Contacts of the helix formed by residues 5 - 21 (chain D) in PDB entry 1UMD
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 5 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D MET* 1.3 75.7 - - - +
6D MET* 1.3 63.9 + - - +
7D VAL* 3.6 6.1 + - - +
8D GLN* 2.9 37.2 + - - +
9D ALA* 3.0 22.3 + - - +
151D PRO* 3.8 2.5 - - - -
177D TYR 3.5 11.6 + - - -
178D ARG* 4.0 27.0 + - + +
180D VAL 3.6 9.0 - - - +
181D LYS* 3.9 23.3 - - + -
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Residues in contact with MET 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D THR* 1.3 74.6 - - - +
7D VAL* 1.3 63.6 + - - +
9D ALA* 3.2 1.4 + - - +
10D LEU* 2.9 39.1 + - + +
148D VAL* 4.0 21.1 - - + +
149D SER* 3.7 35.7 - - - +
150D THR* 3.7 11.2 - - - +
151D PRO* 3.6 19.4 - - + +
154D ALA* 3.8 12.8 - - + -
172D GLU* 4.7 3.8 - - - -
173D PRO* 4.4 6.5 - - + +
176D LEU* 3.5 36.8 + - + +
177D TYR* 3.2 21.4 + - + +
180D VAL 4.4 1.2 + - - -
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Residues in contact with VAL 7 (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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5D THR* 3.2 5.4 - - - +
6D MET* 1.3 77.0 - - - +
8D GLN* 1.3 60.5 + - + +
10D LEU* 3.7 9.0 - - - +
11D ASN* 2.9 28.0 + - + +
38D PHE 3.5 19.1 - - - +
39D LEU* 3.8 17.9 - - + +
40D VAL* 4.1 4.1 - - + +
177D TYR* 3.1 45.3 + - + +
178D ARG* 3.6 29.8 - - - +
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Residues in contact with GLN 8 (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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3D LEU 4.3 1.8 + - - +
4D MET* 3.1 25.9 - - + +
5D THR* 2.9 43.3 + - - +
7D VAL* 1.3 81.1 - - + +
9D ALA* 1.3 57.0 + - - +
11D ASN* 3.4 7.5 + - - +
12D ARG* 2.9 34.2 + - - +
181D LYS* 4.5 7.6 - - - +
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Residues in contact with ALA 9 (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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4D MET* 3.8 16.5 - - - -
5D THR 3.0 15.5 + - - +
6D MET 3.2 4.7 + - - +
8D GLN* 1.3 77.1 - - - +
10D LEU* 1.3 57.2 + - - +
12D ARG* 3.3 4.7 + - - +
13D ALA* 2.9 28.1 + - - +
151D PRO* 3.2 33.9 - - + +
154D ALA* 4.4 0.7 - - + -
155D LYS* 3.6 17.6 - - + +
184D VAL* 4.3 2.7 - - + -
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Residues in contact with LEU 10 (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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6D MET* 2.9 28.0 + - + +
7D VAL 3.7 3.1 - - - +
9D ALA* 1.3 71.5 - - - +
11D ASN* 1.3 66.9 + - - +
13D ALA* 3.2 6.6 + - - +
14D LEU* 3.0 28.6 + - - +
40D VAL* 3.8 17.5 - - + -
154D ALA* 3.6 25.8 - - + +
158D LEU* 3.8 12.4 - - + +
170D PHE* 3.7 26.0 - - + -
172D GLU* 3.5 32.1 - - + +
177D TYR* 3.6 20.2 - - + -
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Residues in contact with ASN 11 (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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7D VAL* 2.9 17.5 + - + +
8D GLN* 3.6 7.5 - - - +
10D LEU* 1.3 75.8 - - - +
12D ARG* 1.3 60.4 + - - +
14D LEU* 3.2 6.1 + - - +
15D ASP* 2.9 34.3 + - - +
39D LEU 4.3 3.7 + - - +
40D VAL* 2.8 29.6 + - - +
41D THR* 3.7 3.2 - - - +
42D GLU* 3.0 36.4 + - - +
44D LEU* 4.2 8.3 - - - +
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Residues in contact with ARG 12 (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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4D MET* 3.8 25.6 - - + +
8D GLN* 2.9 20.9 + - - +
9D ALA* 3.5 8.7 - - - +
11D ASN* 1.3 79.1 + - - +
13D ALA* 1.3 55.6 + - - +
15D ASP* 3.6 8.2 + - - +
16D GLU* 2.8 56.3 + - - +
155D LYS* 4.2 10.5 - - + +
186D GLU* 2.8 38.0 + - - +
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Residues in contact with ALA 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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9D ALA 2.9 14.0 + - - +
10D LEU 3.2 9.6 + - - +
12D ARG* 1.3 75.2 - - - +
14D LEU* 1.3 63.6 + - - +
16D GLU* 3.7 1.9 - - - +
17D GLU* 3.0 30.9 + - - +
155D LYS* 3.8 17.9 - - - +
158D LEU* 4.1 16.8 - - + -
159D LYS* 3.7 28.9 - - + -
162D ILE* 5.2 0.4 - - - -
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Residues in contact with LEU 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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10D LEU 3.0 17.9 + - - +
11D ASN 3.5 5.6 - - - +
13D ALA* 1.3 74.7 - - - +
15D ASP* 1.3 66.2 + - - +
17D GLU* 3.3 1.2 + - - +
18D MET* 2.9 32.8 + - - +
24D VAL* 5.7 1.6 - - + -
26D VAL* 4.4 9.6 - - + -
40D VAL* 4.0 20.0 - - + +
41D THR* 4.0 17.9 - - + -
44D LEU* 3.9 25.8 - - + -
78D VAL* 4.0 28.7 - - + -
116D ARG* 4.9 5.4 - - - +
158D LEU* 4.0 17.0 - - + -
162D ILE* 4.1 15.5 - - + -
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Residues in contact with ASP 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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11D ASN* 2.9 21.8 + - - +
12D ARG* 3.6 10.7 + - - +
14D LEU* 1.3 75.1 - - - +
16D GLU* 1.3 64.1 + - + +
18D MET 3.4 0.2 + - - -
19D ALA* 3.0 11.0 + - - +
44D LEU* 4.0 17.7 - - + +
47D LYS* 2.7 29.8 + - - +
48D TYR* 2.7 51.6 + - - -
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Residues in contact with GLU 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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12D ARG* 2.8 23.8 + - + +
13D ALA 3.7 2.2 - - - +
15D ASP* 1.3 78.0 - - + +
17D GLU* 1.3 62.7 + - - +
19D ALA* 3.3 6.4 + - - +
20D LYS* 3.1 28.9 + - + +
155D LYS* 2.7 39.0 + - - -
159D LYS* 2.8 35.4 + - - +
186D GLU* 3.0 29.4 - - - +
187D GLU 5.1 0.2 - - - -
188D ASP* 3.8 8.6 - - - +
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Residues in contact with GLU 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 ALA 3.0 21.0 + - - +
14D LEU 4.0 1.3 - - - +
16D GLU* 1.3 76.0 - - - +
18D MET* 1.3 57.7 + - - +
20D LYS* 3.2 8.7 + - - +
21D ASP* 2.9 33.3 + - - +
24D VAL* 3.9 5.3 - - + +
159D LYS* 2.6 44.3 + - + -
162D ILE* 3.7 39.6 - - + +
163D ARG* 2.9 40.5 + - - +
188D ASP* 4.1 0.2 - - - +
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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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14D LEU* 2.9 21.7 + - + +
17D GLU* 1.3 75.9 - - - +
19D ALA* 1.3 62.5 + - - +
21D ASP 3.3 10.0 - - - +
22D PRO* 4.2 0.5 - - - +
24D VAL* 3.6 28.0 - - + +
26D VAL* 4.1 20.0 - - + -
44D LEU* 4.2 13.9 - - - -
48D TYR* 3.6 45.8 - - + -
52D ARG* 2.9 63.8 + - + +
53D VAL* 3.9 7.6 - - + -
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Residues in contact with ALA 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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15D ASP* 3.0 13.6 + - - +
16D GLU* 3.7 7.0 - - - +
17D GLU 3.2 0.2 - - - -
18D MET* 1.3 77.1 - - - +
20D LYS* 1.3 61.9 + - + +
21D ASP 5.2 0.2 - - - -
22D PRO* 5.5 1.4 - - - +
47D LYS* 5.0 5.2 - - - +
48D TYR* 3.3 22.4 + - + +
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Residues in contact with LYS 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 GLU* 3.1 16.9 + - + +
17D GLU* 3.2 12.1 + - - +
19D ALA* 1.3 81.7 - - + +
21D ASP* 1.3 58.5 + - + +
22D PRO* 4.1 5.4 - - - +
163D ARG* 2.9 41.4 - - - +
188D ASP* 3.8 18.1 + - - +
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Residues in contact with ASP 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 GLU* 2.9 11.9 + - - +
18D MET 3.3 5.1 - - - +
20D LYS* 1.3 80.5 - - + +
22D PRO* 1.3 70.9 - - - +
23D ARG* 2.7 61.7 + - - +
24D VAL* 3.1 22.5 + - + +
52D ARG* 3.2 10.4 + - - -
76D ARG* 3.5 12.3 + - - -
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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