Contacts of the helix formed by residues 37 - 54 (chain A) in PDB entry 1TF5
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 SER 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ASN 3.8 0.4 + - - -
36A LEU* 1.3 77.2 - - - +
38A ASP* 1.3 54.4 + - - +
39A ASP* 4.0 7.0 + - - +
40A ALA* 2.7 26.4 + - - +
41A LEU* 2.5 35.2 + - - +
75A ARG* 3.8 1.8 - - - +
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Residues in contact with ASP 38 (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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37A SER* 1.3 70.9 - - - +
39A ASP* 1.3 60.5 + - - +
41A LEU* 3.0 2.2 + - - +
42A LYS* 2.8 36.6 + - - +
75A ARG* 2.8 29.0 + - - +
147A PHE* 3.4 35.0 - - + -
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Residues in contact with ASP 39 (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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37A SER* 3.2 6.4 + - - +
38A ASP* 1.3 79.9 - - - +
40A ALA* 1.3 57.6 + - - +
42A LYS* 3.4 10.3 + - - +
43A HIS* 2.9 28.5 + - - +
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Residues in contact with ALA 40 (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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36A LEU* 3.7 25.2 - - + +
37A SER* 2.7 28.2 + - - +
39A ASP* 1.3 74.5 - - - +
41A LEU* 1.3 64.2 + - - +
43A HIS* 3.4 15.4 + - - +
44A LYS* 3.5 14.9 + - - +
47A GLU* 4.7 1.6 - - - +
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Residues in contact with LEU 41 (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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33A TYR* 4.1 31.0 - - + +
36A LEU* 3.8 12.1 - - + +
37A SER 2.5 20.3 + - - +
38A ASP 3.5 5.4 - - - +
40A ALA* 1.3 72.5 - - - +
42A LYS* 1.3 62.4 + - - +
44A LYS* 3.1 22.2 - - + +
68A VAL* 3.9 21.5 - - + +
71A GLU* 3.7 11.2 - - + -
72A ALA* 4.1 8.5 - - - +
75A ARG* 3.5 35.4 - - - +
147A PHE* 4.0 18.2 - - + -
148A LEU* 4.1 11.6 - - + +
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Residues in contact with LYS 42 (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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38A ASP 2.8 16.0 + - - +
39A ASP* 3.6 9.0 - - - +
41A LEU* 1.3 74.3 - - - +
43A HIS* 1.3 62.4 + - - +
44A LYS 2.9 7.1 + - - -
45A THR* 3.1 21.0 + - - -
46A ILE* 4.3 1.0 + - - +
146A GLU 4.6 4.8 + - - -
147A PHE* 3.5 24.2 - - + +
148A LEU* 3.8 16.2 - - - +
149A GLY* 3.5 24.2 - - - +
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Residues in contact with HIS 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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39A ASP 2.9 18.0 + - - +
40A ALA* 3.6 11.2 - - - +
41A LEU 3.3 0.8 - - - -
42A LYS* 1.3 76.7 - - - +
44A LYS* 1.3 62.5 + - - +
46A ILE* 2.9 50.3 + - + +
47A GLU* 3.0 35.5 + - + +
50A GLU* 4.4 4.6 + - - -
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Residues in contact with LYS 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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32A ASP 5.3 1.2 + - - -
33A TYR* 3.9 19.9 + - + -
36A LEU* 3.6 26.6 - - + +
40A ALA 3.5 6.2 + - - +
41A LEU* 3.1 23.1 - - + +
42A LYS 2.9 1.0 - - - -
43A HIS* 1.3 77.5 - - - +
45A THR* 1.3 56.3 + - - +
47A GLU* 3.1 36.2 + - + +
48A PHE* 2.8 54.4 + - + -
64A GLU* 5.4 4.9 + - - +
68A VAL* 4.1 17.3 - - + -
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Residues in contact with THR 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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42A LYS 3.1 9.3 + - - -
43A HIS 3.1 0.2 - - - -
44A LYS* 1.3 77.8 - - - +
46A ILE* 1.3 67.8 + - + +
48A PHE* 3.2 5.0 + - - +
49A LYS* 3.0 52.9 + - - +
115A TYR* 2.8 23.9 + - - -
119A LEU* 3.9 12.1 - - + -
148A LEU* 2.5 31.7 + - - +
149A GLY* 4.7 4.3 - - - +
150A LEU* 4.2 11.2 - - + -
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Residues in contact with ILE 46 (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 5.0 1.6 - - - +
43A HIS* 2.9 43.6 + - + +
45A THR* 1.3 79.2 - - + +
47A GLU* 1.3 64.2 + - - +
49A LYS* 3.3 13.7 + - + +
50A GLU* 3.0 44.6 + - + +
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Residues in contact with GLU 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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40A ALA 4.7 1.4 - - - +
43A HIS* 3.0 41.9 + - + +
44A LYS* 3.2 48.4 + - + +
46A ILE* 1.3 76.7 - - - +
48A PHE* 1.3 64.8 + - + +
50A GLU* 3.3 14.5 + - - +
51A ARG* 3.0 38.8 + - - +
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Residues in contact with PHE 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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33A TYR* 5.3 0.2 - - - -
44A LYS* 2.8 37.9 + - + +
45A THR* 3.6 4.3 - - - +
47A GLU* 1.3 74.3 - - + +
49A LYS* 1.3 58.5 + - - +
51A ARG* 3.4 15.8 + - - +
52A LEU* 2.9 34.8 + - - +
61A LEU* 3.5 21.0 - - + +
64A GLU* 3.9 28.3 - - + -
65A ALA* 3.8 20.2 - - - -
68A VAL* 3.4 33.7 - - + -
115A TYR* 3.3 30.3 - + - -
119A LEU* 3.8 20.0 - - + -
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Residues in contact with LYS 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 THR* 3.0 39.8 + - + +
46A ILE* 3.3 13.4 + - + +
48A PHE* 1.3 74.4 - - - +
50A GLU* 1.3 61.2 + - + +
52A LEU* 3.7 9.5 - - - +
53A GLU* 2.9 28.2 + - - +
118A ALA 5.3 0.4 - - - -
119A LEU* 3.6 34.5 + - + +
121A GLY* 6.0 1.6 - - - +
149A GLY 5.1 2.8 + - - -
150A LEU* 4.1 18.4 - - - +
171A ASP* 4.7 8.7 + - - -
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Residues in contact with GLU 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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43A HIS* 4.4 4.3 + - - -
46A ILE* 3.0 31.1 + - + +
47A GLU* 3.3 28.6 + - - +
48A PHE 3.3 0.2 - - - -
49A LYS* 1.3 76.5 - - + +
51A ARG* 1.3 59.4 + - + +
53A GLU* 3.0 18.0 + - - +
54A LYS* 2.9 41.3 + - - +
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Residues in contact with ARG 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 GLU* 3.0 28.5 + - - +
48A PHE* 3.7 13.1 - - - +
50A GLU* 1.3 77.5 - - + +
52A LEU* 1.3 58.7 + - - +
54A LYS* 3.0 30.5 - - + +
56A ALA* 2.9 32.6 + - + +
60A ASP* 5.0 3.2 + - - +
61A LEU* 3.3 27.6 - - + +
64A GLU* 2.9 42.0 + - - -
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Residues in contact with LEU 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 PHE 2.9 27.6 + - - +
49A LYS* 3.7 7.9 - - - +
51A ARG* 1.3 75.2 - - - +
53A GLU* 1.3 63.2 + - - +
55A GLY* 3.2 10.7 + - - -
56A ALA* 3.4 25.8 - - - +
57A THR* 3.8 14.4 - - - -
58A THR* 4.0 12.6 - - + +
61A LEU* 3.4 22.2 - - + -
119A LEU* 3.5 35.4 - - + +
120A THR* 3.9 22.4 - - + -
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Residues in contact with GLU 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 LYS 2.9 14.6 + - - +
50A GLU* 3.0 23.5 - - - +
52A LEU* 1.3 78.6 - - - +
54A LYS* 1.3 59.9 + - - +
55A GLY 3.3 4.0 + - - -
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Residues in contact with LYS 54 (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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50A GLU* 2.9 29.2 + - - +
51A ARG* 3.0 36.6 - - + +
53A GLU* 1.3 80.8 + - - +
55A GLY* 1.3 55.3 + - - -
56A ALA* 3.6 1.4 + - + +
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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