Contacts of the helix formed by residues 12 - 24 (chain D) in PDB entry 1FTA
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 THR 12 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B THR* 4.2 17.7 + - + +
84B MET* 5.6 3.6 - - + -
59C ILE* 6.0 0.2 - - + -
10D VAL* 4.9 12.1 - - + -
11D VAL* 1.3 80.5 - - - +
13D LEU* 1.3 59.6 + - - +
14D THR* 3.8 2.9 + - - -
15D ARG* 3.2 27.9 + - - +
16D PHE* 3.0 28.8 + - - +
184D PHE* 4.0 3.1 - - - -
192D GLU* 3.5 37.8 + - + +
193D PHE 3.2 9.2 - - - +
194D ILE* 4.6 7.2 - - + +
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Residues in contact with LEU 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D THR* 1.3 71.9 - - - +
14D THR* 1.3 58.8 + - - +
16D PHE* 3.7 0.2 - - - +
17D VAL* 2.8 53.3 + - + +
34D LEU 5.4 1.8 - - - +
38D CYS* 3.5 38.1 - - + -
173D LEU* 4.0 19.7 - - + -
175D LEU* 4.3 10.1 - - + -
184D PHE* 3.6 37.9 - - + -
192D GLU* 4.8 1.0 + - - -
193D PHE* 2.8 36.3 + - + -
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Residues in contact with THR 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B THR* 3.6 31.5 - - + +
32B GLN* 4.9 0.2 - - - -
35B ASN* 3.7 25.1 - - + +
39B THR* 6.1 0.9 - - - -
12D THR* 3.3 6.0 - - - -
13D LEU* 1.3 77.7 - - - +
15D ARG* 1.3 57.5 + - - +
17D VAL* 3.9 1.7 - - - +
18D MET* 3.0 30.0 + - + +
35D ASN* 4.5 15.0 + - - +
38D CYS* 5.2 7.4 - - - -
192D GLU* 3.5 16.0 + - - -
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Residues in contact with ARG 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B GLN* 3.3 27.2 + - - +
35B ASN* 5.8 1.9 - - + +
36B SER* 2.9 30.9 + - - +
84B MET* 3.3 32.6 + - - +
87B SER* 3.3 30.9 + - - -
88B SER* 4.4 4.4 - - - +
10D VAL 3.0 27.1 + - - -
11D VAL* 4.1 14.2 - - + +
12D THR* 3.2 20.5 + - - +
14D THR* 1.3 76.1 - - - +
16D PHE* 1.3 60.3 + - - +
18D MET 3.1 1.2 + - - -
19D GLU* 2.8 55.8 + - - +
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Residues in contact with PHE 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D VAL* 3.6 13.3 - - + +
12D THR 3.0 20.5 + - - +
13D LEU 3.7 1.8 - - - +
15D ARG* 1.3 75.4 - - - +
17D VAL* 1.3 71.5 + - + +
19D GLU* 3.5 7.5 + - - +
20D GLU* 3.0 50.8 + - + +
175D LEU* 4.5 7.6 - - + -
177D MET* 4.0 25.6 - - + -
179D CYS* 4.9 5.4 - - - -
182D ASN* 3.4 33.9 - - + -
184D PHE* 3.8 23.1 - + + -
195D LEU* 4.4 17.5 - - + -
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Residues in contact with VAL 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LEU* 2.8 42.5 + - + +
14D THR 4.0 1.6 - - - +
16D PHE* 1.3 80.3 - - + +
18D MET* 1.3 62.7 + - - +
20D GLU* 3.3 3.6 + - - +
21D GLY 3.0 7.1 + - - -
31D THR* 3.7 22.7 - - + -
34D LEU* 4.2 31.0 - - + -
35D ASN* 3.8 16.4 - - - +
175D LEU* 4.3 7.9 - - + -
177D MET* 5.8 0.9 - - + -
338D AMP 3.0 32.1 + - - +
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Residues in contact with MET 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B MET* 3.4 39.9 - - + +
28B GLY* 4.1 15.9 - - - +
31B THR* 4.2 11.9 - - + -
32B GLN* 3.4 34.1 - - + +
35B ASN* 4.8 3.4 - - - +
14D THR* 3.0 20.2 + - + +
15D ARG 3.6 0.2 - - - +
17D VAL* 1.3 74.4 - - - +
19D GLU* 1.3 62.7 + - - +
21D GLY* 3.0 13.2 + - - -
22D ARG* 3.1 43.9 + - + +
31D THR* 4.2 13.2 - - + -
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Residues in contact with GLU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B GLN* 3.4 13.9 + - + +
89B PHE* 4.9 14.9 - - - +
11D VAL* 3.9 17.9 - - - +
15D ARG* 2.8 43.4 + - - +
16D PHE* 3.8 8.1 - - - +
18D MET* 1.3 71.9 - - - +
20D GLU* 1.3 61.6 + - - +
22D ARG* 3.5 14.7 + - - +
23D LYS* 3.0 40.5 + - - +
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Residues in contact with GLU 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D PHE* 3.0 44.9 + - + +
17D VAL* 3.5 6.3 - - - +
18D MET 3.1 0.2 - - - -
19D GLU* 1.3 78.4 - - - +
21D GLY* 1.3 59.3 + - - +
23D LYS* 3.2 40.0 + - - +
24D ALA* 3.1 28.2 + - - +
177D MET* 4.2 14.4 - - + -
179D CYS* 4.9 12.3 - - - +
338D AMP 3.6 25.4 - - + +
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Residues in contact with GLY 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D VAL 3.0 10.7 + - - -
18D MET* 3.0 5.7 + - - -
20D GLU* 1.3 71.7 - - - +
22D ARG* 1.3 59.0 + - - +
24D ALA* 3.4 1.2 + - - +
25D ARG 3.0 22.7 + - - -
26D GLY* 3.2 14.9 + - - +
28D GLY* 6.5 0.4 - - - -
31D THR* 4.1 6.3 - - - -
338D AMP 3.5 29.8 + - - -
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Residues in contact with ARG 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B THR* 3.0 37.3 + - - +
28B GLY* 3.3 22.5 - - - -
29B GLU* 3.4 13.8 - - - +
32B GLN* 4.6 8.1 - - - +
89B PHE* 6.3 1.4 - - - +
18D MET* 3.1 43.7 + - + +
19D GLU* 3.5 14.8 - - - +
21D GLY* 1.3 73.2 - - - +
23D LYS* 1.3 66.4 + - - +
25D ARG* 3.0 19.7 + - - +
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Residues in contact with LYS 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D GLU* 3.0 28.5 + - - +
20D GLU* 3.2 39.9 + - - +
21D GLY 3.5 0.4 - - - -
22D ARG* 1.3 74.5 - - - +
24D ALA* 1.3 62.2 + - - +
25D ARG* 3.1 14.4 + - - +
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Residues in contact with ALA 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D GLU 3.1 16.2 + - - +
21D GLY 4.0 1.3 - - - +
22D ARG 3.2 0.2 - - - -
23D LYS* 1.3 76.2 - - - +
25D ARG* 1.3 71.6 + - - +
26D GLY 3.3 0.7 + - - -
338D AMP 3.8 40.6 - - + +
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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