Contacts of the helix formed by residues 9 - 22 (chain B) in PDB entry 5Y1Z
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 HIS 9 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B PHE 4.2 0.8 + - - -
7B SER 3.3 0.4 - - - -
8B GLY* 1.3 86.7 + - - +
10B ARG* 1.3 67.2 + - - +
11B LEU 3.3 2.5 - - - -
12B GLU* 3.0 26.9 + - - +
13B LEU* 2.9 31.0 + - + +
35B GLU* 3.0 36.9 + - - -
40B ASP* 3.5 10.4 + - - -
41B LEU 3.3 25.6 - - - +
42B LYS* 4.1 12.0 - - + +
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Residues in contact with ARG 10 (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 PHE* 3.1 29.0 + - - +
7B SER* 3.9 9.5 + - - +
8B GLY 3.7 0.8 - - - -
9B HIS* 1.3 76.4 - - - +
11B LEU* 1.3 63.3 + - - +
13B LEU* 3.3 6.8 + - - +
14B LEU* 3.0 26.4 + - + +
108B PHE* 3.5 23.9 - - + -
285D LEU* 3.6 32.8 - - - +
288D PHE* 3.5 42.2 - - + -
291D TRP* 5.6 1.0 - - - +
307D PHE* 3.9 14.3 - - - +
310D GLN* 3.5 12.7 - - - +
312D ASP* 2.8 42.8 + - - -
314D ALA* 5.6 2.4 - - - +
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Residues in contact with LEU 11 (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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9B HIS 3.3 0.8 - - - -
10B ARG* 1.3 79.0 - - - +
12B GLU* 1.3 58.6 + - - +
14B LEU* 3.8 0.4 - - - -
15B ALA* 2.8 28.5 + - + +
287D GLY 3.4 25.9 + - - +
288D PHE* 3.9 17.4 - - + -
289D PRO* 4.7 8.1 - - + -
334D LYS* 4.2 30.5 - - + -
335D THR* 3.8 25.6 - - + -
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Residues in contact with GLU 12 (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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9B HIS* 3.0 31.3 + - + +
11B LEU* 1.3 81.0 - - - +
13B LEU* 1.3 63.3 + - - +
15B ALA* 3.2 6.5 + - + +
16B ALA* 3.0 23.4 + - - +
43B LEU* 3.7 36.7 + - + +
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Residues in contact with LEU 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 PHE* 4.2 33.0 - - + -
9B HIS* 2.9 30.4 + - + +
10B ARG* 3.8 4.5 - - - +
12B GLU* 1.3 76.3 - - - +
14B LEU* 1.3 62.4 + - - +
16B ALA 3.4 0.2 + - - -
17B TYR 3.1 6.6 + - - -
32B TYR* 2.9 56.8 + - + -
41B LEU* 3.8 22.4 - - + +
42B LYS* 3.7 11.2 - - - -
43B LEU* 3.6 21.3 - - + +
108B PHE* 4.4 5.4 - - + -
109B PHE* 3.7 11.2 - - + -
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Residues in contact with LEU 14 (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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10B ARG* 3.0 13.8 + - + +
11B LEU 4.2 0.4 - - - +
13B LEU* 1.3 75.9 - - - +
15B ALA* 1.3 60.0 + - - +
17B TYR* 3.8 6.4 - - + +
18B GLU* 2.9 28.9 + - - +
108B PHE* 3.8 41.3 - - + +
109B PHE* 4.4 10.1 - - + -
288D PHE* 3.6 30.5 - - + -
291D TRP* 4.8 1.3 - - + -
310D GLN* 3.9 33.0 - - + +
335D THR* 4.1 17.8 - - + +
338D ILE* 4.2 19.1 - - + +
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Residues in contact with ALA 15 (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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11B LEU* 2.8 20.5 + - + +
12B GLU* 3.6 7.9 - - + +
14B LEU* 1.3 74.5 - - - +
16B ALA* 1.3 65.6 + - - +
18B GLU* 3.3 3.3 + - - +
19B GLU* 3.0 28.2 + - - +
334D LYS* 3.9 36.5 - - + +
335D THR* 4.5 0.6 - - - +
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Residues in contact with ALA 16 (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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12B GLU 3.0 13.9 + - - +
15B ALA* 1.3 75.4 - - - +
17B TYR* 1.3 63.1 + - - +
19B GLU* 3.2 13.0 + - - +
20B VAL* 3.1 22.9 + - - +
30B ALA* 4.1 8.1 - - + -
32B TYR* 3.8 13.2 - - + +
43B LEU* 3.8 31.0 - - + -
46B SER* 4.7 9.1 - - - +
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Residues in contact with TYR 17 (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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13B LEU 3.1 10.9 + - - +
14B LEU* 3.4 9.2 + - + +
15B ALA 3.3 0.2 - - - -
16B ALA* 1.3 75.3 - - - +
18B GLU* 1.3 64.6 + - - +
20B VAL* 2.9 26.6 + - + +
21B ILE* 3.0 51.4 + - + +
30B ALA* 5.2 0.2 - - + -
32B TYR* 3.3 7.5 + - - +
67B PHE* 3.2 50.1 - + + -
80B TYR* 3.7 26.8 - + - +
109B PHE* 3.6 55.5 + + + -
110B GLN 4.0 7.4 + - - -
111B GLY 5.1 0.5 - - - -
112B VAL* 4.8 1.2 - - - +
338D ILE* 4.4 6.3 - - + -
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Residues in contact with GLU 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 LEU 2.9 19.3 + - - +
15B ALA 3.3 5.4 + - - +
17B TYR* 1.3 74.1 - - - +
19B GLU* 1.3 65.4 + - + +
21B ILE* 3.1 5.1 + - - +
22B ARG* 2.9 28.4 + - + +
333D LYS 4.8 1.7 - - - +
334D LYS 3.6 17.7 - - - +
335D THR* 3.3 1.9 - - - -
336D LYS* 3.3 16.1 + - - +
337D SER* 2.8 31.1 + - - -
338D ILE* 3.0 42.6 + - + +
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Residues in contact with GLU 19 (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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15B ALA* 3.0 15.8 + - - +
16B ALA* 3.2 13.8 + - - +
18B GLU* 1.3 79.4 - - + +
20B VAL* 1.3 63.4 + - - +
22B ARG* 3.5 8.8 + - - +
25B SER* 3.5 33.0 + - - +
27B ALA* 3.6 28.2 - - + +
46B SER* 5.4 3.8 + - - -
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Residues in contact with VAL 20 (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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16B ALA 3.1 12.1 + - - +
17B TYR* 2.9 25.1 + - + +
19B GLU* 1.3 78.2 - - - +
21B ILE* 1.3 62.8 + - - +
22B ARG 4.0 2.8 - - - +
27B ALA* 3.8 14.4 - - + +
28B ASP* 3.9 9.4 - - - +
29B TRP* 3.6 37.0 - - - +
30B ALA* 3.9 8.5 - - + +
46B SER* 5.8 0.4 - - - -
67B PHE 4.9 1.3 - - - +
68B CYS 4.8 1.3 - - - -
69B SER* 3.8 35.1 + - - +
80B TYR* 4.2 9.5 + - + -
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Residues in contact with ILE 21 (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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17B TYR* 3.0 35.5 + - + +
18B GLU* 3.1 6.2 + - - +
20B VAL* 1.3 78.0 - - - +
22B ARG* 1.3 66.0 + - - +
23B GLU* 3.2 4.3 + - - +
78B PRO* 5.8 1.7 - - - +
80B TYR* 3.7 30.7 + - + +
110B GLN 5.2 3.1 - - - +
337D SER* 4.0 20.2 - - - +
338D ILE* 3.4 32.3 - - + -
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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
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18B GLU* 2.9 22.3 + - + +
19B GLU* 3.5 5.8 + - - +
20B VAL 3.4 4.5 - - - +
21B ILE* 1.3 76.7 - - - +
23B GLU* 1.3 64.8 + - - +
24B GLU* 4.5 2.2 - - + +
25B SER* 3.4 34.9 - - - +
27B ALA 4.9 0.2 - - - +
337D SER* 6.1 2.2 - - - -
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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