Contacts of the helix formed by residues 39 - 57 (chain A) in PDB entry 1TJY
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 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A LEU* 3.7 28.7 + - + -
37A VAL 3.3 0.4 - - - -
38A GLY* 1.3 81.5 - - - +
40A GLY* 1.3 68.2 + - - +
41A PHE* 4.0 7.9 - - + +
42A PHE* 3.0 34.2 + - + +
43A THR* 3.0 12.9 + - - -
195A ASN 5.0 0.7 - - - +
222A ALA* 4.2 19.3 - - + +
223A ASN* 3.7 36.8 - - - +
400A PAV 6.0 0.2 - - + -
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Residues in contact with GLY 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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38A GLY 4.4 0.2 + - - -
39A VAL* 1.3 74.1 - - - +
41A PHE* 1.3 63.1 + - - +
43A THR* 3.3 7.6 + - - -
44A SER* 2.9 30.1 + - - -
247A THR* 4.1 12.8 - - - -
250A VAL* 4.7 14.0 - - - +
340A PHE* 4.5 2.7 - - - -
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Residues in contact with PHE 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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39A VAL* 3.2 6.2 - - + +
40A GLY* 1.3 74.6 - - - +
42A PHE* 1.3 82.6 + + + +
45A GLY* 3.0 22.5 + - - -
115A TRP* 3.9 9.2 - + - -
116A ASP* 3.5 38.4 - - - -
222A ALA* 4.2 17.9 - - + +
247A THR* 3.5 18.4 + - + +
265A LEU* 3.9 17.5 - - + -
266A TRP* 3.6 30.5 - + - -
268A VAL* 3.5 32.8 - - + +
271A GLN* 4.1 2.5 - - - -
400A PAV 3.6 23.1 - + + -
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Residues in contact with PHE 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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32A PHE* 4.9 0.7 - - - -
34A PRO* 3.3 17.7 - - + -
35A LYS* 3.6 25.1 - - + -
36A LEU* 3.4 45.8 - - + +
39A VAL* 3.0 19.7 + - + +
41A PHE* 1.3 89.8 - + - +
43A THR* 1.3 65.9 + - - +
45A GLY* 3.3 0.9 + - - +
46A GLY 2.9 19.8 + - - -
62A TYR* 3.3 18.4 + - - +
91A SER* 4.1 1.6 - - - -
115A TRP* 3.6 20.4 - + - -
116A ASP* 3.5 14.4 - - - -
195A ASN* 5.6 1.1 - - - -
400A PAV 3.5 32.3 - + - -
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Residues in contact with THR 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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38A GLY* 4.3 9.9 + - - -
39A VAL 3.0 20.4 + - - -
40A GLY* 3.7 10.7 - - - -
42A PHE* 1.3 75.2 - - - +
44A SER* 1.3 59.3 + - - +
46A GLY* 3.3 1.7 + - - -
47A ASN* 2.9 44.4 + - - +
62A TYR* 3.5 15.0 + - + -
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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 GLY* 2.9 16.0 + - - -
43A THR* 1.3 75.2 - - - +
45A GLY* 1.3 64.4 + - - +
47A ASN* 3.2 14.1 + - - +
48A GLY 3.1 17.3 + - - -
268A VAL* 3.7 18.4 - - - -
269A VAL* 3.6 14.0 - - - +
340A PHE* 2.7 40.6 + - - +
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Residues in contact with GLY 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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32A PHE* 3.6 8.7 - - - -
41A PHE 3.0 16.5 + - - -
42A PHE 3.3 2.9 + - - -
44A SER* 1.3 76.2 - - - +
46A GLY* 1.3 60.4 + - - +
48A GLY 3.2 2.1 + - - -
49A ALA* 3.0 20.1 + - - +
115A TRP* 4.3 9.4 - - - -
268A VAL* 3.6 25.2 - - - +
272A GLY* 3.5 9.6 - - - -
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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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32A PHE* 3.6 16.5 - - - -
42A PHE 2.9 14.3 + - - -
43A THR 3.7 4.0 - - - -
45A GLY* 1.3 73.2 - - - +
47A ASN* 1.3 61.8 + - - +
49A ALA* 3.3 1.2 + - - +
50A GLN* 2.9 38.5 + - - +
62A TYR* 3.8 19.7 - - - -
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Residues in contact with ASN 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 THR* 2.9 32.8 + - - +
44A SER* 3.4 16.3 + - - +
46A GLY* 1.3 76.0 - - - +
48A GLY* 1.3 58.0 + - - +
50A GLN* 3.4 11.8 + - - +
51A GLU* 3.0 36.6 + - + +
269A VAL* 4.8 6.3 - - + -
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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 3.1 11.5 + - - -
45A GLY 3.2 1.5 + - - -
47A ASN* 1.3 73.7 - - - +
49A ALA* 1.3 63.3 + - - +
51A GLU* 3.5 5.5 + - - +
52A ALA* 3.0 24.3 + - - +
269A VAL* 3.3 34.7 - - - +
273A LYS* 3.6 12.9 - - - +
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Residues in contact with ALA 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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32A PHE* 3.6 35.7 - - + -
45A GLY 3.0 11.0 + - - +
46A GLY 3.6 7.4 - - - +
48A GLY* 1.3 76.8 - - - +
50A GLN* 1.3 58.2 + - - +
52A ALA* 3.3 1.6 + - - +
53A GLY 3.0 22.5 + - - -
60A VAL* 3.7 9.6 - - + +
272A GLY 3.5 14.2 - - - +
276A VAL* 3.5 21.7 - - + +
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Residues in contact with GLN 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 GLY 2.9 22.0 + - - +
47A ASN* 4.0 11.7 + - - +
49A ALA* 1.3 73.4 - - + +
51A GLU* 1.3 69.7 + - - +
53A GLY* 3.2 2.3 + - - -
54A LYS* 3.0 21.5 + - - +
60A VAL* 3.2 39.0 + - + +
61A THR* 4.5 0.2 - - - +
62A TYR* 3.7 28.1 - - + +
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Residues in contact with GLU 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 ASN* 3.0 22.1 + - + +
48A GLY* 3.9 5.8 - - - +
50A GLN* 1.3 80.8 - - - +
52A ALA* 1.3 62.7 + - - +
54A LYS* 3.3 27.3 + - - +
55A ALA* 3.0 22.2 + - - +
269A VAL* 6.3 0.4 - - + -
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Residues in contact with ALA 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 GLY 3.0 17.9 + - - +
49A ALA 3.5 5.2 - - - +
51A GLU* 1.3 74.3 - - - +
53A GLY* 1.3 65.0 + - - +
55A ALA* 3.2 5.2 + - - +
56A LEU* 3.0 28.1 + - - +
273A LYS* 3.9 14.3 - - + +
276A VAL* 3.8 21.1 - - + -
277A TYR* 3.9 24.2 - - + -
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Residues in contact with GLY 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 ALA 3.0 10.7 + - - -
50A GLN 3.2 4.9 + - - -
52A ALA* 1.3 75.9 - - - +
54A LYS* 1.3 55.9 + - - +
56A LEU 3.2 1.0 + - - -
57A GLY* 2.9 11.4 + - - -
58A ILE* 2.9 50.8 + - - +
60A VAL* 3.7 15.3 - - - -
276A VAL* 4.0 3.7 - - - +
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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 GLN 3.0 13.1 + - - +
51A GLU* 3.5 30.0 + - - +
52A ALA 3.3 0.2 - - - -
53A GLY* 1.3 76.1 - - - +
55A ALA* 1.3 62.4 + - - +
56A LEU 3.3 0.7 + - - -
57A GLY* 3.4 8.9 + - - +
58A ILE 4.9 0.4 - - - -
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Residues in contact with ALA 55 (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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51A GLU 3.0 14.3 + - - +
52A ALA* 3.2 10.3 + - - +
54A LYS* 1.3 76.9 - - - +
56A LEU* 1.3 62.1 + - - +
57A GLY 3.9 0.2 + - - -
277A TYR* 3.9 17.9 - - - +
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Residues in contact with LEU 56 (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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52A ALA 3.0 18.3 + - - +
53A GLY 4.0 0.9 - - - +
55A ALA* 1.3 77.4 - - - +
57A GLY* 1.3 62.9 + - - +
58A ILE* 3.9 18.1 - - + +
276A VAL* 4.1 13.7 - - + -
277A TYR* 3.7 48.0 - - + +
280A ASN* 3.8 42.6 - - + +
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Residues in contact with GLY 57 (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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27A ALA* 4.1 18.7 - - - +
28A GLU 4.8 1.0 + - - -
53A GLY 2.9 5.2 + - - -
54A LYS* 3.4 8.8 + - - -
55A ALA 3.5 0.6 - - - -
56A LEU* 1.3 79.4 - - - +
58A ILE* 1.3 60.1 + - - +
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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