Contacts of the helix formed by residues 11 - 22 (chain R) in PDB entry 3K9Q
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 GLY 11 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190O PRO* 5.4 0.9 - - - -
0R NAD 3.2 30.9 + - - -
9R GLY 3.0 9.7 + - - -
10R PHE* 1.3 75.9 - - - +
12R ARG* 1.3 67.5 + - - +
13R ILE 3.4 2.0 - - - -
14R GLY* 4.1 0.6 - - - -
15R ARG* 2.8 35.9 + - - +
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Residues in contact with ARG 12 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187O GLN* 4.3 24.8 + - + -
188O ASP* 3.5 29.2 - - - +
0R NAD 2.8 41.8 + - - +
11R GLY* 1.3 72.6 - - - +
13R ILE* 1.3 64.1 + - - +
15R ARG* 2.9 24.3 - - - +
16R LEU* 3.1 33.7 + - - +
48R ASP* 2.7 45.3 + - - +
50R MET* 5.0 2.6 - - - +
51R GLN* 3.4 8.5 - - - +
182R GLY* 6.1 1.1 - - - +
317R GLU* 2.8 49.1 + - + +
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Residues in contact with ILE 13 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0R NAD 2.9 78.0 + - + +
12R ARG* 1.3 72.8 - - - +
14R GLY* 1.3 54.0 + - - +
16R LEU* 3.3 1.6 + - - +
17R ALA* 2.7 38.2 + - + +
96R CYS* 4.2 4.5 - - + -
120R SER* 3.8 24.0 - - - +
316R ASN 4.2 0.2 - - - +
317R GLU* 4.1 17.0 - - + +
320R TYR* 4.2 5.8 - - + -
321R THR* 3.7 22.1 + - - +
324R LEU* 3.8 17.0 - - + -
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Residues in contact with GLY 14 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0R NAD 4.6 0.2 + - - -
7R ILE* 3.5 23.6 - - - +
9R GLY 3.3 26.7 + - - -
10R PHE* 4.1 6.7 - - - -
11R GLY 3.4 3.5 + - - +
12R ARG 3.4 0.4 - - - -
13R ILE* 1.3 76.9 - - - +
15R ARG* 1.3 54.9 + - - +
17R ALA* 3.3 1.7 + - - +
18R PHE* 2.9 23.2 + - - +
96R CYS* 3.9 9.8 - - - +
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Residues in contact with ARG 15 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188O ASP* 3.1 32.5 + - - +
190O PRO* 4.7 3.6 - - - +
10R PHE* 2.7 74.3 + - + +
11R GLY* 2.8 32.4 + - - +
12R ARG* 2.9 33.5 - - - +
14R GLY* 1.3 69.6 - - - +
16R LEU* 1.3 66.5 + - + +
18R PHE* 3.1 5.1 + - - +
19R ARG* 2.9 32.8 + - - +
41R LEU* 5.9 0.2 - - - +
44R LEU* 3.1 54.7 + - - +
45R LEU* 3.8 9.2 - - + +
47R TYR 5.5 0.2 + - - -
48R ASP* 5.1 1.3 + - - +
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Residues in contact with LEU 16 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12R ARG* 3.1 27.9 + - - +
13R ILE* 5.4 0.2 - - + -
15R ARG* 1.3 75.3 - - + +
17R ALA* 1.3 66.3 + - - +
19R ARG* 3.2 22.7 + - - +
20R ARG* 2.9 25.8 + - - +
48R ASP* 3.6 14.6 - - - +
51R GLN* 3.6 36.8 - - + +
317R GLU* 3.6 39.7 - - + +
318R MET* 4.3 13.6 - - + +
321R THR* 3.4 18.4 - - + +
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Residues in contact with ALA 17 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7R ILE* 4.5 1.1 - - + -
13R ILE 2.7 18.6 + - - +
14R GLY* 3.7 5.4 - - - +
16R LEU* 1.3 76.0 - - - +
18R PHE* 1.3 65.3 + - - +
20R ARG* 3.2 1.0 + - - +
21R ILE* 2.9 31.5 + - + +
94R LEU* 3.5 32.1 - - + -
321R THR* 3.4 15.0 - - + +
324R LEU* 5.0 4.7 - - + -
325R VAL* 4.2 8.5 - - + -
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Residues in contact with PHE 18 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7R ILE* 3.8 6.4 - - + +
10R PHE* 3.8 20.9 - + + -
14R GLY 2.9 13.8 + - - +
15R ARG* 3.2 8.7 - - - +
17R ALA* 1.3 79.4 - - - +
19R ARG* 1.3 65.5 + - - +
21R ILE* 3.3 2.4 + - - +
22R GLN* 3.1 53.4 + - + +
29R VAL* 3.7 41.3 - - + -
45R LEU* 3.7 32.3 - - + -
54R PHE* 4.7 1.3 - + - -
65R PHE* 4.7 3.4 - + - -
67R VAL* 3.7 28.3 - - + -
72R VAL* 3.9 20.6 - - + -
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Residues in contact with ARG 19 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15R ARG* 2.9 18.2 + - - +
16R LEU* 3.2 24.7 + - - +
18R PHE* 1.3 75.5 - - - +
20R ARG* 1.3 63.1 + - - +
22R GLN* 3.1 23.8 + - - +
23R GLU* 4.0 8.1 + - - -
44R LEU 4.8 0.8 + - - -
45R LEU* 3.0 33.6 + - + +
46R LYS 4.0 1.0 + - - -
48R ASP* 3.3 21.4 + - - +
51R GLN* 3.6 22.4 + - - +
52R GLY 2.9 30.3 + - - -
53R ARG 4.1 5.1 + - - -
54R PHE* 3.4 33.9 - - + +
318R MET* 5.2 9.6 - - + +
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Residues in contact with ARG 20 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16R LEU 2.9 17.0 + - - +
17R ALA 3.8 2.9 - - - +
19R ARG* 1.3 79.7 - - - +
21R ILE* 1.3 60.4 + - - +
23R GLU* 3.2 45.8 + - - +
24R VAL* 3.3 20.7 - - + +
287R THR* 3.7 24.6 + - - +
318R MET* 4.4 17.3 - - + -
321R THR* 4.3 4.3 - - + -
322R ALA* 3.8 23.7 + - - +
325R VAL* 4.2 24.0 - - + +
326R ARG* 4.0 25.5 - - - +
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Residues in contact with ILE 21 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5R VAL* 4.4 9.0 - - + -
7R ILE* 4.6 4.0 - - + -
17R ALA* 2.9 26.3 + - + +
18R PHE 3.6 4.3 - - - +
20R ARG* 1.3 72.3 - - - +
22R GLN* 1.3 67.7 + - - +
23R GLU 3.1 2.5 + - - -
24R VAL* 3.4 22.1 + - - +
27R LEU* 3.7 37.1 - - + +
28R GLU* 4.3 0.7 - - - +
29R VAL* 3.8 34.8 - - + +
94R LEU* 4.6 1.1 - - + -
325R VAL* 4.0 20.9 - - + -
328R LEU* 3.9 22.4 - - + -
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Residues in contact with GLN 22 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18R PHE* 3.1 54.3 + - + +
19R ARG 3.1 12.5 + - - +
21R ILE* 1.3 85.2 - - - +
23R GLU* 1.3 57.8 + - + +
24R VAL 3.6 1.5 + - - -
29R VAL* 4.9 2.8 + - - +
54R PHE* 4.2 19.5 - - + -
67R VAL* 4.1 18.0 + - - +
68R ASN* 4.6 8.5 + - - +
70R LYS* 4.7 19.4 - - - +
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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