + -
64T LEU* 4.4 11.2 - - + -
65T ILE* 1.3 76.2 - - - +
67T MET* 1.3 61.2 + - - +
69T VAL* 3.6 16.2 - - + +
73T ASP* 3.4 29.4 - - + +
77T TYR* 4.2 11.0 - - + +
94T ILE* 4.2 20.6 - - + -
96T ILE* 6.4 0.2 - - + -
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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