Contacts of the helix formed by residues 29 - 48 (chain D) in PDB entry 1UFI
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 29 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C LYS* 5.8 6.9 - - - +
27D PRO 3.7 2.1 + - - +
28D ILE* 1.3 81.5 - - - +
30D ASP* 1.3 65.9 + - - +
31D ARG* 3.0 25.1 + - - +
32D VAL* 3.1 20.9 + - - +
33D GLN* 3.6 19.8 + - - +
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Residues in contact with ASP 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ILE 4.9 1.9 - - - +
29D ASP* 1.3 80.7 - - - +
31D ARG* 1.3 63.7 + - - +
32D VAL 3.5 0.2 - - - -
33D GLN* 4.0 18.2 - - - +
34D SER* 3.4 20.8 + - - -
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Residues in contact with ARG 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ASP* 3.7 14.3 + - - -
29D ASP* 3.0 17.7 + - - +
30D ASP* 1.3 75.8 - - - +
32D VAL* 1.3 69.9 + - - +
34D SER* 3.1 7.4 + - - -
35D HIS* 3.0 56.8 + - + +
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Residues in contact with VAL 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU* 4.8 0.2 - - + -
42C ASP* 3.7 38.8 - - + +
46C VAL* 3.9 20.2 - - + -
23D LEU* 4.2 18.4 - - + -
28D ILE* 3.9 34.8 - - + -
29D ASP* 3.1 16.9 + - - +
31D ARG* 1.3 77.8 - - + +
33D GLN* 1.3 63.4 + - - +
35D HIS* 3.0 4.7 + - - +
36D ILE* 2.9 22.3 + - + +
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Residues in contact with GLN 33 (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 LYS* 6.0 1.4 - - - +
24D THR* 4.3 11.6 - - - +
28D ILE* 4.1 23.6 - - + +
29D ASP 3.6 14.2 + - - +
30D ASP* 4.0 21.1 - - - +
31D ARG 3.3 0.4 - - - -
32D VAL* 1.3 76.6 - - - +
34D SER* 1.3 57.8 + - - +
36D ILE* 3.3 12.2 + - - +
37D LEU* 3.0 47.9 + - + +
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Residues in contact with SER 34 (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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30D ASP 3.4 16.2 + - - -
31D ARG* 3.1 6.6 + - - -
32D VAL 3.1 0.6 - - - -
33D GLN* 1.3 79.4 - - - +
35D HIS* 1.3 68.9 + - - +
37D LEU* 3.5 13.3 - - - +
38D HIS* 2.9 49.2 + - - -
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Residues in contact with HIS 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C HIS* 5.1 7.3 - + - +
38C HIS* 3.7 40.0 - + + +
39C LEU* 3.8 18.9 - - + +
42C ASP* 2.4 35.3 + - - +
31D ARG* 3.0 55.4 + - + +
32D VAL 3.0 3.7 + - - +
34D SER* 1.3 78.7 - - - +
36D ILE* 1.3 67.7 + - - +
38D HIS* 4.1 4.3 - - + +
39D LEU* 3.1 22.3 + - - +
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Residues in contact with ILE 36 (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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39C LEU* 3.9 19.9 - - + +
16D PHE* 3.5 19.2 - - + -
20D LYS* 3.7 35.2 - - + +
23D LEU* 3.9 22.2 - - + -
24D THR* 4.1 13.9 - - + -
28D ILE* 3.8 28.9 - - + -
32D VAL* 2.9 15.9 + - + +
33D GLN* 3.3 16.4 + - - +
35D HIS* 1.3 75.8 - - - +
37D LEU* 1.3 67.1 + - + +
39D LEU 3.1 0.2 + - - -
40D GLU* 2.9 24.0 + - - +
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Residues in contact with LEU 37 (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 LYS* 6.1 2.9 - - - +
33D GLN* 3.0 42.1 + - + +
34D SER* 3.5 18.8 - - - +
36D ILE* 1.3 80.2 - - + +
38D HIS* 1.3 68.8 + - + +
40D GLU* 3.6 7.3 + - - +
41D HIS* 3.1 23.9 + - - +
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Residues in contact with HIS 38 (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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35C HIS* 3.7 41.3 - + + +
34D SER* 2.9 40.5 + - - +
35D HIS* 4.2 4.0 - + - +
37D LEU* 1.3 84.9 - - + +
39D LEU* 1.3 68.3 + - - +
41D HIS* 3.4 12.6 + + - +
42D ASP* 3.1 25.8 + - - +
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Residues in contact with LEU 39 (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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16C PHE* 3.7 23.3 - - + -
19C VAL* 4.6 6.7 - - + -
23C LEU* 3.7 26.2 - - + -
32C VAL* 4.5 0.9 - - + +
35C HIS* 3.8 25.3 - - + +
36C ILE* 3.8 14.4 - - + +
39C LEU* 3.6 28.5 - - + -
16D PHE* 4.0 14.8 - - + -
35D HIS 3.1 15.7 + - - +
36D ILE 3.1 4.8 + - - +
38D HIS* 1.3 77.8 - - - +
40D GLU* 1.3 57.3 + - - +
42D ASP* 3.1 12.2 + - - +
43D LEU* 2.9 27.4 + - + +
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Residues in contact with GLU 40 (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 MET* 4.5 17.4 - - + +
16D PHE* 3.5 25.5 - - + -
20D LYS* 3.3 38.5 + - - +
36D ILE* 2.9 18.0 + - - +
37D LEU* 3.8 7.6 - - - +
39D LEU* 1.3 72.5 - - - +
41D HIS* 1.3 66.1 + - - +
43D LEU* 3.2 18.2 + - - +
44D VAL* 3.3 15.5 + - + +
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Residues in contact with HIS 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C HIS* 6.3 0.2 - + - -
37D LEU 3.1 15.9 + - - +
38D HIS* 3.4 12.6 - + + +
40D GLU* 1.3 78.8 - - - +
42D ASP* 1.3 69.4 + - - +
44D VAL* 3.0 5.9 + - - +
45D HIS* 2.9 76.7 + + + +
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Residues in contact with ASP 42 (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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23C LEU* 4.3 3.1 - - + -
32C VAL* 3.5 37.1 - - + +
35C HIS* 2.7 42.5 + - - +
38D HIS 3.1 15.3 + - - +
39D LEU* 3.1 14.2 + - + +
41D HIS* 1.3 87.2 - - - +
43D LEU* 1.3 63.9 + - - +
45D HIS* 4.5 1.6 - - - +
46D VAL* 2.9 32.8 + - - +
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Residues in contact with LEU 43 (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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19C VAL* 4.2 11.4 - - + -
22C TYR* 3.9 22.6 - - + -
23C LEU* 3.8 32.8 - - + -
9D PHE* 3.7 6.0 - - + -
12D ALA* 4.6 9.6 - - + +
13D MET* 3.9 21.3 - - - -
16D PHE* 3.6 45.8 - - + -
39D LEU* 2.9 17.1 + - + +
40D GLU* 3.3 9.4 - - - +
42D ASP* 1.3 78.4 - - - +
44D VAL* 1.3 55.6 + - - +
46D VAL* 4.7 0.3 - - - +
47D THR* 2.6 29.3 + - - -
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Residues in contact with VAL 44 (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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9B PHE* 6.0 0.9 - - + -
9D PHE* 3.9 24.0 - - + -
13D MET* 4.1 17.5 - - + -
40D GLU* 3.3 11.9 + - + +
41D HIS* 3.0 8.5 + - - +
43D LEU* 1.3 79.1 - - - +
45D HIS* 1.3 73.3 + - + +
47D THR* 3.2 7.6 - - - -
48D ARG* 2.9 30.4 + - + +
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Residues in contact with HIS 45 (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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41D HIS* 2.9 63.3 + + + +
42D ASP* 5.0 1.3 - - - -
44D VAL* 1.3 86.0 - - + +
46D VAL* 1.3 63.9 + - - +
47D THR 3.1 1.3 - - - -
48D ARG* 2.9 31.0 + - + +
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Residues in contact with VAL 46 (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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23C LEU* 4.3 9.0 - - + -
26C PHE* 3.5 50.2 - - + -
28C ILE* 3.9 23.6 - - + -
32C VAL* 4.0 19.7 - - + -
42D ASP* 2.9 22.8 + - + +
43D LEU 4.7 0.7 - - - +
45D HIS* 1.3 77.0 - - - +
47D THR* 1.3 61.5 + - - +
48D ARG 3.6 4.2 - - - +
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Residues in contact with THR 47 (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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22C TYR* 2.8 33.0 + - - +
26C PHE* 4.6 9.5 - - + -
9D PHE* 3.7 24.5 - - + -
43D LEU 2.6 20.3 + - - -
44D VAL 3.2 9.8 + - - -
45D HIS 3.1 0.4 - - - -
46D VAL* 1.3 82.2 - - - +
48D ARG* 1.3 59.8 + - + +
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Residues in contact with ARG 48 (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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48B ARG* 5.7 9.5 + - - +
44D VAL* 2.9 20.3 + - + +
45D HIS* 2.9 30.3 + - + +
46D VAL 3.6 5.0 - - - +
47D THR* 1.3 82.2 - - + +
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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
------------------------------------------------------------
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