Contacts of the strand formed by residues 43 - 48 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7G GLU* 5.7 0.2 - - - +
35G ARG* 3.9 29.8 - - + -
36G ILE 3.3 10.5 - - - +
37G THR* 4.4 14.1 - - + +
38G TYR* 4.6 0.4 - - - -
41G GLY 3.7 9.9 - - - +
42G ALA* 1.3 78.1 - - - +
44G GLY* 1.3 59.0 + - - +
45G TRP* 3.5 29.0 + - + +
113G GLN* 2.8 27.4 + - - -
354G ILE 5.3 0.9 - - - +
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Residues in contact with GLY 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G ARG* 3.3 6.4 - - - -
36G ILE 2.9 34.9 + - - -
38G TYR* 3.8 6.6 - - - -
43G VAL* 1.3 74.0 - - - +
45G TRP* 1.3 61.6 + - - -
106G ALA* 3.6 24.1 - - - +
109G ASP* 3.5 11.0 - - - -
110G GLY 4.4 0.2 - - - -
113G GLN* 4.1 1.8 - - - -
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Residues in contact with TRP 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G ILE* 4.1 15.3 - - + -
34G VAL 3.4 3.6 - - - -
35G ARG* 3.5 41.1 - - + -
43G VAL* 3.5 28.9 + - + +
44G GLY* 1.3 78.2 - - - -
46G GLY* 1.3 58.3 + - - +
105G MET* 3.4 1.2 - - - +
106G ALA* 3.1 20.7 + - - +
109G ASP* 3.0 15.1 + - - +
113G GLN* 5.3 0.2 - - - -
302G LEU* 3.6 17.9 - - + -
333G PHE* 4.0 28.3 - + - -
352G LEU* 3.4 16.4 - - + +
354G ILE* 3.6 32.8 + - + -
355G ILE 4.0 5.5 + - - -
356G GLY* 3.8 27.6 - - - -
357G ALA* 4.4 4.7 - - + -
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Residues in contact with GLY 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G ILE* 3.3 5.5 - - - -
34G VAL* 2.8 36.6 + - - -
45G TRP* 1.3 76.3 - - - +
47G GLU* 1.3 59.4 + - - -
102G ALA* 3.5 21.5 - - - -
105G MET* 4.0 8.1 - - - -
302G LEU* 3.5 11.3 - - - +
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Residues in contact with GLU 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G SER* 2.7 34.6 + - - +
32G VAL 3.3 9.0 - - - +
33G ILE* 4.7 4.7 - - + -
46G GLY* 1.3 74.7 - - - +
48G ALA* 1.3 64.5 + - - +
49G PRO* 4.7 2.0 - - + -
102G ALA* 3.7 11.3 - - - +
105G MET* 3.5 10.2 - - - +
270G MET* 3.1 21.0 - - - +
299G GLU* 3.2 16.4 - - + +
300G THR* 2.7 46.1 + - - +
302G LEU* 3.6 13.7 - - + +
303G GLY* 3.0 22.9 + - - +
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Residues in contact with ALA 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G SER* 3.9 3.6 - - - -
32G VAL* 3.0 34.7 + - - +
47G GLU* 1.3 74.9 - - - +
49G PRO* 1.3 68.1 - - - +
50G PRO* 4.6 0.2 - - - +
62G ILE* 3.6 19.7 - - + +
98G SER* 3.1 32.8 - - - +
102G ALA* 3.8 8.9 - - + +
270G MET* 3.7 6.1 - - - -
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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