Contacts of the helix formed by residues 2 - 17 (chain A) in PDB entry 1YLK
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 THR 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A GLY* 1.3 77.5 - - - +
3A VAL* 1.3 64.0 + - - +
4A THR* 3.5 8.8 + - - -
5A ASP* 3.0 33.1 + - - +
6A ASP* 3.2 24.2 + - - +
82B GLU* 3.6 18.6 - - - +
144B THR* 6.1 0.7 - - - +
145B SER* 4.8 11.7 + - - +
147B ARG* 4.4 2.8 + - - -
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Residues in contact with VAL 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A THR* 1.3 71.2 - - - +
4A THR* 1.3 65.8 + - - +
6A ASP* 3.1 14.2 + - + +
7A TYR* 2.9 49.5 + - + +
28B LYS* 3.5 53.8 - - + +
29B HIS* 5.9 0.7 - - - +
30B ILE* 4.1 8.1 - - + -
82B GLU* 3.1 17.0 + - - +
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Residues in contact with THR 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A THR* 3.7 6.7 - - - -
3A VAL* 1.3 76.0 - - - +
5A ASP* 1.3 56.6 + - - +
7A TYR* 3.2 2.3 + - - +
8A LEU* 2.9 35.0 + - + +
30B ILE* 3.7 2.8 - - - +
82B GLU* 2.7 24.8 + - - +
83B ILE 4.8 1.4 + - - -
84B ILE* 3.5 40.4 - - + +
145B SER* 4.1 6.0 + - - -
147B ARG* 3.6 33.9 - - + +
149B PHE* 3.9 14.8 - - + -
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Residues in contact with ASP 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A GLY* 3.6 13.1 + - - -
2A THR* 3.0 36.4 + - - +
4A THR* 1.3 76.3 - - - +
6A ASP* 1.3 59.7 + - - +
8A LEU* 3.5 8.1 + - - +
9A ALA* 3.1 26.5 + - - +
147B ARG* 2.9 25.4 + - - +
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Residues in contact with ASP 6 (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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1A GLY* 5.2 4.2 - - - -
2A THR 3.2 14.1 + - - +
3A VAL* 3.1 16.6 + - + +
5A ASP* 1.3 75.0 - - - +
7A TYR* 1.3 68.0 + - + +
9A ALA* 3.2 9.6 + - - +
10A ASN* 2.9 34.4 + - - +
28B LYS* 5.0 9.8 + - - -
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Residues in contact with TYR 7 (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 VAL* 2.9 37.7 + - + +
4A THR* 3.6 5.6 - - - +
6A ASP* 1.3 76.9 - - + +
8A LEU* 1.3 58.6 + - - +
10A ASN* 3.3 13.0 + - - +
11A ASN* 3.0 26.9 + - - +
28B LYS* 3.8 9.5 - - + +
30B ILE* 4.0 13.2 - - + -
32B ILE* 4.4 2.0 - - + -
46B LEU* 3.3 50.4 - - + +
47B GLY 4.6 0.7 - - - -
48B ILE* 3.7 22.9 - - + +
52B GLU* 2.8 43.2 + - - +
53B ALA* 3.9 8.2 - - + +
84B ILE* 4.2 18.4 - - + -
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Residues in contact with LEU 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A THR* 2.9 21.0 + - + +
5A ASP* 3.7 8.3 - - - +
7A TYR* 1.3 76.0 - - + +
9A ALA* 1.3 62.2 + - - +
11A ASN* 3.1 15.1 + - + +
12A VAL* 3.3 16.1 + - - +
46B LEU* 5.0 2.2 - - + -
84B ILE* 6.0 1.1 - - + -
147B ARG* 3.5 33.4 - - - +
149B PHE* 3.5 35.7 - - + -
158B LEU* 3.8 28.3 - - + -
160B GLU* 5.0 0.2 - - - +
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Residues in contact with ALA 9 (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 ASP 3.1 14.9 + - - +
6A ASP* 3.2 11.9 + - - +
8A LEU* 1.3 75.8 - - - +
10A ASN* 1.3 62.2 + - - +
12A VAL* 3.2 26.1 + - - +
13A ASP* 3.6 9.6 + - - +
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Residues in contact with ASN 10 (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 ASP* 2.9 22.2 + - - +
7A TYR* 3.3 12.3 + - - +
9A ALA* 1.3 76.5 - - - +
11A ASN* 1.3 57.6 + - - +
13A ASP* 3.2 13.8 + - - +
14A TYR* 3.0 25.3 + - - +
44B ARG 5.1 0.7 - - - +
45B MET 4.3 1.6 - - - -
46B LEU 2.9 32.3 + - - +
47B GLY* 3.5 21.3 + - - +
49B LYS* 6.2 0.2 - - - +
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Residues in contact with ASN 11 (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 TYR 3.0 11.4 + - - +
8A LEU* 3.1 14.0 + - + +
10A ASN* 1.3 75.1 - - - +
12A VAL* 1.3 60.2 + - - +
14A TYR* 3.1 3.4 + - - -
15A ALA* 2.8 30.5 + - - +
45B MET* 3.1 39.5 + - - +
156B GLY 3.0 21.2 + - - -
157B LYS* 3.6 4.9 - - - +
158B LEU* 3.0 44.0 + - + +
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Residues in contact with VAL 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU 3.3 14.5 + - - +
9A ALA* 3.2 14.5 + - - +
11A ASN* 1.3 78.8 - - - +
13A ASP* 1.3 66.4 + - - +
15A ALA* 3.5 6.0 + - - +
16A SER* 3.3 21.5 + - - -
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Residues in contact with ASP 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA 3.6 9.2 + - - +
10A ASN* 3.2 13.8 + - - +
11A ASN 3.2 0.4 - - - -
12A VAL* 1.3 81.2 - - - +
14A TYR* 1.3 64.5 + - - +
16A SER* 2.7 24.3 + - - -
17A GLY* 3.8 2.4 + - - -
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Residues in contact with TYR 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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10A ASN 3.0 13.3 + - - +
11A ASN* 3.5 7.9 - - - +
13A ASP* 1.3 77.2 - - - +
15A ALA* 1.3 63.2 + - - +
17A GLY* 3.3 12.8 + - - -
18A PHE* 3.4 38.0 + + + +
50A GLU* 2.5 37.5 + - - -
39B ARG 4.7 1.7 + - - -
41B ASP* 4.9 4.3 + - - +
44B ARG* 3.2 45.1 - - + +
45B MET* 3.8 17.9 - - + +
151B PHE* 4.0 21.0 - + - -
156B GLY 3.7 12.3 - - - -
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Residues in contact with ALA 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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11A ASN* 2.8 20.1 + - - +
12A VAL* 3.9 6.1 - - - +
14A TYR* 1.3 72.2 - - - +
16A SER* 1.3 64.2 + - - +
18A PHE* 3.3 17.6 + - - +
155B THR 3.6 14.0 - - - +
156B GLY 3.7 9.0 - - - +
157B LYS* 3.6 36.9 - - + -
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Residues in contact with SER 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 VAL 3.3 11.9 + - - -
13A ASP* 2.7 25.2 + - - +
15A ALA* 1.3 76.8 - - - +
17A GLY* 1.3 56.9 + - - +
18A PHE 3.5 1.1 + - - +
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Residues in contact with GLY 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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13A ASP 3.8 2.2 + - - -
14A TYR 3.3 9.0 + - - -
15A ALA 3.2 0.4 - - - -
16A SER* 1.3 81.0 + - - +
18A PHE* 1.3 60.7 + - - +
19A LYS* 3.6 24.7 + - - +
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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