Contacts of the strand formed by residues 43 - 48 (chain C) in PDB entry 1TKK
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 VAL 43 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ARG* 4.2 22.0 - - + +
36C ILE 3.3 11.4 - - - +
37C THR* 4.4 16.4 - - + +
38C TYR* 4.6 1.8 - - - -
41C GLY 3.9 9.6 - - - +
42C ALA* 1.3 80.2 - - - +
44C GLY* 1.3 69.1 + - - +
45C TRP* 3.7 33.7 + - + +
109C ASP* 3.8 1.9 - - - +
113C GLN* 2.8 22.6 + - - +
354C ILE 5.5 0.2 - - - +
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Residues in contact with GLY 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ARG* 3.5 4.3 - - - -
36C ILE 2.8 35.1 + - - -
38C TYR* 3.9 6.2 - - - -
43C VAL* 1.3 75.5 - - - +
45C TRP* 1.3 62.1 + - - -
106C ALA* 3.5 24.4 - - - +
109C ASP* 3.2 12.3 - - - -
113C GLN* 4.2 0.7 - - - -
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Residues in contact with TRP 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ILE* 3.9 20.4 - - + -
34C VAL 3.6 3.8 - - - -
35C ARG* 3.5 36.1 - - + -
43C VAL* 3.7 24.4 + - + +
44C GLY* 1.3 78.4 - - - -
46C GLY* 1.3 58.4 + - - +
105C MET* 3.4 6.8 - - - +
106C ALA* 3.3 19.2 + - - +
109C ASP* 3.0 16.7 + - - +
302C LEU* 3.7 18.6 - - + -
333C PHE* 3.9 23.8 - + - -
352C LEU* 3.5 11.7 - - + +
354C ILE* 3.5 31.0 + - + -
355C ILE 3.8 6.7 + - - -
356C GLY* 3.6 28.7 - - - -
357C ALA* 4.2 3.4 - - + -
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Residues in contact with GLY 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ILE* 3.5 2.1 - - - -
34C VAL* 3.0 32.1 + - - +
45C TRP* 1.3 75.9 - - - +
47C GLU* 1.3 62.1 + - - +
102C ALA* 3.4 21.1 - - - -
105C MET* 3.7 10.1 - - - -
106C ALA* 4.0 1.2 - - - +
302C LEU* 3.2 15.2 - - - +
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Residues in contact with GLU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C SER* 2.7 30.4 + - - +
32C VAL 3.2 10.1 - - - +
33C ILE* 4.3 4.3 - - + -
46C GLY* 1.3 74.6 - - - +
48C ALA* 1.3 67.6 + - - +
49C PRO* 4.4 3.1 - - + -
102C ALA* 3.3 12.8 - - - +
105C MET* 3.4 9.7 - - - +
270C MET* 3.2 20.3 - - - +
299C GLU* 3.6 14.6 - - - +
300C THR* 2.7 47.9 + - - +
302C LEU* 3.6 11.5 - - + +
303C GLY* 2.9 24.2 + - - +
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Residues in contact with ALA 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C SER* 3.2 4.2 - - - -
32C VAL* 2.9 36.6 + - - +
47C GLU* 1.3 75.3 - - - +
49C PRO* 1.3 68.8 - - - +
62C ILE* 3.9 20.0 - - + +
98C SER* 3.2 31.4 - - - +
102C ALA* 3.8 6.7 - - + +
270C MET* 3.7 8.3 - - - -
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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