Contacts of the helix formed by residues 12 - 24 (chain A) in PDB entry 1YQZ
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 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ALA* 1.3 74.1 - - - +
13A GLY* 1.3 60.6 + - - +
14A ALA 3.7 0.2 - - - -
15A THR* 3.6 0.9 + - - -
16A CYS* 2.9 32.6 + - - +
112A SER* 3.2 14.6 - - - -
275A ILE* 3.5 13.7 - - - +
298A ALA* 4.0 16.6 - - - -
302A ALA* 3.8 0.9 - - - +
439A FAD 2.9 13.3 + - - -
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Residues in contact with GLY 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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6A VAL* 3.7 19.2 - - - +
8A GLY 3.3 22.6 + - - -
10A VAL 3.5 3.2 + - - +
12A GLY* 1.3 74.4 - - - +
14A ALA* 1.3 65.9 + - - +
16A CYS* 3.4 2.4 + - - +
17A ALA* 3.1 24.4 + - - +
31A ILE* 4.5 1.1 - - - -
112A SER* 3.3 13.7 + - - -
275A ILE* 4.9 0.2 - - - -
439A FAD 4.0 1.4 + - - -
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Residues in contact with ALA 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA* 3.4 21.2 - - - +
10A VAL 3.1 9.1 + - - +
13A GLY* 1.3 74.3 - - - +
15A THR* 1.3 63.2 + - - +
17A ALA* 3.4 0.3 + - - +
18A SER* 3.0 24.8 + - - -
31A ILE* 4.0 11.2 - - - -
38A MET* 4.1 11.7 - - + -
39A SER* 3.6 7.9 - - - +
67A PHE* 3.8 9.8 - - + -
441A COA 3.3 24.9 - - - +
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Residues in contact with THR 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 VAL 3.6 0.4 + - - -
11A ALA 2.5 28.2 + - - +
12A GLY 3.8 1.6 - - - -
13A GLY 3.2 0.6 - - - -
14A ALA* 1.3 79.3 - - - +
16A CYS* 1.3 57.1 + - - +
18A SER* 3.2 3.2 + - - -
19A GLN* 2.8 36.5 + - + +
299A HIS* 3.7 10.5 + - + +
302A ALA* 3.7 15.5 - - + -
441A COA 2.7 37.6 + - - +
427B LYS* 3.5 27.6 - - - +
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Residues in contact with CYS 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 5.6 0.7 - - + -
12A GLY 2.9 19.5 + - - +
13A GLY* 3.9 4.3 - - - +
14A ALA 3.3 0.2 - - - -
15A THR* 1.3 75.0 - - - +
17A ALA* 1.3 63.5 + - - +
19A GLN* 3.1 1.7 + - - +
20A ILE* 2.9 32.9 + - - +
110A ILE* 3.8 24.0 - - + -
275A ILE* 3.8 7.2 - - + -
302A ALA* 3.5 32.0 - - + +
305A VAL* 3.8 28.9 - - - -
306A ALA 4.4 1.1 - - - -
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Residues in contact with ALA 17 (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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6A VAL* 4.3 6.1 - - + +
13A GLY 3.1 18.1 + - - +
14A ALA 3.8 2.0 - - - +
16A CYS* 1.3 76.1 - - - +
18A SER* 1.3 62.7 + - - +
20A ILE* 3.3 9.7 + - - +
21A ARG 3.0 18.4 + - - -
29A ILE* 3.9 20.1 - - + +
31A ILE* 3.6 24.7 - - + -
67A PHE* 4.7 0.2 - - + -
73A ILE* 3.4 21.1 - - + +
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Residues in contact with SER 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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14A ALA 3.0 18.4 + - - -
15A THR 3.5 1.1 - - - -
17A ALA* 1.3 76.7 - - - +
19A GLN* 1.3 62.1 + - - +
21A ARG* 3.2 4.8 + - - +
22A ARG* 3.1 24.8 + - - +
67A PHE* 4.5 2.7 - - - -
71A LYS* 3.1 37.6 + - - -
73A ILE* 3.9 9.8 - - - +
441A COA 2.8 30.9 + - - -
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Residues in contact with GLN 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 THR* 2.8 28.3 + - + +
16A CYS 3.1 2.7 + - - +
18A SER* 1.3 73.4 - - - +
20A ILE* 1.3 65.9 + - - +
22A ARG* 3.4 22.2 + - - +
23A LEU* 3.7 9.4 + - - +
302A ALA 4.2 3.4 - - - +
303A SER* 3.4 26.1 + - - +
306A ALA* 3.5 23.1 - - + +
441A COA 2.8 76.6 + - - -
427B LYS* 4.0 5.8 - - - +
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Residues in contact with ILE 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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4A ILE* 3.5 38.4 - - + -
16A CYS* 2.9 21.7 + - - +
17A ALA* 3.6 10.1 - - - +
19A GLN* 1.3 77.5 - - - +
21A ARG* 1.3 58.5 + - - +
23A LEU* 3.0 8.5 + - - +
24A ASP* 2.8 31.5 + - + +
29A ILE* 3.9 9.6 - - + -
110A ILE* 3.6 31.6 - - + -
306A ALA* 3.8 23.3 - - - +
309A ILE* 4.1 9.4 - - + -
310A ALA* 4.4 14.1 - - + -
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Residues in contact with ARG 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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17A ALA 3.0 13.8 + - - +
18A SER* 3.2 8.5 + - - +
20A ILE* 1.3 78.3 - - - +
22A ARG* 1.3 62.5 + - - +
23A LEU 3.2 0.5 + - - -
24A ASP 2.9 27.1 + - - +
25A LYS* 2.9 60.3 + - + +
27A SER* 2.9 31.5 + - - +
28A ASP* 4.7 0.8 - - - +
29A ILE* 3.8 27.7 - - + +
71A LYS* 2.8 34.5 + - + +
72A GLN* 2.8 32.6 + - - +
73A ILE* 4.1 8.9 - - + +
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Residues in contact with ARG 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 SER* 3.1 22.0 + - - +
19A GLN* 3.5 17.9 - - - +
20A ILE 3.2 0.4 - - - -
21A ARG* 1.3 76.9 - - - +
23A LEU* 1.3 62.8 + - + +
25A LYS* 2.9 20.9 + - - +
71A LYS* 5.9 1.8 - - - +
441A COA 3.1 95.2 + - - +
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Residues in contact with LEU 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 GLN 3.8 13.0 - - - +
20A ILE 3.0 6.5 + - - +
21A ARG 4.2 0.2 - - - -
22A ARG* 1.3 82.9 - - + +
24A ASP* 1.3 57.7 + - - +
25A LYS* 4.3 1.8 - - - -
306A ALA* 3.6 34.1 - - + +
307A GLU* 4.1 20.0 - - - +
310A ALA* 3.7 18.4 - - + +
311A GLY* 3.9 16.6 - - - +
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Residues in contact with ASP 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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2A PRO* 4.0 9.4 - - - +
4A ILE* 5.3 0.3 - - - +
20A ILE* 2.8 16.7 + - + +
21A ARG* 2.9 33.8 + - - +
23A LEU* 1.3 81.6 - - - +
25A LYS* 1.3 58.7 + - - +
26A GLU* 2.8 21.5 + - - +
27A SER* 2.6 34.8 + - - -
310A ALA* 3.8 19.6 - - + +
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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