Contacts of the helix formed by residues 40 - 60 (chain A) in PDB entry 1TFR
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 LEU 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A ASN* 1.3 74.2 - - - +
41A SER* 1.3 53.8 + - - +
43A VAL* 3.3 1.9 + - - -
44A ARG* 2.7 61.2 + - - +
107A SER* 3.7 30.1 + - - +
110A LYS* 3.9 18.6 - - + -
111A VAL* 3.8 24.5 - - + -
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Residues in contact with SER 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 ASN* 2.9 12.5 + - - -
40A LEU* 1.3 78.3 - - - +
42A MET* 1.3 55.4 + - - +
44A ARG* 3.9 14.2 + - - +
45A HIS* 2.7 52.5 + - - +
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Residues in contact with MET 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* 3.4 45.1 - - + -
33A PRO* 5.0 9.0 - - + -
36A GLU* 5.6 3.1 - - + +
37A LYS* 3.5 20.2 - - - +
38A ILE* 3.7 5.2 - - + -
39A ASN* 2.9 51.4 + - - +
41A SER* 1.3 79.1 - - - +
43A VAL* 1.3 58.7 + - + +
45A HIS* 3.6 5.0 - - - +
46A LEU* 2.9 28.6 + - - +
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Residues in contact with VAL 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PHE* 3.6 15.5 - - + -
38A ILE* 3.4 32.5 - - + -
39A ASN 3.2 6.0 + - - +
40A LEU 3.9 4.7 - - - +
42A MET* 1.3 74.4 - - - +
44A ARG* 1.3 62.0 + - - +
45A HIS 3.2 0.2 - - - -
46A LEU* 4.2 1.8 - - + -
47A ILE* 2.8 49.4 + - + +
104A TYR* 3.7 18.2 - - + +
107A SER* 4.0 12.3 - - - -
108A SER* 3.8 31.4 - - - +
111A VAL* 4.3 2.0 - - + -
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Residues in contact with ARG 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 2.7 54.8 + - - +
41A SER* 3.9 13.8 + - - +
43A VAL* 1.3 70.1 - - - +
45A HIS* 1.3 67.6 + - - +
47A ILE* 3.4 0.9 + - - +
48A LEU* 3.0 32.2 + - + +
110A LYS* 4.6 0.2 - - - +
111A VAL* 3.7 15.4 - - + +
114A GLU* 2.4 44.0 + - - +
289A TYR* 3.4 19.5 - - - +
293A ALA* 3.7 23.9 + - - +
295A LEU* 3.5 28.2 - - + +
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Residues in contact with HIS 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 SER* 2.7 35.9 + - - +
42A MET* 3.6 6.1 - - - +
44A ARG* 1.3 81.3 - - - +
46A LEU* 1.3 63.6 + - - +
48A LEU* 3.9 2.5 - - - +
49A ASN* 3.1 36.5 + - - +
293A ALA 5.8 0.7 - - - -
294A GLY 5.1 7.4 - - - -
295A LEU* 3.6 31.1 - - + +
298A LEU* 5.8 2.4 - - + +
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Residues in contact with LEU 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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24A ALA* 3.7 25.4 - - - +
27A THR* 3.9 22.1 - - + +
28A ALA* 3.5 26.5 - - + +
31A ASN* 4.0 12.6 - - + +
32A PHE* 3.5 28.9 - - + -
42A MET 2.9 21.9 + - - +
43A VAL* 3.9 3.4 - - - +
44A ARG 3.3 0.2 - - - -
45A HIS* 1.3 74.7 - - - +
47A ILE* 1.3 76.3 + - + +
49A ASN* 3.9 5.4 - - - +
50A SER* 3.1 21.3 + - - -
104A TYR* 5.3 1.6 - - + -
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Residues in contact with ILE 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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20A PHE* 3.4 37.8 - - + -
24A ALA* 4.0 16.4 - - + -
43A VAL* 2.8 46.6 + - + +
46A LEU* 1.3 81.3 - - + +
48A LEU* 1.3 62.2 + - + +
50A SER* 3.3 5.6 + - - -
51A ILE* 3.1 39.9 + - + +
104A TYR* 4.4 5.2 - - - +
108A SER* 4.5 10.8 - - - +
111A VAL* 3.7 29.4 - - + -
112A ILE* 5.1 1.8 - - + -
115A LEU* 4.2 5.6 - - + -
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Residues in contact with LEU 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 ARG* 3.0 29.0 + - + +
45A HIS 4.1 1.3 - - - +
47A ILE* 1.3 72.8 - - + +
49A ASN* 1.3 60.6 - - - +
51A ILE* 3.3 4.8 + - + +
52A LYS* 3.0 24.3 + - - +
111A VAL* 5.4 0.7 - - + -
115A LEU* 4.1 23.3 - - + -
119A MET* 3.9 27.4 - - + -
289A TYR* 3.9 10.1 - - + +
290A PHE* 4.0 8.1 - - + -
295A LEU* 3.3 35.4 - - + -
298A LEU* 3.9 22.4 - - + -
305A PHE* 3.4 16.2 - - + -
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Residues in contact with ASN 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 HIS* 3.1 29.4 + - - +
46A LEU* 3.9 5.6 - - - +
48A LEU* 1.3 76.6 - - - +
50A SER* 1.3 63.7 + - - +
52A LYS* 3.7 24.2 + - - +
53A PHE* 3.1 25.8 + - - +
298A LEU* 4.3 16.6 - - - +
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Residues in contact with SER 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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20A PHE* 5.8 3.1 - - - -
23A ILE* 3.7 26.0 + - - +
24A ALA* 5.4 4.0 - - - -
27A THR* 4.1 13.4 + - - +
46A LEU* 3.1 24.4 + - - -
47A ILE* 3.5 8.1 - - - -
48A LEU 3.1 0.4 - - - -
49A ASN* 1.3 80.0 - - - +
51A ILE* 1.3 57.8 + - - +
53A PHE* 3.5 2.8 + - - +
54A ASN* 2.8 40.3 + - - +
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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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18A ILE* 6.0 1.3 - - - -
20A PHE* 3.7 30.3 - - + -
47A ILE* 3.1 16.6 - - + +
48A LEU* 3.5 11.2 - - + +
50A SER* 1.3 73.4 - - - +
52A LYS* 1.3 56.2 + - - +
54A ASN* 3.2 3.6 + - - +
55A VAL* 2.6 45.9 + - + +
68A LEU* 3.7 24.2 - - + -
115A LEU* 3.8 24.5 - - + -
119A MET* 5.3 0.4 - - + -
121A TYR* 3.3 37.9 - - + +
305A PHE* 4.1 6.5 - - + -
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Residues in contact with LYS 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 LEU 3.0 15.7 + - - +
49A ASN* 3.7 26.4 + - - +
51A ILE* 1.3 76.6 - - - +
53A PHE* 1.3 59.8 + - - +
55A VAL* 3.9 1.5 - - - +
56A LYS* 2.9 33.2 + - - +
298A LEU* 4.2 11.9 - - + +
301A SER* 4.4 3.5 + - - -
304A GLU* 3.7 55.6 - - + +
305A PHE* 3.7 29.4 - - + -
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Residues in contact with PHE 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 ASN 3.1 14.3 + - - +
50A SER* 3.8 4.9 - - - +
52A LYS* 1.3 81.8 - - - +
54A ASN* 1.3 80.9 + - - +
56A LYS* 3.6 7.0 - - - +
57A LYS* 3.4 23.6 + - + +
170A TRP* 5.6 4.5 - + - -
172A PRO* 4.7 6.1 - - + -
175A LYS* 3.3 43.5 - - + -
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Residues in contact with ASN 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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18A ILE* 4.1 13.7 - - + -
23A ILE* 4.3 12.4 - - - +
50A SER* 2.8 39.7 + - - +
51A ILE* 4.0 2.0 - - - +
53A PHE* 1.3 90.8 - - - +
55A VAL* 1.3 66.1 + - - +
56A LYS 3.1 1.8 - - - -
57A LYS* 3.2 7.2 + - - +
58A ALA* 3.1 21.8 + - - +
152A ILE* 3.5 29.6 - - + +
170A TRP* 4.8 3.5 + - - -
172A PRO* 3.4 26.3 - - - +
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Residues in contact with VAL 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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18A ILE* 5.0 4.0 - - + -
51A ILE* 2.6 47.1 + - + +
52A LYS* 4.0 2.7 - - - +
54A ASN* 1.3 70.7 - - - +
56A LYS* 1.3 53.1 + - - +
58A ALA* 3.2 6.4 + - - +
59A LYS* 2.8 55.2 + - + +
66A ILE* 3.9 22.0 - - + -
121A TYR* 3.8 17.3 - - + +
304A GLU 3.9 11.7 - - - +
305A PHE* 3.6 20.0 - - - +
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Residues in contact with LYS 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 LYS* 2.9 18.6 + - + +
53A PHE* 3.6 8.5 - - - +
54A ASN 3.1 0.2 - - - -
55A VAL* 1.3 78.4 - - - +
57A LYS* 1.3 64.8 + - - +
59A LYS* 4.1 3.0 - - - +
60A THR* 2.9 45.8 + - + +
304A GLU* 4.7 23.1 + - + +
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Residues in contact with LYS 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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53A PHE* 3.4 17.5 + - + +
54A ASN* 3.2 12.4 + - - +
56A LYS* 1.3 81.6 - - - +
58A ALA* 1.3 63.5 + - - +
60A THR* 4.0 4.0 - - - +
61A LEU* 3.0 58.9 + - + +
150A LEU* 5.3 1.1 - - + -
152A ILE* 4.9 5.4 - - + -
170A TRP* 3.5 65.3 - - + +
177A TRP* 4.0 4.6 - - - +
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Residues in contact with ALA 58 (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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16A CYS* 3.8 28.5 - - + -
54A ASN 3.1 9.1 + - - +
55A VAL* 3.4 8.3 - - - +
57A LYS* 1.3 78.2 - - - +
59A LYS* 1.3 67.2 + - - +
61A LEU* 3.0 14.0 + - - +
62A GLY 3.1 0.5 + - - -
63A TYR* 3.0 31.2 + - - +
66A ILE* 3.8 8.1 - - + -
150A LEU* 3.8 15.0 - - + +
152A ILE* 4.7 0.2 - - + -
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Residues in contact with LYS 59 (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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55A VAL* 2.8 39.5 + - + +
56A LYS* 4.1 2.9 - - - +
58A ALA* 1.3 71.9 - - - +
60A THR* 1.3 62.3 + - - +
62A GLY* 2.8 20.8 + - - -
63A TYR 3.5 15.3 - - - +
64A THR* 3.4 41.3 + - + +
66A ILE* 4.4 6.5 - - + -
121A TYR* 6.0 0.4 - - - -
283A ARG* 3.6 25.3 - - - +
303A ASN 5.7 0.8 + - - -
304A GLU 6.4 0.2 - - - -
305A PHE* 4.0 8.0 + - - -
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Residues in contact with THR 60 (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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56A LYS* 2.9 39.8 + - + +
57A LYS* 4.0 5.4 - - - +
59A LYS* 1.3 76.7 - - - +
61A LEU* 1.3 64.4 + - + +
62A GLY 3.6 0.3 + - - -
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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