Contacts of the helix formed by residues 11 - 24 (chain A) in PDB entry 4OQZ
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLY 3.6 4.2 + - - -
10A LEU* 1.3 81.0 - - - +
12A PRO* 1.3 75.3 - - - +
13A MET* 3.1 4.1 + - - -
14A GLY 3.4 1.8 + - - +
15A GLN* 3.0 19.4 + - - +
32A ASN* 4.5 0.4 + - - -
37A ARG* 3.7 8.7 - - - -
65A SER 5.0 2.6 + - - -
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Residues in contact with PRO 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLY* 1.3 81.7 - - - +
13A MET* 1.3 61.4 + - + +
15A GLN* 3.8 10.2 - - + +
16A ALA* 3.1 24.9 + - - +
37A ARG* 3.7 13.0 - - - +
122A PRO* 3.5 25.6 - - + +
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Residues in contact with MET 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLY 3.2 1.2 - - - -
12A PRO* 1.3 77.1 - - + +
14A GLY* 1.3 57.2 + - - +
16A ALA* 3.2 6.6 + - - +
17A MET* 3.1 39.8 + - + +
65A SER* 3.8 14.1 - - - +
118A VAL* 3.9 20.9 - - + +
120A SER 3.2 27.1 - - - +
121A PRO 3.8 0.9 - - - -
122A PRO* 3.6 31.2 - - + -
125A ILE* 3.8 20.2 - - + +
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Residues in contact with GLY 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 3.6 10.5 - - - +
9A GLY 3.4 20.5 + - - -
10A LEU* 3.9 7.1 - - - +
11A GLY* 3.4 4.6 + - - +
13A MET* 1.3 74.3 - - - +
15A GLN* 1.4 59.5 + - - +
17A MET* 3.6 5.6 - - - +
18A ALA* 3.0 30.0 + - - +
65A SER* 3.7 16.4 + - - -
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Residues in contact with GLN 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 3.2 31.0 + - + +
11A GLY 3.0 13.2 + - - +
12A PRO* 3.8 8.0 - - + +
14A GLY* 1.4 74.3 - - - +
16A ALA* 1.4 63.3 + - - +
18A ALA 3.7 0.2 + - - -
19A ALA* 3.2 23.7 + - - +
37A ARG* 2.7 55.8 + - - +
41A LEU* 3.9 21.9 - - + +
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Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PRO 3.1 18.9 + - - +
13A MET 3.2 4.9 + - - +
15A GLN* 1.4 77.4 - - - +
17A MET* 1.4 55.0 + - - +
19A ALA* 3.5 7.2 + - - +
20A ALA* 3.1 28.8 + - - +
122A PRO* 3.3 29.6 - - + +
125A ILE* 3.6 14.8 - - + +
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Residues in contact with MET 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 4.7 6.5 - - + -
13A MET* 3.1 45.5 + - + +
14A GLY* 3.3 8.2 + - - +
16A ALA* 1.4 72.0 - - - +
18A ALA* 1.3 60.3 + - - +
20A ALA* 3.1 6.2 + - - +
21A TYR* 2.9 39.1 + - + -
63A ILE* 4.1 11.4 - - + -
65A SER* 4.1 22.9 - - - +
91A LEU* 3.5 35.7 - - + -
118A VAL* 4.2 7.4 - - + -
125A ILE* 3.7 23.1 - - + -
151A ILE* 4.1 17.3 - - + -
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Residues in contact with ALA 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 4.1 14.2 - - + +
10A LEU* 4.6 0.2 - - + -
14A GLY 3.0 16.3 + - - +
15A GLN 4.0 0.2 - - - +
17A MET* 1.3 75.5 - - - +
19A ALA* 1.3 50.4 + - - +
21A TYR* 3.2 6.1 + - - +
22A LEU* 2.8 37.6 + - + +
28A VAL* 4.2 5.8 - - + +
30A LEU* 3.7 30.5 - - + -
41A LEU* 3.8 19.7 - - + -
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Residues in contact with ALA 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLN 3.2 16.4 + - - +
16A ALA* 3.7 7.4 - - - +
17A MET 3.3 0.2 - - - -
18A ALA* 1.3 73.6 - - - +
20A ALA* 1.4 55.6 + - - +
22A LEU* 3.4 4.3 + - - +
23A ASP* 2.8 43.5 + - - +
41A LEU* 3.8 10.0 - - + +
44A ARG* 3.5 24.3 + - - +
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Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ALA 3.1 15.1 + - - +
17A MET* 3.1 9.8 + - - +
19A ALA* 1.4 72.3 - - - +
21A TYR* 1.4 63.3 + - - +
23A ASP* 3.3 12.1 + - - +
24A ARG* 3.1 33.1 + - - +
125A ILE* 4.3 12.6 - - + +
126A GLY* 4.4 4.7 - - - -
150A VAL* 3.6 28.8 - - + +
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Residues in contact with TYR 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A VAL* 3.6 21.5 - - + -
7A VAL* 4.3 8.5 - - + -
17A MET* 2.9 30.7 + - + -
18A ALA* 3.6 7.4 - - - +
20A ALA* 1.4 75.8 - - + +
22A LEU* 1.4 59.0 + - - +
24A ARG 3.2 6.8 + - - -
26A TYR* 2.9 62.1 + + + +
28A VAL* 3.6 16.8 - - + -
61A LEU* 4.6 0.2 - - - +
63A ILE* 3.7 22.6 - - + +
147A ALA* 2.6 36.5 + - + +
150A VAL* 3.6 18.6 - - + -
151A ILE* 3.6 29.6 - - + +
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ALA 2.8 23.0 + - - +
19A ALA* 3.4 4.7 + - - +
21A TYR* 1.4 71.2 - - - +
23A ASP* 1.3 61.3 + - - +
25A GLY* 3.1 14.6 + - - -
26A TYR 3.9 10.5 - - - +
28A VAL* 3.8 26.0 - - + +
41A LEU* 4.0 31.2 - - + +
44A ARG* 4.0 31.2 - - + +
45A GLY* 4.4 5.2 - - - +
46A ALA* 4.0 29.2 - - + +
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Residues in contact with ASP 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ALA* 2.8 29.4 + - - +
20A ALA* 3.5 10.9 - - - +
21A TYR 3.3 0.2 - - - -
22A LEU* 1.3 72.2 - - - +
24A ARG* 1.4 63.4 + - + +
25A GLY 3.4 1.1 + - - -
44A ARG* 2.7 28.9 + - - +
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Residues in contact with ARG 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLN 5.7 0.7 + - - -
20A ALA* 3.1 17.4 + - - +
21A TYR 3.2 0.2 + - - -
22A LEU 3.2 1.0 - - - -
23A ASP* 1.4 80.7 - - - +
25A GLY* 1.3 59.4 + - - +
26A TYR* 3.4 25.9 + - + -
126A GLY* 3.0 28.7 + - - -
128A PRO* 5.9 0.8 - - - +
149A GLU 4.6 2.4 + - - -
150A VAL* 3.1 54.7 + - + +
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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