Contacts of the helix formed by residues 11 - 22 (chain D) in PDB entry 1M6X
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 PRO 11 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A GLN* 3.3 17.5 - - - +
127A PHE* 3.5 24.5 - - + -
9D LYS 3.7 5.6 - - - +
10D THR* 1.4 90.8 - - + +
12D PRO* 1.3 73.0 - - + +
13D LYS* 4.7 2.2 - - + -
14D VAL* 2.7 37.2 + - + +
15D LEU* 3.0 10.4 + - - +
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Residues in contact with PRO 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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120A VAL* 4.0 13.7 - - + +
123A LEU* 3.5 13.0 - - + +
124A GLN* 3.1 39.7 - - + +
127A PHE* 3.4 27.6 - - + -
10D THR 3.6 2.2 - - - +
11D PRO* 1.3 80.8 - - + -
13D LYS* 1.3 63.4 + - - +
15D LEU* 2.9 20.9 + - + +
16D VAL* 3.0 14.9 + - - +
40D TYR* 3.9 22.0 - - + +
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Residues in contact with LYS 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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120A VAL* 4.2 9.8 - - + +
121A SER* 6.4 0.2 - - - -
124A GLN* 2.7 53.8 + - + +
128A GLU* 5.3 4.2 + - - -
11D PRO* 5.2 1.8 - - - -
12D PRO* 1.3 72.7 - - - +
14D VAL* 1.3 69.2 + - + +
16D VAL* 3.7 3.1 - - - +
17D ARG* 2.7 59.0 + - - +
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Residues in contact with VAL 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 THR* 3.6 18.2 - - + -
11D PRO* 2.7 44.1 + - + +
13D LYS* 1.3 83.9 - - + +
15D LEU* 1.3 55.4 + - - +
17D ARG* 3.0 11.5 - - + +
18D GLN* 2.8 53.3 + - + +
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Residues in contact with LEU 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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7D LEU* 3.8 30.5 - - + +
10D THR* 3.4 39.7 - - + +
11D PRO 3.0 7.5 + - - +
12D PRO* 2.9 10.6 + - + +
14D VAL* 1.3 77.4 - - - +
16D VAL* 1.3 64.9 + - - +
18D GLN* 3.1 13.3 + - - +
19D PHE* 2.9 23.2 + - - +
37D GLU* 4.0 18.4 - - + +
40D TYR* 3.5 46.9 - - + +
41D LEU* 5.9 1.3 - - + -
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Residues in contact with VAL 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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117A THR* 6.2 0.9 - - + -
120A VAL* 3.3 44.9 - - + -
12D PRO* 3.0 6.2 + - + +
13D LYS* 3.8 5.8 - - - +
15D LEU* 1.3 76.2 - - + +
17D ARG* 1.3 67.0 + - - +
19D PHE* 3.3 7.9 + - - +
20D VAL* 3.0 29.1 + - + +
40D TYR* 5.6 2.2 - - + -
41D LEU* 4.2 16.6 - - + +
96D LEU* 3.8 36.8 - - + -
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Residues in contact with ARG 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 LYS* 2.7 51.4 + - - +
14D VAL* 3.0 17.1 - - + +
16D VAL* 1.3 74.1 - - - +
18D GLN* 1.3 55.6 + - + +
20D VAL* 2.8 30.1 + - - +
21D GLU* 3.1 31.1 + - + +
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Residues in contact with GLN 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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10D THR* 4.1 11.3 + - - +
14D VAL* 2.8 43.3 + - + +
15D LEU* 3.5 14.9 - - - +
17D ARG* 1.3 73.8 - - + +
19D PHE* 1.3 61.8 + - - +
21D GLU* 3.6 19.0 + - - +
22D ARG* 3.3 28.0 + - - +
37D GLU* 3.4 20.7 - - - +
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Residues in contact with PHE 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 LEU 2.9 12.0 + - - +
16D VAL* 3.5 11.0 - - - +
17D ARG 3.0 0.2 + - - -
18D GLN* 1.3 76.7 - - - +
20D VAL* 1.3 61.3 + - - +
22D ARG* 3.4 7.3 - - - +
23D PHE* 3.1 43.1 - + - -
34D CYS* 3.6 33.0 - - + -
37D GLU* 3.0 27.0 + - + +
38D LEU* 3.9 27.8 - - + -
41D LEU* 3.3 27.8 - - + -
77D LEU* 6.0 0.2 - - + -
93D LEU* 4.6 7.2 - - + -
96D LEU* 4.0 16.8 - - + -
97D ILE* 3.6 20.0 - - + -
102D PHE* 4.7 8.3 - + - -
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Residues in contact with VAL 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 VAL* 3.0 26.5 - - + +
17D ARG* 2.8 9.9 + - - +
19D PHE* 1.3 74.6 - - + +
21D GLU* 1.3 55.7 + - + +
22D ARG 3.0 1.8 - - - -
23D PHE* 2.7 28.8 + - + +
24D GLU* 3.4 20.7 + - + +
96D LEU* 4.4 30.3 - - + +
97D ILE* 4.5 11.9 - - + -
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Residues in contact with GLU 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 ARG* 3.1 31.2 + - + +
18D GLN* 3.6 24.0 + - - +
19D PHE 3.5 0.2 - - - -
20D VAL* 1.3 76.9 - - + +
22D ARG* 1.3 62.4 + - + +
24D GLU* 3.1 32.4 + - - +
30D LYS* 3.3 15.6 + - - -
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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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18D GLN* 3.3 13.3 + - - +
19D PHE* 3.4 10.3 - - - +
20D VAL 2.9 0.4 + - - -
21D GLU* 1.3 79.4 - - - +
23D PHE* 1.3 66.6 + - + +
26D PRO* 4.2 4.3 - - - +
29D GLU 4.9 0.2 + - - -
30D LYS* 2.9 64.5 + - + +
31D ILE* 3.3 13.9 - - + +
33D SER* 3.6 28.5 + - - -
34D CYS* 3.6 23.2 - - - +
37D GLU* 2.8 41.1 + - - -
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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