Contacts of the helix formed by residues 4 - 18 (chain B) in PDB entry 1AYZ
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 PRO 4 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B THR* 1.3 89.0 - - - +
5B ALA* 1.3 63.6 + - - +
7B ARG* 3.3 23.2 + - + +
8B ARG* 3.0 25.3 + - - +
11B ARG* 4.9 1.4 + - - -
61B GLU* 5.3 1.3 - - - +
63B TYR 4.9 1.1 - - - +
64B PRO* 6.1 0.7 - - - -
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Residues in contact with ALA 5 (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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3B THR* 3.3 1.2 + - - -
4B PRO* 1.3 80.0 - - - +
6B ARG* 1.3 57.8 + - - +
8B ARG* 3.3 4.0 + - - +
9B LEU* 2.9 34.1 + - - +
34B MET* 4.6 3.6 - - + -
60B ASP 3.6 20.6 - - - +
61B GLU* 3.2 29.7 + - - +
63B TYR* 3.5 27.5 + - + +
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Residues in contact with ARG 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B SER* 3.9 17.9 - - - +
3B THR* 3.0 36.5 + - - +
5B ALA* 1.3 77.3 - - - +
7B ARG* 1.3 56.9 + - - +
9B LEU* 3.3 10.1 + - - +
10B MET* 3.0 32.3 + - + +
32B ASN* 4.4 6.7 + - - +
33B VAL* 3.9 24.3 - - + +
34B MET* 3.3 34.3 - - + +
61B GLU* 2.6 32.0 + - - +
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Residues in contact with ARG 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B SER* 3.2 30.6 + - - +
3B THR* 2.8 35.9 + - - +
4B PRO* 3.6 31.5 - - + +
6B ARG* 1.3 70.2 - - - +
8B ARG* 1.3 65.8 - - - +
10B MET* 3.0 20.1 + - + +
11B ARG* 3.0 28.0 + - - +
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Residues in contact with ARG 8 (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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4B PRO 3.0 13.3 + - - +
5B ALA* 3.4 10.1 - - - +
7B ARG* 1.3 78.0 - - - +
9B LEU* 1.3 57.5 + - - +
11B ARG* 2.9 54.8 + - - +
12B ASP* 2.8 55.4 + - - +
63B TYR* 3.0 25.5 + - + -
64B PRO* 3.4 23.5 - - + +
98B PRO 2.9 22.4 + - - -
99B THR* 4.1 4.6 + - - +
100B TYR 2.7 24.4 + - - -
101B ASP* 3.7 3.2 - - - +
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Residues in contact with LEU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ALA 2.9 17.9 + - - +
6B ARG* 3.4 9.9 - - - +
8B ARG* 1.3 78.1 - - - +
10B MET* 1.3 56.0 + - - +
12B ASP* 3.2 9.5 + - - +
13B PHE* 2.9 23.4 + - - +
33B VAL* 3.1 34.1 - - + +
34B MET* 3.7 24.0 - - - -
36B TRP* 3.4 21.9 - - + +
59B PHE* 3.7 34.8 - - + -
63B TYR* 3.3 28.3 - - + -
102B VAL* 4.6 0.2 - - + -
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Residues in contact with MET 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B SER* 5.5 3.1 - - - +
6B ARG* 3.0 20.6 + - + +
7B ARG* 3.0 15.0 + - + +
9B LEU* 1.3 75.6 - - - +
11B ARG* 1.3 58.3 + - + +
13B PHE* 3.2 23.7 + - + +
14B LYS* 3.0 25.8 + - - +
17B LYS* 6.2 1.1 - - - +
28B PRO* 6.2 0.2 - - - -
33B VAL* 3.9 24.7 - - - -
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Residues in contact with ARG 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PRO 4.9 1.2 + - - -
7B ARG* 3.0 20.5 + - - +
8B ARG* 2.9 53.8 + - - +
10B MET* 1.3 75.8 - - + +
12B ASP* 1.3 67.0 + - - +
14B LYS* 3.3 12.9 + - + +
15B ARG* 3.2 21.0 + - - +
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Residues in contact with ASP 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ARG* 2.8 38.9 + - - +
9B LEU* 3.4 12.3 - - - +
11B ARG* 1.3 77.3 - - - +
13B PHE* 1.3 57.7 + - - +
15B ARG* 3.4 8.1 + - - +
16B MET* 3.1 31.0 + - - +
36B TRP* 4.0 2.9 - - + -
63B TYR* 2.6 29.1 + - - -
101B ASP* 3.6 15.3 - - + +
102B VAL* 3.2 29.9 + - + +
103B ALA 5.8 0.2 + - - -
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Residues in contact with PHE 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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9B LEU 2.9 12.3 + - - +
10B MET* 3.3 30.1 - - + +
12B ASP* 1.3 76.6 - - - +
14B LYS* 1.3 65.4 + - - +
16B MET* 3.2 2.0 + - + -
17B LYS* 2.9 65.9 + - + +
26B ALA 4.5 5.4 - - - -
27B SER* 4.0 17.3 - - - -
28B PRO* 3.6 40.4 - - + -
33B VAL* 6.0 0.2 - - + -
36B TRP* 3.5 13.9 - + + -
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Residues in contact with LYS 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 MET 3.0 12.7 + - - +
11B ARG* 3.3 15.5 + - + +
13B PHE* 1.3 74.7 - - - +
15B ARG* 1.3 66.8 + - - +
17B LYS* 3.2 12.7 + - - +
18B GLU* 3.0 52.0 + - - +
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Residues in contact with ARG 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 ARG 3.2 10.0 + - - +
12B ASP* 3.6 11.0 - - - +
13B PHE 3.2 0.2 - - - -
14B LYS* 1.3 83.2 - - + +
16B MET* 1.3 58.0 + - - +
18B GLU* 5.1 0.9 - - - -
19B ASP* 2.7 76.1 + - - +
21B PRO* 3.4 26.7 - - - +
101B ASP* 3.9 15.3 + - - +
103B ALA* 3.8 25.2 - - + +
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Residues in contact with MET 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ASP 3.1 21.6 + - - +
13B PHE* 3.2 7.4 + - + +
15B ARG* 1.3 75.1 - - - +
17B LYS* 1.3 64.5 + - - +
20B ALA* 3.0 35.8 - - + +
21B PRO* 3.9 17.5 - - - -
24B VAL* 4.1 7.4 - - + +
25B SER* 3.8 12.8 - - - -
26B ALA 3.5 42.5 - - - +
36B TRP* 4.4 3.4 - - + -
102B VAL* 4.2 17.3 - - + -
103B ALA* 3.9 23.1 - - - +
106B LEU* 3.9 13.5 - - + -
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Residues in contact with LYS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B MET* 6.2 0.8 - - - +
13B PHE* 2.9 63.1 + - + +
14B LYS* 3.2 8.9 + - - +
16B MET* 1.3 79.6 - - - +
18B GLU* 1.3 65.8 - - + +
20B ALA* 5.5 0.2 - - - +
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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 LYS* 3.0 46.3 + - - +
15B ARG* 5.0 0.8 - - - -
17B LYS* 1.3 85.4 - - + +
19B ASP* 1.3 63.0 + - + +
20B ALA* 3.4 4.5 + - - +
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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