Contacts of the helix formed by residues 42 - 53 (chain B) in PDB entry 1TAD
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 LYS 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B LEU* 3.4 33.0 - - + +
35B LEU* 3.7 9.2 - - - +
36B GLY 3.0 28.4 + - - +
37B ALA 2.8 25.1 + - - -
40B SER* 3.5 7.2 + - - +
41B GLY* 1.3 76.7 - - - +
43B SER* 1.3 63.1 + - - +
45B ILE* 3.2 10.0 + - - +
46B VAL* 3.2 9.9 + - - +
196B ASP* 4.8 5.2 - - + +
197B VAL 3.0 29.4 - - - +
199B GLY* 3.8 2.2 - - - +
207B TRP* 5.5 1.6 - - + -
220B ILE* 3.6 18.6 - - + -
351B GDP 2.8 24.4 + - - +
355B ALF 2.8 20.3 - - - -
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Residues in contact with SER 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LYS* 1.3 73.3 - - - +
44B THR* 1.3 56.8 + - - +
46B VAL* 3.2 13.2 + - - +
47B LYS* 3.0 43.6 + - - +
175B VAL 5.5 1.6 - - - -
177B THR* 3.7 15.4 + - - +
181B ILE* 5.5 1.0 - - - +
196B ASP* 3.9 8.0 + - - -
351B GDP 2.8 22.7 + - - -
352B CA 2.4 25.4 - - - -
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Residues in contact with THR 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B GLY 3.4 9.0 - - - -
42B LYS 3.1 0.4 - - - -
43B SER* 1.3 73.9 - - - +
45B ILE* 1.3 64.8 + - - +
47B LYS* 3.2 13.4 + - - +
48B GLN* 3.1 25.6 + - - +
171B LEU* 3.8 16.1 + - + +
322B ALA* 3.5 33.4 - - + +
323B THR* 3.8 20.0 - - + -
351B GDP 2.7 41.7 + - + -
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Residues in contact with ILE 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 4.2 19.5 - - + -
41B GLY 3.2 15.2 + - - +
42B LYS 3.2 7.6 + - - +
44B THR* 1.3 75.3 - - - +
46B VAL* 1.3 61.3 + - - +
48B GLN* 3.2 7.8 + - - +
49B MET* 3.0 39.8 + - + +
194B MET* 5.0 4.7 - - + -
218B ILE* 5.5 2.2 - - + -
220B ILE* 3.8 17.5 - - + -
263B PHE* 4.0 29.6 - - + -
265B ASN* 5.3 1.6 - - - +
320B THR* 5.4 1.8 - - - +
322B ALA* 3.7 26.5 - - + -
328B VAL* 4.1 15.9 - - + -
332B PHE* 5.7 0.9 - - + -
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Residues in contact with VAL 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 3.5 15.5 - - + -
42B LYS 3.4 14.1 - - - +
43B SER* 3.2 12.0 + - - +
45B ILE* 1.3 78.0 - - - +
47B LYS* 1.3 63.1 + - + +
49B MET* 3.1 19.4 + - - +
50B LYS* 3.2 11.7 + - + +
181B ILE* 5.1 6.1 - - + -
183B THR* 3.2 28.1 - - + +
194B MET* 4.7 4.3 - - + -
196B ASP* 3.3 28.5 - - + +
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Residues in contact with LYS 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B SER* 3.0 32.4 + - - +
44B THR* 3.2 12.0 + - - +
46B VAL* 1.3 76.1 - - + +
48B GLN* 1.3 63.1 + - - +
50B LYS* 3.1 8.7 + - - +
51B ILE* 3.0 26.0 + - - +
57B TYR* 3.2 23.0 - - + +
65B PHE* 4.0 18.1 - - - -
170B VAL* 3.5 28.5 - - + +
171B LEU* 3.6 23.9 + - + +
173B SER* 3.9 18.1 + - - -
175B VAL* 6.1 2.8 - - - +
351B GDP 5.7 1.6 + - - -
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Residues in contact with GLN 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B THR 3.1 10.6 + - - +
45B ILE* 3.2 8.3 + - - +
47B LYS* 1.3 76.7 - - - +
49B MET* 1.3 53.8 + - - +
51B ILE* 3.8 8.2 - - - +
52B ILE* 2.7 43.6 + - + +
171B LEU* 3.4 12.2 - - + +
322B ALA 2.6 30.8 + - - +
323B THR 3.3 10.7 + - - -
324B ASP 3.4 1.0 + - - -
325B THR* 2.8 54.9 + - - +
328B VAL* 3.7 24.7 - - + -
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Residues in contact with MET 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ILE* 3.0 32.4 + - + +
46B VAL 3.1 8.9 + - - +
48B GLN* 1.3 77.9 - - - +
50B LYS* 1.3 56.4 + - - +
52B ILE* 4.9 1.8 - - + -
53B HIS* 2.7 48.3 + - + +
54B GLN* 3.3 5.7 + - - +
183B THR* 4.1 8.7 - - + -
185B PHE* 3.6 33.4 - - + -
194B MET* 3.7 30.3 - - + -
328B VAL* 3.8 25.1 - - + -
332B PHE* 3.9 25.4 - - + -
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Residues in contact with LYS 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A PRO* 6.3 0.2 - - - +
46B VAL 3.2 6.7 + - - +
47B LYS* 3.1 12.2 + - - +
49B MET* 1.3 79.5 - - - +
51B ILE* 1.3 62.1 + - - +
54B GLN* 3.2 40.1 + - + +
55B ASP 6.0 0.2 - - - +
56B GLY 3.0 41.4 + - - +
57B TYR* 3.5 41.1 - - + +
61B GLU* 2.9 38.7 + - - -
183B THR* 5.3 0.9 - - + +
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Residues in contact with ILE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LYS 3.0 16.8 + - - +
48B GLN* 3.2 22.0 + - - +
50B LYS* 1.3 78.9 - - - +
52B ILE* 1.3 60.0 + - + +
54B GLN 4.3 5.2 - - - +
55B ASP 5.3 0.2 - - - -
56B GLY* 4.1 12.4 + - - -
57B TYR* 3.6 25.6 - - + -
167B GLU* 3.9 35.7 - - + +
171B LEU* 4.0 25.6 - - + -
325B THR* 4.1 22.2 - - + +
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Residues in contact with ILE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B GLN* 2.7 37.8 + - + +
49B MET* 4.9 3.6 - - + -
51B ILE* 1.3 75.3 - - + +
53B HIS* 1.3 87.9 + - + +
54B GLN 3.6 2.9 + - - +
325B THR* 3.7 29.8 - - + +
328B VAL* 4.2 4.9 - - + -
329B LYS* 3.7 54.7 - - + +
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Residues in contact with HIS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B MET* 2.7 37.0 + - + +
52B ILE* 1.3 100.9 - - + +
54B GLN* 1.3 63.9 + - - +
185B PHE* 3.4 33.0 - + + +
186B SER 4.5 8.5 + - - +
187B PHE* 3.7 42.1 - + + -
329B LYS* 5.7 4.1 + - - +
332B PHE* 3.5 33.7 - + + -
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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