Contacts of the helix formed by residues 12 - 24 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ALA* 1.3 74.5 - - - +
13B GLY* 1.3 58.4 + - - +
14B ALA 3.7 0.2 - - - -
16B CYS* 2.8 33.3 + - - +
112B SER* 3.3 13.7 - - - -
275B ILE* 3.5 14.2 - - - +
276B GLY* 5.3 0.2 - - - -
298B ALA* 4.1 16.4 - - - -
302B ALA* 3.7 1.6 - - - +
440B FAD 2.9 15.9 + - - -
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Residues in contact with GLY 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 3.7 17.7 - - - +
8B GLY 3.3 21.7 + - - -
10B VAL 3.5 2.8 + - - +
12B GLY* 1.3 73.6 - - - +
14B ALA* 1.3 61.1 + - - +
16B CYS* 3.3 3.6 + - - +
17B ALA* 3.0 29.5 + - - +
31B ILE* 4.5 1.3 - - - -
112B SER* 3.3 13.9 + - - -
275B ILE* 4.8 0.4 - - - -
440B FAD 4.0 1.4 + - - -
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Residues in contact with ALA 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ALA* 3.4 20.3 - - - +
10B VAL 3.0 11.0 + - - +
13B GLY* 1.3 69.0 - - - -
15B THR* 1.3 66.5 + - - +
17B ALA* 3.4 1.7 + - - +
18B SER* 3.0 24.9 + - - -
31B ILE* 4.1 11.9 - - + -
38B MET* 4.2 13.5 - - + -
67B PHE* 4.0 5.3 - - + -
442B COA 3.3 34.5 - - + +
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Residues in contact with THR 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LYS* 3.7 26.5 - - - +
10B VAL 3.6 1.4 + - - -
11B ALA 2.6 26.4 + - - +
12B GLY 3.8 1.6 - - - -
13B GLY 3.2 0.2 - - - -
14B ALA* 1.3 79.6 - - - +
16B CYS* 1.3 61.9 + - - +
18B SER* 3.3 2.9 + - - -
19B GLN* 2.9 30.7 + - + +
299B HIS* 3.8 13.0 - - + +
302B ALA* 3.7 15.9 - - + -
442B COA 2.6 39.4 + - - +
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Residues in contact with CYS 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 5.7 0.9 - - + -
12B GLY 2.8 20.0 + - - +
13B GLY* 3.8 4.3 - - - +
14B ALA 3.3 0.2 - - - -
15B THR* 1.3 77.9 - - - +
17B ALA* 1.3 57.2 + - - +
19B GLN* 3.2 3.6 + - - +
20B ILE* 2.9 37.5 + - - +
110B ILE* 3.9 23.3 - - + -
275B ILE* 3.9 8.1 - - + -
302B ALA* 3.5 32.5 - - + +
305B VAL* 3.8 28.0 - - - -
306B ALA 4.3 1.1 - - - -
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Residues in contact with ALA 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 4.5 5.7 - - + +
13B GLY 3.0 17.0 + - - +
14B ALA 3.7 2.9 - - - +
16B CYS* 1.3 76.3 - - - +
18B SER* 1.3 63.2 + - - +
20B ILE* 3.3 13.2 + - - +
21B ARG* 3.0 17.8 + - - +
29B ILE* 3.9 16.7 - - + +
31B ILE* 3.6 25.6 - - + -
67B PHE* 4.8 0.2 - - + -
73B ILE* 3.5 22.3 - - + +
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Residues in contact with SER 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ALA 3.0 18.8 + - - -
15B THR 3.6 4.5 - - - -
17B ALA* 1.3 77.7 - - - +
19B GLN* 1.3 62.2 + - - +
21B ARG* 3.2 4.9 + - - +
22B ARG* 3.1 25.2 + - - +
67B PHE* 4.5 2.9 - - - -
71B LYS* 3.0 38.2 + - - -
73B ILE* 4.0 8.7 - - - +
442B COA 3.2 26.8 + - - -
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Residues in contact with GLN 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LYS* 4.1 6.2 - - - +
15B THR* 2.9 28.4 + - + +
16B CYS 3.2 2.4 + - - +
18B SER* 1.3 73.1 - - - +
20B ILE* 1.3 65.2 + - - +
22B ARG* 3.3 23.6 + - - +
23B LEU* 3.6 11.4 + - - +
302B ALA 4.3 2.2 - - - +
303B SER* 3.6 26.3 + - - +
306B ALA* 3.5 20.6 - - + +
442B COA 2.8 76.7 + - - -
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Residues in contact with ILE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 3.8 35.7 - - + -
6B VAL* 5.7 0.2 - - + -
16B CYS* 2.9 23.8 + - - +
17B ALA* 3.6 10.3 - - - +
19B GLN* 1.3 77.2 - - - +
21B ARG* 1.3 58.1 + - - +
23B LEU* 2.9 9.6 + - - +
24B ASP* 2.8 39.8 + - + +
29B ILE* 3.9 10.8 - - + -
110B ILE* 3.6 31.0 - - + -
306B ALA* 3.8 24.0 - - - +
309B ILE* 4.2 9.9 - - + -
310B ALA* 4.5 7.9 - - + -
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Residues in contact with ARG 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ALA 3.0 13.1 + - - +
18B SER* 3.2 9.1 + - - +
20B ILE* 1.3 78.2 - - - +
22B ARG* 1.3 61.0 + - - +
23B LEU 3.3 0.3 + - - -
24B ASP 2.9 28.2 + - - +
25B LYS* 2.9 53.1 + - + +
27B SER* 2.9 30.5 + - - +
28B ASP* 4.6 0.8 - - - +
29B ILE* 3.7 28.1 - - + +
71B LYS* 2.9 34.4 + - + +
72B GLN* 3.0 31.7 + - - +
73B ILE* 4.1 10.8 - - + +
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Residues in contact with ARG 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B SER* 3.1 22.0 + - - +
19B GLN* 3.4 23.3 - - - +
20B ILE 3.2 0.4 - - - -
21B ARG* 1.3 76.7 - - - +
23B LEU* 1.3 62.9 + - + +
25B LYS* 3.3 23.6 + - - +
71B LYS* 6.0 1.6 - - - +
442B COA 3.3 89.6 + - - +
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLN 3.6 13.0 + - - +
20B ILE* 2.9 5.7 + - - +
22B ARG* 1.3 81.7 - - + +
24B ASP* 1.3 57.7 + - - +
25B LYS* 4.2 3.4 + - - +
306B ALA* 3.4 35.4 - - + +
307B GLU* 4.2 17.0 - - - +
310B ALA* 3.7 20.0 - - + +
311B GLY* 4.0 17.7 - - - +
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Residues in contact with ASP 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B PRO* 4.1 8.3 - - - +
4B ILE* 5.0 0.9 - - - +
20B ILE* 2.8 20.2 + - + +
21B ARG* 2.9 33.9 + - - +
23B LEU* 1.3 75.5 - - - +
25B LYS* 1.3 57.3 + - - +
26B GLU* 2.8 20.8 + - - +
27B SER* 2.6 34.9 + - - -
309B ILE* 5.6 0.3 - - - +
310B ALA* 3.7 21.0 - - + +
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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