Contacts of the strand formed by residues 43 - 48 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35H ARG* 4.2 17.0 - - + -
36H ILE 3.2 8.1 - - - +
37H THR* 3.5 21.1 - - + +
38H TYR* 4.6 0.9 - - - -
41H GLY 3.7 9.0 - - - +
42H ALA* 1.3 77.1 - - - +
44H GLY* 1.3 66.7 + - - +
45H TRP* 3.6 38.6 + - + +
113H GLN* 3.3 20.8 + - - +
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Residues in contact with GLY 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H ARG* 3.3 5.4 - - - -
36H ILE 2.6 40.6 + - - -
38H TYR* 3.8 9.4 - - - -
43H VAL* 1.3 73.9 - - - +
45H TRP* 1.3 60.2 + - - -
106H ALA* 3.6 24.9 - - - +
109H ASP* 3.5 10.1 - - - -
113H GLN* 4.5 0.7 - - - -
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Residues in contact with TRP 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H ILE* 4.2 15.9 - - + -
34H VAL 3.5 4.7 - - - -
35H ARG* 3.4 40.2 - - + -
43H VAL* 3.6 31.1 + - + +
44H GLY* 1.3 72.2 - - - -
46H GLY* 1.3 57.9 + - - +
105H MET* 3.3 5.7 - - - +
106H ALA* 3.0 21.1 + - - +
109H ASP* 3.1 16.0 + - - +
302H LEU* 3.7 19.1 - - + -
333H PHE* 3.9 27.1 - + - -
352H LEU* 3.4 12.6 - - + +
354H ILE* 3.2 31.4 + - + -
355H ILE 4.0 4.9 + - - -
356H GLY* 3.5 26.2 - - - -
357H ALA* 4.1 6.7 - - + -
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Residues in contact with GLY 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H ILE* 3.5 2.4 - - - -
34H VAL* 2.9 36.7 + - - -
45H TRP* 1.3 76.5 - - - +
47H GLU* 1.3 61.1 + - - -
102H ALA 3.6 18.2 - - - -
105H MET* 3.9 7.6 - - - -
106H ALA 4.3 0.2 - - - -
302H LEU* 3.1 16.3 - - - +
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Residues in contact with GLU 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H SER* 2.4 34.0 + - - +
32H VAL 3.3 11.0 - - - +
33H ILE* 4.1 8.3 - - + -
46H GLY* 1.3 74.4 - - - +
48H ALA* 1.3 61.8 + - - +
102H ALA* 3.4 11.9 - - - +
105H MET* 3.4 10.4 - - + +
270H MET* 3.1 21.5 - - - +
299H GLU* 3.3 17.7 - - - +
300H THR* 2.7 45.0 + - - -
302H LEU* 3.6 9.9 - - + +
303H GLY* 2.9 25.9 + - - +
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Residues in contact with ALA 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H SER* 3.8 3.6 - - - -
32H VAL* 2.9 35.6 + - + +
47H GLU* 1.3 76.5 - - - +
49H PRO* 1.3 69.0 - - - +
62H ILE* 3.9 17.1 - - + +
98H SER 3.2 34.3 - - - +
102H ALA* 3.8 7.9 - - + -
270H MET* 3.8 4.7 - - - -
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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