Contacts of the helix formed by residues 35 - 48 (chain A) in PDB entry 1TFZ
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 ASP 35 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A CYS* 3.9 2.2 - - - +
34A GLY* 1.3 76.8 - - - +
36A ALA* 1.3 65.4 + - - +
37A THR* 3.4 10.6 + - - -
38A ASN* 2.7 48.9 + - + +
39A VAL* 3.4 24.2 + - - +
80A ALA* 4.2 0.9 - - - -
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Residues in contact with ALA 36 (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 CYS* 4.3 10.5 - - - -
35A ASP* 1.3 70.5 - - - +
37A THR* 1.3 58.6 + - - +
39A VAL* 3.4 1.9 + - - +
40A ALA* 2.9 33.3 + - - +
65A ALA* 3.6 18.6 - - + +
67A TYR* 3.8 14.8 - - + -
78A PHE* 3.4 28.6 - - - +
79A THR 4.1 0.2 - - - -
80A ALA* 3.5 18.7 - - + +
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Residues in contact with THR 37 (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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35A ASP* 3.4 11.2 + - - -
36A ALA* 1.3 79.1 - - - +
38A ASN* 1.3 63.3 + - - +
40A ALA* 4.0 1.4 - - - +
41A ARG* 3.0 57.4 + - + +
67A TYR* 3.7 25.4 + - + -
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Residues in contact with ASN 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ASP* 2.7 39.5 + - + +
36A ALA 3.4 0.2 - - - -
37A THR* 1.3 81.0 - - - +
39A VAL* 1.3 67.3 + - + +
41A ARG* 4.1 4.0 - - - +
42A ARG* 3.2 24.1 + - - +
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Residues in contact with VAL 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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33A CYS* 4.0 19.5 - - + -
34A GLY 5.5 0.4 - - - +
35A ASP* 3.4 17.9 - - + +
36A ALA 3.4 3.0 + - - +
38A ASN* 1.3 78.0 - - + +
40A ALA* 1.3 57.2 + - - +
42A ARG* 3.2 4.4 + - - +
43A PHE* 2.9 55.3 + - + -
78A PHE* 3.6 20.2 - - + -
116A LEU* 4.0 27.8 - - + -
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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 ALA 2.9 18.7 + - - +
37A THR* 4.0 3.8 - - - +
39A VAL* 1.3 77.1 - - - +
41A ARG* 1.3 57.4 + - + +
43A PHE 3.4 0.2 + - - -
44A SER* 2.8 30.8 + - - -
67A TYR* 4.3 16.4 - - + -
69A LEU* 3.3 13.0 - - + +
78A PHE* 3.7 34.0 - - + -
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Residues in contact with ARG 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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37A THR* 3.0 37.4 + - + +
38A ASN* 4.2 4.5 - - - +
40A ALA* 1.3 75.0 - - + +
42A ARG* 1.3 63.1 + - - +
44A SER* 3.6 7.6 + - - -
45A TRP* 3.3 23.2 + - - +
51A PHE* 5.4 12.1 - - - -
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Residues in contact with ARG 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 ASN 3.2 18.7 + - - +
39A VAL* 3.5 6.1 - - - +
41A ARG* 1.3 76.0 - - - +
43A PHE* 1.3 68.6 + - + +
45A TRP* 3.5 3.1 + - - +
46A GLY* 2.9 24.9 + - - -
116A LEU* 5.9 0.4 - - - +
309A GLY* 3.3 25.3 + - - +
310A GLY 2.9 20.4 + - - -
311A PHE* 3.4 35.2 - - - +
312A ASP* 5.3 1.0 - - - +
363A PRO 5.3 1.8 + - - -
364A LEU* 2.8 29.7 + - - +
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Residues in contact with PHE 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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31A PHE* 3.8 24.0 - + - -
39A VAL* 2.9 42.7 + - + +
40A ALA 3.7 0.9 - - - +
42A ARG* 1.3 87.6 - - - +
44A SER* 1.3 60.3 + - - +
47A LEU* 2.9 54.9 + - + +
49A MET* 4.6 0.5 + - - +
69A LEU* 4.0 4.6 - - + +
76A PHE* 4.1 6.3 - + - -
78A PHE* 3.6 28.5 - + + -
116A LEU* 4.6 8.3 - - + -
311A PHE* 3.6 24.2 - + - -
364A LEU* 3.5 37.2 - - + -
372A ILE* 4.5 0.4 - - + -
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Residues in contact with SER 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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40A ALA 2.8 17.9 + - - -
41A ARG* 3.7 9.6 - - - -
42A ARG 3.3 0.2 - - - -
43A PHE* 1.3 75.9 - - - +
45A TRP* 1.3 56.6 + - - +
48A GLY* 2.8 27.0 + - - -
49A MET 2.6 33.3 + - - +
51A PHE* 4.8 5.5 + - - +
69A LEU* 3.6 15.5 - - - +
196A LEU* 3.5 14.1 - - - +
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Residues in contact with TRP 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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41A ARG 3.3 14.2 + - - +
42A ARG* 3.9 2.9 - - - +
44A SER* 1.3 81.0 - - - +
46A GLY* 1.3 61.7 + - - +
196A LEU* 4.2 21.7 - - + +
198A TYR* 2.7 39.7 + - - -
305A ARG* 3.2 52.1 - - + +
308A ILE* 3.0 41.6 + - + +
309A GLY* 4.0 17.3 - - - -
310A GLY 4.2 1.3 - - - -
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Residues in contact with GLY 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 ARG 2.9 17.3 + - - -
45A TRP* 1.3 78.7 - - - +
47A LEU* 1.3 57.8 + - - +
198A TYR* 3.7 4.0 - - - -
302A MET* 3.5 29.8 - - - +
305A ARG* 4.9 3.1 - - - -
310A GLY* 3.7 25.4 - - - -
311A PHE* 3.8 13.8 + - - -
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Residues in contact with LEU 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 PHE* 2.9 43.4 + - + +
46A GLY* 1.3 74.2 - - - +
48A GLY* 1.3 64.1 + - - +
49A MET* 3.8 18.7 - - + +
76A PHE* 4.0 12.8 - - + -
198A TYR* 3.4 16.9 + - - +
200A ILE* 3.8 34.3 - - + +
290A LEU* 4.1 11.4 - - + -
302A MET* 3.5 26.9 - - + +
311A PHE* 3.5 13.9 - - + -
372A ILE* 3.9 21.5 - - + -
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Residues in contact with GLY 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 SER 2.8 10.0 + - - -
47A LEU* 1.3 81.1 - - - +
49A MET* 1.3 59.7 + - - +
71A SER* 3.9 9.0 + - - -
196A LEU* 3.3 23.1 - - - +
197A ASP* 3.3 10.7 - - - -
198A TYR* 3.1 35.7 + - - -
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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