Contacts of the helix formed by residues 2 - 17 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C GLY* 1.3 80.5 - - - +
3C VAL* 1.3 64.0 + - - +
4C THR* 3.6 6.6 + - - -
5C ASP* 3.2 33.1 + - - +
6C ASP* 3.2 25.6 + - - +
82D GLU* 3.4 21.5 + - - +
144D THR* 6.0 2.0 - - - +
145D SER* 4.8 12.0 + - - +
147D ARG* 4.1 4.0 + - - -
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Residues in contact with VAL 3 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C THR* 1.3 72.0 - - - +
4C THR* 1.3 61.0 + - - +
6C ASP* 3.1 15.3 + - + +
7C TYR* 2.9 52.2 + - + -
28D LYS* 3.6 48.2 - - + +
30D ILE* 3.8 18.2 - - + -
82D GLU* 3.2 15.6 + - - +
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Residues in contact with THR 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C THR* 3.2 5.8 - - - -
3C VAL* 1.3 76.3 - - - +
5C ASP* 1.3 56.4 + - - +
7C TYR* 3.2 2.9 + - - +
8C LEU* 3.0 35.0 + - + +
30D ILE* 3.6 3.7 - - - +
82D GLU* 2.8 24.3 + - - +
83D ILE 4.7 1.7 + - - -
84D ILE* 3.5 40.4 - - + +
145D SER* 4.2 5.7 + - - -
147D ARG* 3.7 34.8 - - + +
149D PHE* 4.0 15.0 - - + -
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Residues in contact with ASP 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C GLY* 3.8 12.7 + - - +
2C THR* 3.2 35.3 + - - +
4C THR* 1.3 76.7 - - - +
6C ASP* 1.3 63.1 + - - +
8C LEU* 3.4 8.3 + - - +
9C ALA* 3.2 22.7 + - - +
147D ARG* 2.7 32.4 + - - +
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Residues in contact with ASP 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C GLY 4.9 6.1 + - - -
2C THR 3.4 15.1 - - - +
3C VAL* 3.1 21.8 + - + +
5C ASP* 1.3 77.6 - - - +
7C TYR* 1.3 63.4 + - + +
9C ALA* 3.4 7.7 + - - +
10C ASN* 3.1 32.9 + - - +
28D LYS* 4.7 10.2 + - - -
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Residues in contact with TYR 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C VAL* 2.9 33.8 + - + +
4C THR 3.7 4.5 - - - +
6C ASP* 1.3 77.0 - - + +
8C LEU* 1.3 61.3 + - + +
10C ASN* 3.4 14.0 + - - +
11C ASN 3.0 20.4 + - - -
28D LYS* 4.1 6.9 - - + +
30D ILE* 4.0 28.3 - - + -
32D ILE* 4.4 2.2 - - + -
46D LEU* 3.2 54.4 - - + +
47D GLY 4.4 1.8 - - - -
48D ILE* 3.7 24.0 - - + +
52D GLU* 2.8 44.8 + - - +
53D ALA* 4.0 3.0 - - + +
84D ILE* 4.2 9.2 - - + -
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Residues in contact with LEU 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C THR* 3.0 22.5 + - + +
5C ASP* 3.8 7.2 - - - +
6C ASP 3.4 0.2 - - - -
7C TYR* 1.3 75.2 - - + +
9C ALA* 1.3 62.9 + - - +
11C ASN* 3.1 19.4 + - + +
12C VAL* 3.3 12.1 + - - +
46D LEU* 5.0 2.7 - - + -
84D ILE* 6.1 0.7 - - + -
147D ARG* 3.4 31.9 - - - +
149D PHE* 3.4 41.7 - - + -
158D LEU* 4.0 25.4 - - + +
160D GLU* 4.4 0.9 - - - +
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Residues in contact with ALA 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ASP 3.2 13.4 + - - +
6C ASP* 3.6 10.8 - - - +
8C LEU* 1.3 76.2 - - - +
10C ASN* 1.3 63.5 + - - +
12C VAL* 3.3 25.3 + - - +
13C ASP* 3.8 9.9 + - - +
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Residues in contact with ASN 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ASP* 3.1 18.0 + - - +
7C TYR* 3.4 12.3 - - - +
8C LEU 3.2 0.2 - - - -
9C ALA* 1.3 76.5 - - - +
11C ASN* 1.3 63.6 + - - +
13C ASP* 3.3 13.9 + - - +
14C TYR* 3.1 19.2 + - - +
44D ARG 5.1 0.7 - - - +
45D MET 4.4 1.1 - - - -
46D LEU 3.0 33.2 + - - +
47D GLY* 3.4 22.0 + - - +
49D LYS* 5.6 2.4 - - - +
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Residues in contact with ASN 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C TYR 3.0 12.0 + - - +
8C LEU* 3.1 12.7 + - + +
10C ASN* 1.3 74.3 - - - +
12C VAL* 1.3 67.9 + - - +
14C TYR* 3.0 4.1 + - - -
15C ALA* 2.8 24.1 + - - +
45D MET* 3.1 40.1 + - - +
156D GLY 3.0 20.8 + - - -
157D LYS* 3.5 6.8 - - - +
158D LEU* 3.0 42.9 + - + +
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Residues in contact with VAL 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU 3.6 13.5 - - - +
9C ALA* 3.4 14.1 - - - +
10C ASN 3.2 0.6 - - - -
11C ASN* 1.3 80.9 - - - +
13C ASP* 1.3 63.9 + - - +
15C ALA* 3.3 13.8 + - - +
16C SER* 3.4 13.2 + - - +
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Residues in contact with ASP 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ALA 3.9 10.6 - - - +
10C ASN* 3.3 12.4 + - - +
11C ASN 3.2 0.6 - - - -
12C VAL* 1.3 74.8 - - - +
14C TYR* 1.3 65.9 + - - +
16C SER* 3.3 24.4 + - - -
17C GLY 4.2 1.2 + - - -
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Residues in contact with TYR 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ASN 3.1 10.4 + - - +
11C ASN* 3.0 8.8 + - - +
13C ASP* 1.3 76.0 - - - +
15C ALA* 1.3 65.0 + - - +
16C SER 3.2 1.4 + - - -
17C GLY* 3.4 12.0 + - - -
18C PHE* 3.2 39.1 + + + +
50C GLU* 2.6 36.0 + - - -
39D ARG 4.8 1.2 + - - -
41D ASP* 4.6 4.4 + - - +
44D ARG* 3.3 44.4 - - + +
45D MET* 3.8 19.2 - - + +
151D PHE* 4.0 15.1 - + - -
156D GLY 3.7 18.2 - - - -
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Residues in contact with ALA 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ASN 2.8 19.1 + - - +
12C VAL* 3.6 9.0 - - - +
13C ASP 3.3 0.2 - - - -
14C TYR* 1.3 70.7 - - - +
16C SER* 1.3 63.9 + - - +
17C GLY 3.4 0.4 + - - -
18C PHE* 3.8 9.2 + - - +
155D THR 3.6 18.3 - - - +
156D GLY 3.8 10.1 - - - +
157D LYS* 3.6 38.2 - - + -
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Residues in contact with SER 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C VAL* 3.4 10.3 + - - +
13C ASP* 3.3 18.9 + - - -
14C TYR 3.1 0.6 - - - -
15C ALA* 1.3 80.1 - - - +
17C GLY* 1.3 57.0 - - - +
18C PHE 3.8 0.5 + - - -
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Residues in contact with GLY 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ASP 4.2 1.4 + - - -
14C TYR 3.4 7.9 + - - -
16C SER* 1.3 78.3 - - - +
18C PHE* 1.3 63.6 + - - +
19C LYS* 3.5 3.8 + - - +
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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