Contacts of the helix formed by residues 42 - 53 (chain A) in PDB entry 1TAG
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A LEU* 3.4 32.7 - - + +
35A LEU 4.2 4.0 - - - -
36A GLY 3.0 21.4 + - - +
37A ALA 3.0 22.2 + - - -
38A GLY* 4.2 2.6 - - - -
40A SER* 4.0 7.0 - - - +
41A GLY* 1.3 76.2 - - - +
43A SER* 1.3 61.5 + - - +
45A ILE 3.2 2.8 + - - -
46A VAL* 3.1 25.7 + - - +
196A ASP* 4.0 15.9 - - + +
197A VAL 3.5 24.2 - - - +
198A GLY* 4.0 5.5 - - - +
200A GLN* 5.3 3.1 - - - +
203A GLU* 5.4 0.9 - - - -
220A ILE* 3.7 18.4 - - + -
351A GDP 2.8 36.7 + - - +
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Residues in contact with SER 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LYS* 1.3 72.6 - - - +
44A THR* 1.3 57.5 + - - +
46A VAL* 3.2 11.8 + - - +
47A LYS* 2.9 41.5 + - - +
196A ASP* 3.6 10.8 + - - -
351A GDP 2.9 20.4 + - - -
352A MG 2.2 28.4 - - - -
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Residues in contact with THR 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLY 3.6 5.6 - - - -
42A LYS 3.2 0.4 - - - -
43A SER* 1.3 74.4 - - - +
45A ILE* 1.3 64.6 + - - +
47A LYS* 3.1 15.6 + - - +
48A GLN* 2.9 26.4 + - - +
171A LEU* 3.9 14.1 - - + +
322A ALA* 3.3 36.3 - - + +
323A THR* 3.9 17.7 - - + -
351A GDP 2.8 43.1 + - + -
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Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.0 23.6 - - + -
41A GLY 3.1 14.9 + - - +
42A LYS 3.2 7.6 + - - +
44A THR* 1.3 74.4 - - - +
46A VAL* 1.3 61.7 + - - +
48A GLN* 3.1 6.1 + - - +
49A MET* 3.0 38.1 + - + +
194A MET* 4.9 1.8 - - + -
218A ILE* 5.6 1.6 - - + -
220A ILE* 3.8 17.5 - - + -
263A PHE* 4.2 24.7 - - + -
265A ASN* 5.4 1.6 - - - +
320A THR* 5.5 1.8 - - - +
322A ALA* 3.7 22.9 - - + -
328A VAL* 3.9 24.0 - - + -
332A PHE* 5.7 2.2 - - + -
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Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 3.5 18.2 - - + -
42A LYS 3.1 14.3 + - - +
43A SER* 3.4 11.4 - - - +
45A ILE* 1.3 77.4 - - - +
47A LYS* 1.3 64.0 + - + +
49A MET* 3.1 19.2 + - - +
50A LYS* 3.3 11.1 + - - +
181A ILE* 5.2 8.1 - - + -
183A THR* 3.5 25.1 - - + +
194A MET* 4.5 8.5 - - + +
195A PHE 5.5 0.2 - - - -
196A ASP* 3.9 26.9 - - + +
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Residues in contact with LYS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A SER* 2.9 23.1 + - - +
44A THR* 3.1 29.0 + - - +
46A VAL* 1.3 77.8 - - + +
48A GLN* 1.3 61.6 + - - +
50A LYS* 3.1 7.0 + - - +
51A ILE* 3.1 24.8 + - - +
57A TYR* 3.4 25.6 + - + +
65A PHE* 5.1 6.3 - - + -
170A VAL* 3.4 28.9 - - + +
171A LEU* 3.2 37.6 + - + -
173A SER* 3.6 19.7 + - - -
174A ARG* 6.0 0.2 - - - +
175A VAL* 6.3 3.4 - - - -
351A GDP 5.1 0.8 + - - -
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Residues in contact with GLN 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A THR 2.9 14.3 + - - +
45A ILE* 3.1 8.7 + - - +
47A LYS* 1.3 77.6 - - - +
49A MET* 1.3 54.6 + - - +
51A ILE* 3.3 8.7 + - - +
52A ILE* 2.8 41.8 + - + +
171A LEU* 3.5 13.0 - - + +
322A ALA 2.8 29.5 + - - +
323A THR 3.3 11.7 + - - -
324A ASP 3.5 1.4 + - - -
325A THR* 2.7 55.8 + - - +
328A VAL* 3.7 26.0 - - + -
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Residues in contact with MET 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ILE* 3.0 22.8 + - + +
46A VAL 3.1 8.3 + - - +
48A GLN* 1.3 78.9 - - - +
50A LYS* 1.3 57.0 + - - +
52A ILE* 4.2 7.9 - - + -
53A HIS* 2.7 51.7 + - + +
54A GLN* 3.3 7.9 + - - +
183A THR* 4.1 8.3 - - + -
185A PHE* 3.8 24.5 - - + -
194A MET* 3.6 32.1 - - + -
328A VAL* 3.8 28.3 - - + -
332A PHE* 3.9 24.5 - - + -
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Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A VAL 3.3 7.8 + - - +
47A LYS* 3.1 11.0 + - - +
49A MET* 1.3 80.7 - - - +
51A ILE* 1.3 57.9 + - - +
54A GLN* 3.1 45.7 + - + +
55A ASP 5.8 0.4 - - - +
56A GLY* 2.9 46.9 + - - +
57A TYR* 3.4 40.2 - - + +
61A GLU* 3.1 24.3 + - - -
183A THR* 5.9 0.4 - - + -
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Residues in contact with ILE 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LYS 3.1 13.4 + - - +
48A GLN* 3.7 20.0 - - - +
50A LYS* 1.3 78.6 - - - +
52A ILE* 1.3 60.7 + - - +
54A GLN 4.1 5.4 - - - +
55A ASP* 4.9 0.5 - - - +
56A GLY* 3.9 10.2 + - - -
57A TYR* 3.9 19.7 - - + -
167A GLU* 3.8 36.1 - - + +
171A LEU* 3.9 27.4 - - + -
325A THR* 4.0 25.1 - - + +
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Residues in contact with ILE 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A GLN* 2.8 37.6 + - + +
49A MET* 4.2 6.1 - - + -
51A ILE* 1.3 77.3 - - - +
53A HIS* 1.3 87.1 + - + +
54A GLN 3.6 3.0 - - - +
325A THR* 3.7 29.2 - - + +
328A VAL* 4.2 5.2 - - + -
329A LYS* 3.8 49.6 - - + +
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Residues in contact with HIS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A MET* 2.7 44.0 + - - +
52A ILE* 1.3 96.4 + - + +
54A GLN* 1.3 64.1 + - - +
185A PHE* 3.5 35.7 - + + +
186A SER 4.8 6.5 + - - +
187A PHE* 3.5 47.0 - + - +
329A LYS* 5.8 2.7 + - + -
332A PHE* 3.7 17.6 - - - +
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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